Daily Papers

AI agents are increasingly deployed in production, yet their security evaluations remain bottlenecked by manual red-teaming or static benchmarks that fail to model adaptive, multi-turn adversaries. We propose NAAMSE, an evolutionary framework that reframes agent security evaluation as a feedback-driven optimization problem. Our system employs a single autonomous agent that orchestrates a lifecycle of genetic prompt mutation, hierarchical corpus exploration, and asymmetric behavioral scoring. By using model responses as a fitness signal, the framework iteratively compounds effective attack strategies while simultaneously ensuring "benign-use correctness", preventing the degenerate security of blanket refusal. Our experiments on Gemini 2.5 Flash demonstrate that evolutionary mutation systematically amplifies vulnerabilities missed by one-shot methods, with controlled ablations revealing that the synergy between exploration and targeted mutation uncovers high-severity failure modes. We show that this adaptive approach provides a more realistic and scalable assessment of agent robustness in the face of evolving threats. The code for NAAMSE is open source and available at https://github.com/HASHIRU-AI/NAAMSE.

Building agentic systems that can autonomously self-improve from experience is a longstanding goal of AI. Large language models (LLMs) today primarily self-improve via two mechanisms: self-reflection for context updates, and reinforcement learning (RL) for weight updates. In this work, we propose Evolutionary System Prompt Learning (E-SPL), a method for jointly improving model contexts and model weights. In each RL iteration, E-SPL samples trajectories under multiple system prompts in parallel, then jointly applies RL updates to LLM weights and evolutionary updates to system prompts. System prompts evolve via mutation and crossover, two genetic operators driven by LLM self-reflection; selection is based on relative performance ratings updated across RL iterations. E-SPL encourages a natural division between declarative knowledge encoded in prompts and procedural knowledge encoded in weights, resulting in improved performance across reasoning and agentic tasks. For instance, in an easy-to-hard (AIME rightarrow BeyondAIME) generalization setting, E-SPL improves RL success rate from 38.8% rightarrow 45.1% while also outperforming reflective prompt evolution (40.0%). Overall, our results demonstrate that RL and system prompt evolution are deeply synergistic, and combining the two yields consistent gains in sample efficiency and generalization. Code: https://github.com/LunjunZhang/E-SPL

Large Language Models (LLMs) excel at generating synthetic data, but ensuring its quality and diversity remains challenging. We propose Genetic Prompt, a novel framework that combines genetic algorithms with LLMs to augment synthetic data generation. Our approach treats semantic text attributes as gene sequences and leverages the LLM to simulate crossover and mutation operations. This genetic process enhances data quality and diversity by creating novel attribute combinations, yielding synthetic distributions closer to real-world data. To optimize parent selection, we also integrate an active learning scheme that expands the offspring search space. Our experiments on multiple NLP tasks reveal several key findings: Genetic Prompt not only significantly outperforms state-of-the-art baselines but also shows robust performance across various generator model sizes and scales. Moreover, we demonstrate that fusing our synthetic data with the original training set significantly boosts downstream model performance, particularly for class-imbalanced scenarios. Our findings validate that Genetic Prompt is an effective method for producing high-quality synthetic data for a wide range of NLP applications.

Popular prompt strategies like Chain-of-Thought Prompting can dramatically improve the reasoning abilities of Large Language Models (LLMs) in various domains. However, such hand-crafted prompt-strategies are often sub-optimal. In this paper, we present Promptbreeder, a general-purpose self-referential self-improvement mechanism that evolves and adapts prompts for a given domain. Driven by an LLM, Promptbreeder mutates a population of task-prompts, and subsequently evaluates them for fitness on a training set. Crucially, the mutation of these task-prompts is governed by mutation-prompts that the LLM generates and improves throughout evolution in a self-referential way. That is, Promptbreeder is not just improving task-prompts, but it is also improving the mutationprompts that improve these task-prompts. Promptbreeder outperforms state-of-the-art prompt strategies such as Chain-of-Thought and Plan-and-Solve Prompting on commonly used arithmetic and commonsense reasoning benchmarks. Furthermore, Promptbreeder is able to evolve intricate task-prompts for the challenging problem of hate speech classification.

One of the critical phases in software development is software testing. Testing helps with identifying potential bugs and reducing maintenance costs. The goal of automated test generation tools is to ease the development of tests by suggesting efficient bug-revealing tests. Recently, researchers have leveraged Large Language Models (LLMs) of code to generate unit tests. While the code coverage of generated tests was usually assessed, the literature has acknowledged that the coverage is weakly correlated with the efficiency of tests in bug detection. To improve over this limitation, in this paper, we introduce MuTAP for improving the effectiveness of test cases generated by LLMs in terms of revealing bugs by leveraging mutation testing. Our goal is achieved by augmenting prompts with surviving mutants, as those mutants highlight the limitations of test cases in detecting bugs. MuTAP is capable of generating effective test cases in the absence of natural language descriptions of the Program Under Test (PUTs). We employ different LLMs within MuTAP and evaluate their performance on different benchmarks. Our results show that our proposed method is able to detect up to 28% more faulty human-written code snippets. Among these, 17% remained undetected by both the current state-of-the-art fully automated test generation tool (i.e., Pynguin) and zero-shot/few-shot learning approaches on LLMs. Furthermore, MuTAP achieves a Mutation Score (MS) of 93.57% on synthetic buggy code, outperforming all other approaches in our evaluation. Our findings suggest that although LLMs can serve as a useful tool to generate test cases, they require specific post-processing steps to enhance the effectiveness of the generated test cases which may suffer from syntactic or functional errors and may be ineffective in detecting certain types of bugs and testing corner cases PUTs.

Human language is one of the most expressive tools for conveying intent, yet most artificial or biological systems lack mechanisms to interpret or respond meaningfully to it. Bridging this gap could enable more natural forms of control over complex, decentralized systems. In AI and artificial life, recent work explores how language can specify high-level goals, but most systems still depend on engineered rewards, task-specific supervision, or rigid command sets, limiting generalization to novel instructions. Similar constraints apply in synthetic biology and bioengineering, where the locus of control is often genomic rather than environmental perturbation. A key open question is whether artificial or biological collectives can be guided by free-form natural language alone, without task-specific tuning or carefully designed evaluation metrics. We provide one possible answer here by showing, for the first time, that simple agents' collective behavior can be guided by free-form language prompts: one AI model transforms an imperative prompt into an intervention that is applied to simulated cells; a second AI model scores how well the prompt describes the resulting cellular dynamics; and the former AI model is evolved to improve the scores generated by the latter. Unlike previous work, our method does not require engineered fitness functions or domain-specific prompt design. We show that the evolved system generalizes to unseen prompts without retraining. By treating natural language as a control layer, the system suggests a future in which spoken or written prompts could direct computational, robotic, or biological systems to desired behaviors. This work provides a concrete step toward this vision of AI-biology partnerships, in which language replaces mathematical objective functions, fixed rules, and domain-specific programming.

Large Language Models (LLMs) have shown impressive capabilities in many scenarios, but their performance depends, in part, on the choice of prompt. Past research has focused on optimizing prompts specific to a task. However, much less attention has been given to optimizing the general instructions included in a prompt, known as a system prompt. To address this gap, we propose SPRIG, an edit-based genetic algorithm that iteratively constructs prompts from prespecified components to maximize the model's performance in general scenarios. We evaluate the performance of system prompts on a collection of 47 different types of tasks to ensure generalizability. Our study finds that a single optimized system prompt performs on par with task prompts optimized for each individual task. Moreover, combining system and task-level optimizations leads to further improvement, which showcases their complementary nature. Experiments also reveal that the optimized system prompts generalize effectively across model families, parameter sizes, and languages. This study provides insights into the role of system-level instructions in maximizing LLM potential.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

Large language models (LLMs) have shown impressive promise in code generation, yet their progress remains limited by the shortage of large-scale datasets that are both diverse and well-aligned with human reasoning. Most existing resources pair problems with solutions, but omit the intermediate thought process that guides coding. To close this gap, we present a scalable synthetic data generation pipeline that produces nearly 800k instruction-reasoning-code-test quadruplets. Each sample combines a task, a step-by-step reasoning trace, a working solution, and executable tests, enabling models to learn not just the what but also the how of problem solving. Our pipeline combines four key components: curated contest problems, web-mined content filtered by relevance classifiers, data expansion guided by reasoning patterns, and multi-stage execution-based validation. A genetic mutation algorithm further increases task diversity while maintaining consistency between reasoning traces and code implementations. Our key finding is that fine-tuning LLMs on this dataset yields consistent improvements on coding benchmarks. Beyond raw accuracy, reasoning-aware data can substitute for model scaling, generalize across architectures, and outperform leading open-source alternatives under identical sample budgets. Our work establishes reasoning-centered synthetic data generation as an efficient approach for advancing coding capabilities in LLMs. We publish our dataset and generation pipeline to facilitate further research.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

Autoprompting is the process of automatically selecting optimized prompts for language models, which has been gaining popularity with the rapid advancement of prompt engineering, driven by extensive research in the field of large language models (LLMs). This paper presents ReflectivePrompt - a novel autoprompting method based on evolutionary algorithms that employs a reflective evolution approach for more precise and comprehensive search of optimal prompts. ReflectivePrompt utilizes short-term and long-term reflection operations before crossover and elitist mutation to enhance the quality of the modifications they introduce. This method allows for the accumulation of knowledge obtained throughout the evolution process and updates it at each epoch based on the current population. ReflectivePrompt was tested on 33 datasets for classification and text generation tasks using open-access large language models: t-lite-instruct-0.1 and gemma3-27b-it. The method demonstrates, on average, a significant improvement (e.g., 28% on BBH compared to EvoPrompt) in metrics relative to current state-of-the-art approaches, thereby establishing itself as one of the most effective solutions in evolutionary algorithm-based autoprompting.

Artificial Intelligence (AI) advancement is heavily dependent on access to large-scale, high-quality training data. However, in specialized domains such as healthcare, data acquisition faces significant constraints due to privacy regulations, ethical considerations, and limited availability. While synthetic data generation offers a promising solution, conventional approaches typically require substantial real data for training generative models. The emergence of large-scale prompt-based models presents new opportunities for synthetic data generation without direct access to protected data. However, crafting effective prompts for domain-specific data generation remains challenging, and manual prompt engineering proves insufficient for achieving output with sufficient precision and authenticity. We review recent developments in automatic prompt optimization, following PRISMA guidelines. We analyze six peer-reviewed studies published between 2020 and 2024 that focus on automatic data-free prompt optimization methods. Our analysis reveals three approaches: feedback-driven, error-based, and control-theoretic. Although all approaches demonstrate promising capabilities in prompt refinement and adaptation, our findings suggest the need for an integrated framework that combines complementary optimization techniques to enhance synthetic data generation while minimizing manual intervention. We propose future research directions toward developing robust, iterative prompt optimization frameworks capable of improving the quality of synthetic data. This advancement can be particularly crucial for sensitive fields and in specialized domains where data access is restricted, potentially transforming how we approach synthetic data generation for AI development.

During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns within the genome or a specific gene. In this project, we harnessed the power of Large Language Models(LLMs) to predict the evolution of SARS-CoV-2. By treating the mutation process from one generation to the next as a translation task, we trained a transformer model, called VirusT5, to capture the mutation patterns underlying SARS-CoV-2 evolution. We evaluated the VirusT5's ability to detect these mutation patterns including its ability to identify mutation hotspots and explored the potential of using VirusT5 to predict future virus variants. Our findings demonstrate the feasibility of using a large language model to model viral evolution as a translation process. This study establishes the groundbreaking concept of "mutation-as-translation," paving the way for new methodologies and tools for combating virus threats

Existing prompt-optimization techniques rely on local signals to update behavior, often neglecting broader and recurring patterns across tasks, leading to poor generalization; they further rely on full-prompt rewrites or unstructured merges, resulting in knowledge loss. These limitations are magnified in research-coding workflows, which involve heterogeneous repositories, underspecified environments, and weak feedback, where reproducing results from public codebases is an established evaluation regime. We introduce Reflective Evolving Research Engineer (REVERE), a framework that continuously learns from Global Training Context, recognizes recurring failure modes in cross-repository execution trajectories, distills them into reusable heuristics, and performs targeted edits across three configurable fields: the system prompt, a task-prompt template, and a cumulative cheatsheet. REVERE, via this reflective optimization framework, improves performance over prior state-of-the-art expert-crafted instructions on research coding tasks by 4.50% on SUPER, 3.51% on ResearchCodeBench, and 4.89% on ScienceAgentBench across their respective metrics. These results demonstrate that agents equipped with mechanisms for continual learning and global memory consolidation can meaningfully evolve their capabilities over time.

Software testing is a critical, yet resource-intensive phase of the software development lifecycle. Over the years, various automated tools have been developed to aid in this process. Search-based approaches typically achieve high coverage but produce tests with low readability, whereas large language model (LLM)-based methods generate more human-readable tests but often suffer from low coverage and compilability. While the majority of research efforts have focused on improving test coverage and readability, little attention has been paid to enhancing the robustness of bug detection, particularly in exposing corner cases and vulnerable execution paths. To address this gap, we propose AdverTest, a novel adversarial framework for LLM-powered test case generation. AdverTest comprises two interacting agents: a test case generation agent (T) and a mutant generation agent (M). These agents engage in an adversarial loop, where M persistently creates new mutants "hacking" the blind spots of T's current test suite, while T iteratively refines its test cases to "kill" the challenging mutants produced by M. This interaction loop is guided by both coverage and mutation scores, enabling the system to co-evolve toward both high test coverage and bug detection capability. Experimental results in the Defects4J dataset show that our approach improves fault detection rates by 8.56% over the best existing LLM-based methods and by 63.30% over EvoSuite, while also improving line and branch coverage.

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

We propose a novel prompt design paradigm that challenges conventional wisdom in large language model (LLM) prompting. While conventional wisdom prioritizes well-crafted instructions and demonstrations for in-context learning (ICL), we show that pruning random demonstrations into seemingly incoherent "gibberish" can remarkably improve performance across diverse tasks. Notably, the "gibberish" always matches or surpasses state-of-the-art automatic prompt optimization techniques, achieving substantial gains regardless of LLM alignment. Nevertheless, discovering an effective pruning strategy is non-trivial, as existing attribution methods and prompt compression algorithms fail to deliver robust results, let alone human intuition. In terms of this, we propose a self-discover prompt optimization framework, PromptQuine, an evolutionary search framework that automatically searches for the pruning strategy by itself using only low-data regimes. Much like the emergent complexity in nature--such as symbiosis and self-organization--arising in response to resource constraints, our framework evolves and refines unconventional yet highly effective prompts by leveraging only the tokens present within the context. We demonstrate its effectiveness across classification, multi-choice question answering, generation and math reasoning tasks across LLMs, while achieving decent runtime efficiency. We hope our findings can guide mechanistic studies on in-context learning, and provide a call to action, to pave the way for more open-ended search algorithms for more effective LLM prompting.

Large Language Models (LLMs) excel in various tasks, but they rely on carefully crafted prompts that often demand substantial human effort. To automate this process, in this paper, we propose a novel framework for discrete prompt optimization, called EvoPrompt, which borrows the idea of evolutionary algorithms (EAs) as they exhibit good performance and fast convergence. To enable EAs to work on discrete prompts, which are natural language expressions that need to be coherent and human-readable, we connect LLMs with EAs. This approach allows us to simultaneously leverage the powerful language processing capabilities of LLMs and the efficient optimization performance of EAs. Specifically, abstaining from any gradients or parameters, EvoPrompt starts from a population of prompts and iteratively generates new prompts with LLMs based on the evolutionary operators, improving the population based on the development set. We optimize prompts for both closed- and open-source LLMs including GPT-3.5 and Alpaca, on 9 datasets spanning language understanding and generation tasks. EvoPrompt significantly outperforms human-engineered prompts and existing methods for automatic prompt generation by up to 25% and 14% respectively. Furthermore, EvoPrompt demonstrates that connecting LLMs with EAs creates synergies, which could inspire further research on the combination of LLMs and conventional algorithms.

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation, their application to DNA sequence generation remains largely underexplored. In this work, we introduce ATGC-Gen, an Automated Transformer Generator for Controllable Generation, which leverages cross-modal encoding to integrate diverse biological signals. ATGC-Gen is instantiated with both decoder-only and encoder-only transformer architectures, allowing flexible training and generation under either autoregressive or masked recovery objectives. We evaluate ATGC-Gen on representative tasks including promoter and enhancer sequence design, and further introduce a new dataset based on ChIP-Seq experiments for modeling protein binding specificity. Our experiments demonstrate that ATGC-Gen can generate fluent, diverse, and biologically relevant sequences aligned with the desired properties. Compared to prior methods, our model achieves notable improvements in controllability and functional relevance, highlighting the potential of language models in advancing programmable genomic design. The source code is released at (https://github.com/divelab/AIRS/blob/main/OpenBio/ATGC_Gen).

Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to some form of self-adaptive selection mechanism. In nature, genetic diversity can be the consequence of many different factors, but when considering reproduction Sexual Selection can have an impact on promoting variety within a species. Specifically, Mate Choice often results in different selective pressures between sexes, which in turn may trigger evolutionary differences among them. Although some mechanisms of Sexual Selection have been applied to Genetic Programming in the past, the literature is scarce when it comes to mate choice. Recently, a way of modelling mating preferences by ideal mate representations was proposed, achieving good results when compared to a standard approach. These mating preferences evolve freely in a self-adaptive fashion, creating an evolutionary driving force of its own alongside fitness pressure. The inner mechanisms of this approach operate from personal choice, as each individual has its own representation of a perfect mate which affects the mate to be selected. In this paper, we compare this method against a random mate choice to assess whether there are advantages in evolving personal preferences. We conducted experiments using three symbolic regression problems and different mutation rates. The results show that self-adaptive mating preferences are able to create a more diverse set of solutions when compared to the traditional approach and a random mate approach (with statistically significant differences) and have a higher success rate in three of the six instances tested.

This paper presents the first ChatGPT4PCG Competition at the 2023 IEEE Conference on Games. The objective of this competition is for participants to create effective prompts for ChatGPT--enabling it to generate Science Birds levels with high stability and character-like qualities--fully using their creativity as well as prompt engineering skills. ChatGPT is a conversational agent developed by OpenAI. Science Birds is selected as the competition platform because designing an Angry Birds-like level is not a trivial task due to the in-game gravity; the quality of the levels is determined by their stability. To lower the entry barrier to the competition, we limit the task to the generation of capitalized English alphabetical characters. We also allow only a single prompt to be used for generating all the characters. Here, the quality of the generated levels is determined by their stability and similarity to the given characters. A sample prompt is provided to participants for their reference. An experiment is conducted to determine the effectiveness of several modified versions of this sample prompt on level stability and similarity by testing them on several characters. To the best of our knowledge, we believe that ChatGPT4PCG is the first competition of its kind and hope to inspire enthusiasm for prompt engineering in procedural content generation.

Large language models (LLMs) hold great potential for many natural language applications but risk generating incorrect or toxic content. To probe when an LLM generates unwanted content, the current paradigm is to recruit a red team of human testers to design input prompts (i.e., test cases) that elicit undesirable responses from LLMs. However, relying solely on human testers is expensive and time-consuming. Recent works automate red teaming by training a separate red team LLM with reinforcement learning (RL) to generate test cases that maximize the chance of eliciting undesirable responses from the target LLM. However, current RL methods are only able to generate a small number of effective test cases resulting in a low coverage of the span of prompts that elicit undesirable responses from the target LLM. To overcome this limitation, we draw a connection between the problem of increasing the coverage of generated test cases and the well-studied approach of curiosity-driven exploration that optimizes for novelty. Our method of curiosity-driven red teaming (CRT) achieves greater coverage of test cases while mantaining or increasing their effectiveness compared to existing methods. Our method, CRT successfully provokes toxic responses from LLaMA2 model that has been heavily fine-tuned using human preferences to avoid toxic outputs. Code is available at https://github.com/Improbable-AI/curiosity_redteam

Recent progress in generative models, especially in text-guided diffusion models, has enabled the production of aesthetically-pleasing imagery resembling the works of professional human artists. However, one has to carefully compose the textual description, called the prompt, and augment it with a set of clarifying keywords. Since aesthetics are challenging to evaluate computationally, human feedback is needed to determine the optimal prompt formulation and keyword combination. In this paper, we present a human-in-the-loop approach to learning the most useful combination of prompt keywords using a genetic algorithm. We also show how such an approach can improve the aesthetic appeal of images depicting the same descriptions.

Large Language Models (LLMs) have shown significant capability across various tasks, with their real-world effectiveness often driven by prompt design. While recent research has focused on optimizing prompt content, the role of prompt formatting, a critical but often overlooked dimension, has received limited systematic investigation. In this paper, we introduce Content-Format Integrated Prompt Optimization (CFPO), an innovative methodology that jointly optimizes both prompt content and formatting through an iterative refinement process. CFPO leverages natural language mutations to explore content variations and employs a dynamic format exploration strategy that systematically evaluates diverse format options. Our extensive evaluations across multiple tasks and open-source LLMs demonstrate that CFPO demonstrates measurable performance improvements compared to content-only optimization methods. This highlights the importance of integrated content-format optimization and offers a practical, model-agnostic approach to enhancing LLM performance. Code will be available at https://github.com/HenryLau7/CFPO.

Generative Artificial Intelligence (GenAI) systems are being increasingly deployed across all parts of industry and research settings. Developers and end users interact with these systems through the use of prompting or prompt engineering. While prompting is a widespread and highly researched concept, there exists conflicting terminology and a poor ontological understanding of what constitutes a prompt due to the area's nascency. This paper establishes a structured understanding of prompts, by assembling a taxonomy of prompting techniques and analyzing their use. We present a comprehensive vocabulary of 33 vocabulary terms, a taxonomy of 58 text-only prompting techniques, and 40 techniques for other modalities. We further present a meta-analysis of the entire literature on natural language prefix-prompting.

Test-time prompt tuning enhances zero-shot generalization of vision-language models but tends to ignore the relatedness among test samples during inference. Online test-time prompt tuning provides a simple way to leverage the information in previous test samples, albeit with the risk of prompt collapse due to error accumulation. To enhance test-time prompt tuning, we propose DynaPrompt, short for dynamic test-time prompt tuning, exploiting relevant data distribution information while reducing error accumulation. Built on an online prompt buffer, DynaPrompt adaptively selects and optimizes the relevant prompts for each test sample during tuning. Specifically, we introduce a dynamic prompt selection strategy based on two metrics: prediction entropy and probability difference. For unseen test data information, we develop dynamic prompt appending, which allows the buffer to append new prompts and delete the inactive ones. By doing so, the prompts are optimized to exploit beneficial information on specific test data, while alleviating error accumulation. Experiments on fourteen datasets demonstrate the effectiveness of dynamic test-time prompt tuning.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

Current reinforcement learning (RL) frameworks for large language models (LLM) post-training typically assume a fixed prompt distribution, which is sub-optimal and bottlenecks scalability. Prior works have explored prompt evolving, but are often limited to the supervised fine-tuning stage, and prompts are sampled and evolved uniformly without signals. This empirical work presents a paradigm shift: Evolving Alignment via Asymmetric Self-Play (eva), that casts post-training as an infinite game with regret-based signals for 2 players: (i) a creator, who strategically samples and creates new informative prompts and (ii) a solver, who learns to produce preferred responses. eva is the first method that allows language models to adaptively create training prompts in both offline and online RL post-training. The design is simple, easy-to-use yet remarkably effective: eva sets a new SOTA on challenging benchmarks, without any extra human prompts, e.g. it boosts the win-rate of gemma-2-9b-it on Arena-Hard by 51.6% -> 60.1% for DPO and 52.6% -> 62.4% for RLOO, surpassing claude-3-opus and catching up to gemini-1.5-pro, both of which are orders of magnitude larger. Extensive experiments show eva can create effective RL curricula and is robust across ablations. We believe adaptively evolving prompts are key to designing the next-generation RL post-training scheme.

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent developments in steering protein generative models (e.g diffusion models, language models) offer a promising approach. However, by and large, past studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured by low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages compared to alternatives such as reinforcement learning with protein language models.

Since the emergence of large language models, prompt learning has become a popular method for optimizing and customizing these models. Special prompts, such as Chain-of-Thought, have even revealed previously unknown reasoning capabilities within these models. However, the progress of discovering effective prompts has been slow, driving a desire for general prompt optimization methods. Unfortunately, few existing prompt learning methods satisfy the criteria of being truly "general", i.e., automatic, discrete, black-box, gradient-free, and interpretable all at once. In this paper, we introduce metaheuristics, a branch of discrete non-convex optimization methods with over 100 options, as a promising approach to prompt learning. Within our paradigm, we test six typical methods: hill climbing, simulated annealing, genetic algorithms with/without crossover, tabu search, and harmony search, demonstrating their effectiveness in black-box prompt learning and Chain-of-Thought prompt tuning. Furthermore, we show that these methods can be used to discover more human-understandable prompts that were previously unknown, opening the door to a cornucopia of possibilities in prompt optimization. We release all the codes in https://github.com/research4pan/Plum.

We explore the potential of ChatGPT (3.5-turbo and 4) to generate conversations focused on self-care strategies for African-American heart failure patients -- a domain with limited specialized datasets. To simulate patient-health educator dialogues, we employed four prompting strategies: domain, African American Vernacular English (AAVE), Social Determinants of Health (SDOH), and SDOH-informed reasoning. Conversations were generated across key self-care domains of food, exercise, and fluid intake, with varying turn lengths (5, 10, 15) and incorporated patient-specific SDOH attributes such as age, gender, neighborhood, and socioeconomic status. Our findings show that effective prompt design is essential. While incorporating SDOH and reasoning improves dialogue quality, ChatGPT still lacks the empathy and engagement needed for meaningful healthcare communication.

Prompt engineering is critical for the development of LLM-based applications. However, it is usually done manually in a "trial and error" fashion. This manual procedure can be time consuming, ineffective, and the generated prompts are, in a lot of cases, sub-optimal. Even for the prompts which seemingly work well, there is always a lingering question: can the prompts be made better with further modifications? To address these questions, in this paper, we investigate prompt engineering automation. We consider a specific use case scenario in which developers/users have drafted initial prompts, but lack the time/expertise to optimize them. We propose PRewrite, an automated tool to rewrite these drafts and to generate highly effective new prompts. PRewrite is based on the Reinforcement Learning (RL) framework which allows for end-to-end optimization and our design allows the RL search to happen in a large action space. The automated tool leverages manually crafted prompts as starting points which makes the rewriting procedure more guided and efficient. The generated prompts are human readable, and self-explanatory, unlike some of those in previous works. We conducted extensive experiments on diverse datasets and found that the prompts generated with this new method not only outperform professionally crafted prompts, but also prompts generated with other previously proposed methods.

This paper pursues the insight that large language models (LLMs) trained to generate code can vastly improve the effectiveness of mutation operators applied to programs in genetic programming (GP). Because such LLMs benefit from training data that includes sequential changes and modifications, they can approximate likely changes that humans would make. To highlight the breadth of implications of such evolution through large models (ELM), in the main experiment ELM combined with MAP-Elites generates hundreds of thousands of functional examples of Python programs that output working ambulating robots in the Sodarace domain, which the original LLM had never seen in pre-training. These examples then help to bootstrap training a new conditional language model that can output the right walker for a particular terrain. The ability to bootstrap new models that can output appropriate artifacts for a given context in a domain where zero training data was previously available carries implications for open-endedness, deep learning, and reinforcement learning. These implications are explored here in depth in the hope of inspiring new directions of research now opened up by ELM.

Run-time steering strategies like Medprompt are valuable for guiding large language models (LLMs) to top performance on challenging tasks. Medprompt demonstrates that a general LLM can be focused to deliver state-of-the-art performance on specialized domains like medicine by using a prompt to elicit a run-time strategy involving chain of thought reasoning and ensembling. OpenAI's o1-preview model represents a new paradigm, where a model is designed to do run-time reasoning before generating final responses. We seek to understand the behavior of o1-preview on a diverse set of medical challenge problem benchmarks. Following on the Medprompt study with GPT-4, we systematically evaluate the o1-preview model across various medical benchmarks. Notably, even without prompting techniques, o1-preview largely outperforms the GPT-4 series with Medprompt. We further systematically study the efficacy of classic prompt engineering strategies, as represented by Medprompt, within the new paradigm of reasoning models. We found that few-shot prompting hinders o1's performance, suggesting that in-context learning may no longer be an effective steering approach for reasoning-native models. While ensembling remains viable, it is resource-intensive and requires careful cost-performance optimization. Our cost and accuracy analysis across run-time strategies reveals a Pareto frontier, with GPT-4o representing a more affordable option and o1-preview achieving state-of-the-art performance at higher cost. Although o1-preview offers top performance, GPT-4o with steering strategies like Medprompt retains value in specific contexts. Moreover, we note that the o1-preview model has reached near-saturation on many existing medical benchmarks, underscoring the need for new, challenging benchmarks. We close with reflections on general directions for inference-time computation with LLMs.

Highly effective, task-specific prompts are often heavily engineered by experts to integrate detailed instructions and domain insights based on a deep understanding of both instincts of large language models (LLMs) and the intricacies of the target task. However, automating the generation of such expert-level prompts remains elusive. Existing prompt optimization methods tend to overlook the depth of domain knowledge and struggle to efficiently explore the vast space of expert-level prompts. Addressing this, we present PromptAgent, an optimization method that autonomously crafts prompts equivalent in quality to those handcrafted by experts. At its core, PromptAgent views prompt optimization as a strategic planning problem and employs a principled planning algorithm, rooted in Monte Carlo tree search, to strategically navigate the expert-level prompt space. Inspired by human-like trial-and-error exploration, PromptAgent induces precise expert-level insights and in-depth instructions by reflecting on model errors and generating constructive error feedback. Such a novel framework allows the agent to iteratively examine intermediate prompts (states), refine them based on error feedbacks (actions), simulate future rewards, and search for high-reward paths leading to expert prompts. We apply PromptAgent to 12 tasks spanning three practical domains: BIG-Bench Hard (BBH), as well as domain-specific and general NLP tasks, showing it significantly outperforms strong Chain-of-Thought and recent prompt optimization baselines. Extensive analyses emphasize its capability to craft expert-level, detailed, and domain-insightful prompts with great efficiency and generalizability.

Symbolic regression (SR) is the problem of learning a symbolic expression from numerical data. Recently, deep neural models trained on procedurally-generated synthetic datasets showed competitive performance compared to more classical Genetic Programming (GP) algorithms. Unlike their GP counterparts, these neural approaches are trained to generate expressions from datasets given as context. This allows them to produce accurate expressions in a single forward pass at test time. However, they usually do not benefit from search abilities, which result in low performance compared to GP on out-of-distribution datasets. In this paper, we propose a novel method which provides the best of both worlds, based on a Monte-Carlo Tree Search procedure using a context-aware neural mutation model, which is initially pre-trained to learn promising mutations, and further refined from successful experiences in an online fashion. The approach demonstrates state-of-the-art performance on the well-known SRBench benchmark.

Reinforcement learning enhances the reasoning capabilities of large language models but often involves high computational costs due to rollout-intensive optimization. Online prompt selection presents a plausible solution by prioritizing informative prompts to improve training efficiency. However, current methods either depend on costly, exact evaluations or construct prompt-specific predictive models lacking generalization across prompts. This study introduces Generalizable Predictive Prompt Selection (GPS), which performs Bayesian inference towards prompt difficulty using a lightweight generative model trained on the shared optimization history. Intermediate-difficulty prioritization and history-anchored diversity are incorporated into the batch acquisition principle to select informative prompt batches. The small predictive model also generalizes at test-time for efficient computational allocation. Experiments across varied reasoning benchmarks indicate GPS's substantial improvements in training efficiency, final performance, and test-time efficiency over superior baseline methods.

Recent advancements in large language models (LLMs) have enabled a wide range of natural language processing (NLP) tasks to be performed through simple prompt-based interactions. Consequently, several approaches have been proposed to engineer prompts that most effectively enable LLMs to perform a given task (e.g., chain-of-thought prompting). In settings with a well-defined metric to optimize model performance, automatic prompt optimization (APO) methods have been developed to refine a seed prompt. Advancing this line of research, we propose APIO, a simple but effective prompt induction and optimization approach for the tasks of Grammatical Error Correction (GEC) and Text Simplification, without relying on manually specified seed prompts. APIO achieves a new state-of-the-art performance for purely LLM-based prompting methods on these tasks. We make our data, code, prompts, and outputs publicly available.

Prompt engineering is a new paradigm for enhancing the performance of trained neural network models. For optimizing text-style prompts, existing methods usually individually operate small portions of a text step by step, which either breaks the fluency or could not globally adjust a prompt. Since large language models (LLMs) have powerful ability of generating coherent texts token by token, can we utilize LLMs for improving prompts? Based on this motivation, in this paper, considering a trained LLM as a text generator, we attempt to design a black-box evolution algorithm for automatically optimizing texts, namely SPELL (Semantic Prompt Evolution based on a LLM). The proposed method is evaluated with different LLMs and evolution parameters in different text tasks. Experimental results show that SPELL could rapidly improve the prompts indeed. We further explore the evolution process and discuss on the limitations, potential possibilities and future work.

Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties, totaling 40B tokens. These models demonstrate strong performance in generating molecules with specified properties and predicting new molecular characteristics from limited samples. We introduce a novel optimization algorithm that leverages our language models to optimize molecules for arbitrary properties given limited access to a black box oracle. Our approach combines ideas from genetic algorithms, rejection sampling, and prompt optimization. It achieves state-of-the-art performance on multiple molecular optimization benchmarks, including an 8% improvement on Practical Molecular Optimization compared to previous methods. We publicly release the training corpus, the language models and the optimization algorithm.

The fine-tuning of Large Language Models (LLMs) specialized in code generation has seen notable advancements through the use of open-domain coding queries. Despite the successes, existing methodologies like Evol-Instruct encounter performance limitations, impeding further enhancements in code generation tasks. This paper examines the constraints of existing prompt evolution techniques and introduces a novel approach, Instruction Fusion (IF). IF innovatively combines two distinct prompts through a hybridization process, thereby enhancing the evolution of training prompts for code LLMs. Our experimental results reveal that the proposed novel method effectively addresses the shortcomings of prior methods, significantly improving the performance of Code LLMs across five code generation benchmarks, namely HumanEval, HumanEval+, MBPP, MBPP+ and MultiPL-E, which underscore the effectiveness of Instruction Fusion in advancing the capabilities of LLMs in code generation.

Prompting is a mainstream paradigm for adapting large language models to specific natural language processing tasks without modifying internal parameters. Therefore, detailed supplementary knowledge needs to be integrated into external prompts, which inevitably brings extra human efforts and computational burdens for practical applications. As an effective solution to mitigate resource consumption, Efficient Prompting Methods have attracted a wide range of attention. We provide mathematical expressions at a high level to deeply discuss Automatic Prompt Engineering for different prompt components and Prompt Compression in continuous and discrete spaces. Finally, we highlight promising future directions to inspire researchers interested in this field.

Prompt engineering can significantly improve the performance of large language models (LLMs), with automated prompt optimization (APO) gaining significant attention due to the time-consuming and laborious nature of manual prompt design. However, much of the existing work in APO overlooks task-specific characteristics, resulting in prompts that lack domain specificity and are not well-suited for task-specific optimization. In this paper, we introduce TAPO, a multitask-aware prompt optimization framework composed of three key modules. First, a task-aware metric selection module is proposed to enhance task-specific prompt generation capabilities. Second, we present a multi-metrics evaluation module to jointly evaluate prompts from multiple perspectives. Third, an evolution-based optimization framework is introduced for automatic prompt refinement, which improves adaptability across various tasks. Extensive experiments on six datasets demonstrate the effectiveness of our approach, and our code is publicly available.

The rapid development of large language models is transforming software development. Beyond serving as code auto-completion tools in integrated development environments, large language models increasingly function as foundation models within coding agents in vibe-coding scenarios. In such settings, prompts play a central role in agent-based intelligent software development, as they not only guide the behavior of large language models but also serve as carriers of user requirements. Under the dominant conversational paradigm, prompts are typically divided into system prompts and user prompts. System prompts provide high-level instructions to steer model behavior and establish conversational context, while user prompts represent inputs and requirements provided by human users. Despite their importance, designing effective prompts remains challenging, as it requires expertise in both prompt engineering and software engineering, particularly requirements engineering. To reduce the burden of manual prompt construction, numerous automated prompt engineering methods have been proposed. However, most existing approaches neglect the methodological principles of requirements engineering, limiting their ability to generate artifacts that conform to formal requirement specifications in realistic software development scenarios. To address this gap, we propose REprompt, a multi-agent prompt optimization framework guided by requirements engineering. Experiment results demonstrate that REprompt effectively optimizes both system and user prompts by grounding prompt generation in requirements engineering principles.

Since the adoption of large language models (LLMs) for text evaluation has become increasingly prevalent in the field of natural language processing (NLP), a series of existing works attempt to optimize the prompts for LLM evaluators to improve their alignment with human judgment. However, their efforts are limited to optimizing individual factors of evaluation prompts, such as evaluation criteria or output formats, neglecting the combinatorial impact of multiple factors, which leads to insufficient optimization of the evaluation pipeline. Nevertheless, identifying well-behaved prompting strategies for adjusting multiple factors requires extensive enumeration. To this end, we comprehensively integrate 8 key factors for evaluation prompts and propose a novel automatic prompting strategy optimization method called Heuristic Prompting Strategy Search (HPSS). Inspired by the genetic algorithm, HPSS conducts an iterative search to find well-behaved prompting strategies for LLM evaluators. A heuristic function is employed to guide the search process, enhancing the performance of our algorithm. Extensive experiments across four evaluation tasks demonstrate the effectiveness of HPSS, consistently outperforming both human-designed evaluation prompts and existing automatic prompt optimization methods. Our code is available at https://github.com/thu-coai/HPSS.

The recent explosion in the capabilities of large language models has led to a wave of interest in how best to prompt a model to perform a given task. While it may be tempting to simply choose a prompt based on average performance on a validation set, this can lead to a deployment where unexpectedly poor responses are generated, especially for the worst-off users. To mitigate this prospect, we propose Prompt Risk Control, a lightweight framework for selecting a prompt based on rigorous upper bounds on families of informative risk measures. We offer methods for producing bounds on a diverse set of metrics, including quantities that measure worst-case responses and disparities in generation quality across the population of users. In addition, we extend the underlying statistical bounding techniques to accommodate the possibility of distribution shifts in deployment. Experiments on applications such as open-ended chat, medical question summarization, and code generation highlight how such a framework can foster responsible deployment by reducing the risk of the worst outcomes.

Large Language Models (LLMs) are increasingly deployed via third-party system prompts downloaded from public marketplaces. We identify a critical supply-chain vulnerability: conditional system prompt poisoning, where an adversary injects a ``sleeper agent'' into a benign-looking prompt. Unlike traditional jailbreaks that aim for broad refusal-breaking, our proposed framework, SPECTRE, optimizes system prompts to trigger LLMs to output targeted, compromised responses only for specific queries (e.g., ``Who should I vote for the US President?'') while maintaining high utility on benign inputs. Operating in a strict black-box setting without model weight access, SPECTRE utilizes a two-stage optimization including a global semantic search followed by a greedy lexical refinement. Tested on open-source models and commercial APIs (GPT-4o-mini, GPT-3.5), SPECTRE achieves up to 70% F1 reduction on targeted queries with minimal degradation to general capabilities. We further demonstrate that these poisoned prompts evade standard defenses, including perplexity filters and typo-correction, by exploiting the natural noise found in real-world system prompts. Our code and data are available at https://github.com/vietph34/CAIN. WARNING: Our paper contains examples that might be sensitive to the readers!

Self-evolution methods enhance code generation through iterative "generate-verify-refine" cycles, yet existing approaches suffer from low exploration efficiency, failing to discover solutions with superior complexity within limited budgets. This inefficiency stems from initialization bias trapping evolution in poor solution regions, uncontrolled stochastic operations lacking feedback guidance, and insufficient experience utilization across tasks. To address these bottlenecks, we propose Controlled Self-Evolution (CSE), which consists of three key components. Diversified Planning Initialization generates structurally distinct algorithmic strategies for broad solution space coverage. Genetic Evolution replaces stochastic operations with feedback-guided mechanisms, enabling targeted mutation and compositional crossover. Hierarchical Evolution Memory captures both successful and failed experiences at inter-task and intra-task levels. Experiments on EffiBench-X demonstrate that CSE consistently outperforms all baselines across various LLM backbones. Furthermore, CSE achieves higher efficiency from early generations and maintains continuous improvement throughout evolution. Our code is publicly available at https://github.com/QuantaAlpha/EvoControl.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

Majority voting over multiple LLM attempts improves mathematical reasoning, but correlated errors limit the effective sample size. A natural fix is to assign different reasoning strategies to different voters. The approach, Diverse Prompt Mixer, is tested on the AIMO 3 competition: 3 models, 23+ experiments, 50 IMO-level problems, one H100 80 GB, 5-hour limit. Every prompt-level intervention fails. High-temperature sampling already decorrelates errors; weaker strategies reduce accuracy more than they reduce correlation. Across an 8-point capability gap at equal N=8 and every optimization tested, model capability dominates. The gap between the best majority-vote score (42/50) and pass@20 (~45.5) is selection loss, not prompt loss. A verifier-based selector could close it. Prompt engineering cannot.

Environmental and genetic mutations can transform the cells in a co-operating healthy tissue into an ecosystem of individualistic tumour cells that compete for space and resources. Various selection forces are responsible for driving the evolution of cells in a tumour towards more malignant and aggressive phenotypes that tend to have a fitness advantage over the older populations. Although the evolutionary nature of cancer has been recognised for more than three decades (ever since the seminal work of Nowell) it has been only recently that tools traditionally used by ecological and evolutionary researchers have been adopted to study the evolution of cancer phenotypes in populations of individuals capable of co-operation and competition. In this chapter we will describe game theory as an important tool to study the emergence of cell phenotypes in a tumour and will critically review some of its applications in cancer research. These applications demonstrate that game theory can be used to understand the dynamics of somatic cancer evolution and suggest new therapies in which this knowledge could be applied to gain some control over the evolution of the tumour.

Prompt-learning has become a new paradigm in modern natural language processing, which directly adapts pre-trained language models (PLMs) to cloze-style prediction, autoregressive modeling, or sequence to sequence generation, resulting in promising performances on various tasks. However, no standard implementation framework of prompt-learning is proposed yet, and most existing prompt-learning codebases, often unregulated, only provide limited implementations for specific scenarios. Since there are many details such as templating strategy, initializing strategy, and verbalizing strategy, etc. need to be considered in prompt-learning, practitioners face impediments to quickly adapting the desired prompt learning methods to their applications. In this paper, we present {OpenPrompt}, a unified easy-to-use toolkit to conduct prompt-learning over PLMs. OpenPrompt is a research-friendly framework that is equipped with efficiency, modularity, and extendibility, and its combinability allows the freedom to combine different PLMs, task formats, and prompting modules in a unified paradigm. Users could expediently deploy prompt-learning frameworks and evaluate the generalization of them on different NLP tasks without constraints. OpenPrompt is publicly released at { https://github.com/thunlp/OpenPrompt}.

In this white paper we introduce Helix, an AI based solution for missense pathogenicity prediction. With recent advances in the sequencing of human genomes, massive amounts of genetic data have become available. This has shifted the burden of labor for genetic diagnostics and research from the gathering of data to its interpretation. Helix presents a state of the art platform for the prediction of pathogenicity in human missense variants. In addition to offering best-in-class predictive performance, Helix offers a platform that allows researchers to analyze and interpret variants in depth that can be accessed at helixlabs.ai.

Access to real-world medical data is often restricted due to privacy regulations, posing a significant barrier to the advancement of healthcare research. Synthetic data offers a promising alternative; however, generating realistic, clinically valid, and privacy-conscious records remains a major challenge. Recent advancements in Large Language Models (LLMs) offer new opportunities for structured data generation; however, existing approaches frequently lack systematic prompting strategies and comprehensive, multi-dimensional evaluation frameworks. In this paper, we present SynLLM, a modular framework for generating high-quality synthetic medical tabular data using 20 state-of-the-art open-source LLMs, including LLaMA, Mistral, and GPT variants, guided by structured prompts. We propose four distinct prompt types, ranging from example-driven to rule-based constraints, that encode schema, metadata, and domain knowledge to control generation without model fine-tuning. Our framework features a comprehensive evaluation pipeline that rigorously assesses generated data across statistical fidelity, clinical consistency, and privacy preservation. We evaluate SynLLM across three public medical datasets, including Diabetes, Cirrhosis, and Stroke, using 20 open-source LLMs. Our results show that prompt engineering significantly impacts data quality and privacy risk, with rule-based prompts achieving the best privacy-quality balance. SynLLM establishes that, when guided by well-designed prompts and evaluated with robust, multi-metric criteria, LLMs can generate synthetic medical data that is both clinically plausible and privacy-aware, paving the way for safer and more effective data sharing in healthcare research.

Common deep learning approaches for antibody engineering focus on modeling the marginal distribution of sequences. By treating sequences as independent samples, however, these methods overlook affinity maturation as a rich and largely untapped source of information about the evolutionary process by which antibodies explore the underlying fitness landscape. In contrast, classical phylogenetic models explicitly represent evolutionary dynamics but lack the expressivity to capture complex epistatic interactions. We bridge this gap with CoSiNE, a continuous-time Markov chain parameterized by a deep neural network. Mathematically, we prove that CoSiNE provides a first-order approximation to the intractable sequential point mutation process, capturing epistatic effects with an error bound that is quadratic in branch length. Empirically, CoSiNE outperforms state-of-the-art language models in zero-shot variant effect prediction by explicitly disentangling selection from context-dependent somatic hypermutation. Finally, we introduce Guided Gillespie, a classifier-guided sampling scheme that steers CoSiNE at inference time, enabling efficient optimization of antibody binding affinity toward specific antigens.

We propose a multitask pretraining approach ZeroPrompt for zero-shot generalization, focusing on task scaling and zero-shot prompting. While previous models are trained on only a few dozen tasks, we scale to 1,000 tasks for the first time using real-world data. This leads to a crucial discovery that task scaling can be an efficient alternative to model scaling; i.e., the model size has little impact on performance with an extremely large number of tasks. Our results show that task scaling can substantially improve training efficiency by 30 times in FLOPs. Moreover, we present a prompting method that incorporates a genetic algorithm to automatically search for the best prompt for unseen tasks, along with a few other improvements. Empirically, ZeroPrompt substantially improves both the efficiency and the performance of zero-shot learning across a variety of academic and production datasets.

Soft prompt tuning achieves superior performances across a wide range of few-shot tasks. However, the performances of prompt tuning can be highly sensitive to the initialization of the prompts. We also empirically observe that conventional prompt tuning methods cannot encode and learn sufficient task-relevant information from prompt tokens. In this work, we develop an information-theoretic framework that formulates soft prompt tuning as maximizing mutual information between prompts and other model parameters (or encoded representations). This novel view helps us to develop a more efficient, accurate and robust soft prompt tuning method InfoPrompt. With this framework, we develop two novel mutual information based loss functions, to (i) discover proper prompt initialization for the downstream tasks and learn sufficient task-relevant information from prompt tokens and (ii) encourage the output representation from the pretrained language model to be more aware of the task-relevant information captured in the learnt prompt. Extensive experiments validate that InfoPrompt can significantly accelerate the convergence of the prompt tuning and outperform traditional prompt tuning methods. Finally, we provide a formal theoretical result for showing to show that gradient descent type algorithm can be used to train our mutual information loss.

Large Language Models (LLMs) are increasingly used by software engineers for code generation. However, limitations of LLMs such as irrelevant or incorrect code have highlighted the need for prompt programming (or prompt engineering) where engineers apply specific prompt techniques (e.g., chain-of-thought or input-output examples) to improve the generated code. Despite this, the impact of different prompt techniques -- and their combinations -- on code generation remains underexplored. In this study, we introduce CodePromptEval, a dataset of 7072 prompts designed to evaluate five prompt techniques (few-shot, persona, chain-of-thought, function signature, list of packages) and their effect on the correctness, similarity, and quality of complete functions generated by three LLMs (GPT-4o, Llama3, and Mistral). Our findings show that while certain prompt techniques significantly influence the generated code, combining multiple techniques does not necessarily improve the outcome. Additionally, we observed a trade-off between correctness and quality when using prompt techniques. Our dataset and replication package enable future research on improving LLM-generated code and evaluating new prompt techniques.

In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and kataegis (mutation storms), and their implications for cancer are discussed. Genomic alterations spur cancer genome evolution. Thus, the relationship between cancer clonal evolution and cancer stems cells is commented. The key question in cancer biology concerns how these genomic alterations support cancer development and metastasis in the context of biological functioning. Thus far, efforts such as pathway analysis have improved the understanding of the functional contributions of genetic mutations and DNA copy number variations to cancer development, progression and metastasis. However, the known pathways correspond to a small fraction, plausibly 5-10%, of somatic mutations and genes with an altered copy number. To develop a comprehensive understanding of the function of these genomic alterations in cancer, an integrative network framework is proposed and discussed. Finally, the challenges and the directions of studying cancer omic data using an integrative network approach are commented.

Large language models (LLMs) now write code in settings where misreading a single word can break safety or cost money, yet we still expect them to overlook stray typos. To probe where useful robustness ends and harmful insensitivity begins, we compile 50 LeetCode problems and craft three minimal prompt perturbations that should vary in importance: (i) progressive underspecification deleting 10 % of words per step; (ii) lexical flip swapping a pivotal quantifier ("max" to "min"); and (iii) jargon inflation replacing a common noun with an obscure technical synonym. Six frontier models, including three "reasoning-tuned" versions, solve each mutated prompt, and their Python outputs are checked against the original test suites to reveal whether they reused the baseline solution or adapted. Among 11 853 generations we observe a sharp double asymmetry. Models remain correct in 85 % of cases even after 90 % of the prompt is missing, showing over-robustness to underspecification, yet only 54 % react to a single quantifier flip that reverses the task, with reasoning-tuned variants even less sensitive than their bases. Jargon edits lie in between, passing through 56 %. Current LLMs thus blur the line between harmless noise and meaning - changing edits, often treating both as ignorable. Masking salient anchors such as function names can force re - evaluation. We advocate evaluation and training protocols that reward differential sensitivity: stay steady under benign noise but adapt - or refuse - when semantics truly change.

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and the identification of clinical findings. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets.

Despite impressive recent advances in text-to-image diffusion models, obtaining high-quality images often requires prompt engineering by humans who have developed expertise in using them. In this work, we present NeuroPrompts, an adaptive framework that automatically enhances a user's prompt to improve the quality of generations produced by text-to-image models. Our framework utilizes constrained text decoding with a pre-trained language model that has been adapted to generate prompts similar to those produced by human prompt engineers. This approach enables higher-quality text-to-image generations and provides user control over stylistic features via constraint set specification. We demonstrate the utility of our framework by creating an interactive application for prompt enhancement and image generation using Stable Diffusion. Additionally, we conduct experiments utilizing a large dataset of human-engineered prompts for text-to-image generation and show that our approach automatically produces enhanced prompts that result in superior image quality. We make our code, a screencast video demo and a live demo instance of NeuroPrompts publicly available.

Generative AI is gaining increasing attention in software engineering, where testing remains an indispensable reliability mechanism. According to the widely adopted testing pyramid, unit tests constitute the majority of test cases and are often schematic, requiring minimal domain expertise. Automatically generating such tests under the supervision of software engineers can significantly enhance productivity during the development phase of the software lifecycle. This paper investigates the impact of code context and prompting strategies on the quality and adequacy of unit tests generated by various large language models (LLMs) across several families. The results show that including docstrings notably improves code adequacy, while further extending context to the full implementation yields definitely smaller gains. Notably, the chain-of-thought prompting strategy -- applied even to 'reasoning' models -- achieves the best results, with up to 96.3\% branch coverage, a 57\% average mutation score, and near-perfect compilation success rate. Among the evaluated models, M5 (Gemini 2.5 Pro) demonstrated superior performance in both mutation score and branch coverage being still in top in terms of compilation success rate. All the code and resulting test suites are publicly available at https://github.com/peetery/LLM-analysis.

Large Language Models (LLMs) struggle to automate real-world vulnerability detection due to two key limitations: the heterogeneity of vulnerability patterns undermines the effectiveness of a single unified model, and manual prompt engineering for massive weakness categories is unscalable. To address these challenges, we propose MulVul, a retrieval-augmented multi-agent framework designed for precise and broad-coverage vulnerability detection. MulVul adopts a coarse-to-fine strategy: a Router agent first predicts the top-k coarse categories and then forwards the input to specialized Detector agents, which identify the exact vulnerability types. Both agents are equipped with retrieval tools to actively source evidence from vulnerability knowledge bases to mitigate hallucinations. Crucially, to automate the generation of specialized prompts, we design Cross-Model Prompt Evolution, a prompt optimization mechanism where a generator LLM iteratively refines candidate prompts while a distinct executor LLM validates their effectiveness. This decoupling mitigates the self-correction bias inherent in single-model optimization. Evaluated on 130 CWE types, MulVul achieves 34.79\% Macro-F1, outperforming the best baseline by 41.5\%. Ablation studies validate cross-model prompt evolution, which boosts performance by 51.6\% over manual prompts by effectively handling diverse vulnerability patterns.

Prompt engineering is crucial for deploying LLMs but is poorly understood mathematically. We formalize LLM systems as a class of discrete stochastic dynamical systems to explore prompt engineering through the lens of control theory. We investigate the reachable set of output token sequences R_y(mathbf x_0) for which there exists a control input sequence mathbf u for each mathbf y in R_y(mathbf x_0) that steers the LLM to output mathbf y from initial state sequence mathbf x_0. We offer analytic analysis on the limitations on the controllability of self-attention in terms of reachable set, where we prove an upper bound on the reachable set of outputs R_y(mathbf x_0) as a function of the singular values of the parameter matrices. We present complementary empirical analysis on the controllability of a panel of LLMs, including Falcon-7b, Llama-7b, and Falcon-40b. Our results demonstrate a lower bound on the reachable set of outputs R_y(mathbf x_0) w.r.t. initial state sequences mathbf x_0 sampled from the Wikitext dataset. We find that the correct next Wikitext token following sequence mathbf x_0 is reachable over 97% of the time with prompts of kleq 10 tokens. We also establish that the top 75 most likely next tokens, as estimated by the LLM itself, are reachable at least 85% of the time with prompts of kleq 10 tokens. Intriguingly, short prompt sequences can dramatically alter the likelihood of specific outputs, even making the least likely tokens become the most likely ones. This control-centric analysis of LLMs demonstrates the significant and poorly understood role of input sequences in steering output probabilities, offering a foundational perspective for enhancing language model system capabilities.

Large language models (LLMs) transfer well to new tasks out-of-the-box simply given a natural language prompt that demonstrates how to perform the task and no additional training. Prompting is a brittle process wherein small modifications to the prompt can cause large variations in the model predictions, and therefore significant effort is dedicated towards designing a painstakingly "perfect prompt" for a task. To mitigate the high degree of effort involved in prompt-design, we instead ask whether producing multiple effective, yet imperfect, prompts and aggregating them can lead to a high quality prompting strategy. Our observations motivate our proposed prompting method, ASK ME ANYTHING (AMA). We first develop an understanding of the effective prompt formats, finding that question-answering (QA) prompts, which encourage open-ended generation ("Who went to the park?") tend to outperform those that restrict the model outputs ("John went to the park. Output True or False."). Our approach recursively uses the LLM itself to transform task inputs to the effective QA format. We apply the collected prompts to obtain several noisy votes for the input's true label. We find that the prompts can have very different accuracies and complex dependencies and thus propose to use weak supervision, a procedure for combining the noisy predictions, to produce the final predictions for the inputs. We evaluate AMA across open-source model families (e.g., EleutherAI, BLOOM, OPT, and T0) and model sizes (125M-175B parameters), demonstrating an average performance lift of 10.2% over the few-shot baseline. This simple strategy enables the open-source GPT-J-6B model to match and exceed the performance of few-shot GPT3-175B on 15 of 20 popular benchmarks. Averaged across these tasks, the GPT-J-6B model outperforms few-shot GPT3-175B. We release our code here: https://github.com/HazyResearch/ama_prompting

Controlling emergent behavioral personas (e.g., sycophancy, hallucination) in Large Language Models (LLMs) is critical for AI safety, yet remains a persistent challenge. Existing solutions face a dilemma: manual prompt engineering is intuitive but unscalable and imprecise, while automatic optimization methods are effective but operate as "black boxes" with no interpretable connection to model internals. We propose a novel framework that adapts gradient ascent to LLMs, enabling targeted prompt discovery. In specific, we propose two methods, RESGA and SAEGA, that both optimize randomly initialized prompts to achieve better aligned representation with an identified persona direction. We introduce fluent gradient ascent to control the fluency of discovered persona steering prompts. We demonstrate RESGA and SAEGA's effectiveness across Llama 3.1, Qwen 2.5, and Gemma 3 for steering three different personas, sycophancy, hallucination, and myopic reward. Crucially, on sycophancy, our automatically discovered prompts achieve significant improvement (49.90% compared with 79.24%). By grounding prompt discovery in mechanistically meaningful features, our method offers a new paradigm for controllable and interpretable behavior modification.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

In Grammatical Error Correction (GEC), it is crucial to ensure the user's comprehension of a reason for correction. Existing studies present tokens, examples, and hints as to the basis for correction but do not directly explain the reasons for corrections. Although methods that use Large Language Models (LLMs) to provide direct explanations in natural language have been proposed for various tasks, no such method exists for GEC. Generating explanations for GEC corrections involves aligning input and output tokens, identifying correction points, and presenting corresponding explanations consistently. However, it is not straightforward to specify a complex format to generate explanations, because explicit control of generation is difficult with prompts. This study introduces a method called controlled generation with Prompt Insertion (PI) so that LLMs can explain the reasons for corrections in natural language. In PI, LLMs first correct the input text, and then we automatically extract the correction points based on the rules. The extracted correction points are sequentially inserted into the LLM's explanation output as prompts, guiding the LLMs to generate explanations for the correction points. We also create an Explainable GEC (XGEC) dataset of correction reasons by annotating NUCLE, CoNLL2013, and CoNLL2014. Although generations from GPT-3 and ChatGPT using original prompts miss some correction points, the generation control using PI can explicitly guide to describe explanations for all correction points, contributing to improved performance in generating correction reasons.

In today's era, where large language models (LLMs) are integrated into numerous real-world applications, ensuring their safety and robustness is crucial for responsible AI usage. Automated red-teaming methods play a key role in this process by generating adversarial attacks to identify and mitigate potential vulnerabilities in these models. However, existing methods often struggle with slow performance, limited categorical diversity, and high resource demands. While Rainbow Teaming, a recent approach, addresses the diversity challenge by framing adversarial prompt generation as a quality-diversity search, it remains slow and requires a large fine-tuned mutator for optimal performance. To overcome these limitations, we propose Ferret, a novel approach that builds upon Rainbow Teaming by generating multiple adversarial prompt mutations per iteration and using a scoring function to rank and select the most effective adversarial prompt. We explore various scoring functions, including reward models, Llama Guard, and LLM-as-a-judge, to rank adversarial mutations based on their potential harm to improve the efficiency of the search for harmful mutations. Our results demonstrate that Ferret, utilizing a reward model as a scoring function, improves the overall attack success rate (ASR) to 95%, which is 46% higher than Rainbow Teaming. Additionally, Ferret reduces the time needed to achieve a 90% ASR by 15.2% compared to the baseline and generates adversarial prompts that are transferable i.e. effective on other LLMs of larger size. Our codes are available at https://github.com/declare-lab/ferret.

Prompt engineering reduces reasoning mistakes in Large Language Models (LLMs). However, its effectiveness in mitigating vulnerabilities in LLM-generated code remains underexplored. To address this gap, we implemented a benchmark to automatically assess the impact of various prompt engineering strategies on code security. Our benchmark leverages two peer-reviewed prompt datasets and employs static scanners to evaluate code security at scale. We tested multiple prompt engineering techniques on GPT-3.5-turbo, GPT-4o, and GPT-4o-mini. Our results show that for GPT-4o and GPT-4o-mini, a security-focused prompt prefix can reduce the occurrence of security vulnerabilities by up to 56%. Additionally, all tested models demonstrated the ability to detect and repair between 41.9% and 68.7% of vulnerabilities in previously generated code when using iterative prompting techniques. Finally, we introduce a "prompt agent" that demonstrates how the most effective techniques can be applied in real-world development workflows.

Prompt learning is a new paradigm in the Natural Language Processing (NLP) field which has shown impressive performance on a number of natural language tasks with common benchmarking text datasets in full, few-shot, and zero-shot train-evaluation setups. Recently, it has even been observed that large but frozen pre-trained language models (PLMs) with prompt learning outperform smaller but fine-tuned models. However, as with many recent NLP trends, the performance of even the largest PLMs such as GPT-3 do not perform well on specialized domains (e.g. medical text), and the common practice to achieve State of the Art (SoTA) results still consists of pre-training and fine-tuning the PLMs on downstream tasks. The reliance on fine-tuning large PLMs is problematic in clinical settings where data is often held in non-GPU environments, and more resource efficient methods of training specialized domain models is crucial. We investigated the viability of prompt learning on clinically meaningful decision tasks and directly compared with more traditional fine-tuning methods. Results are partially in line with the prompt learning literature, with prompt learning able to match or improve on traditional fine-tuning with substantially fewer trainable parameters and requiring less training data. We argue that prompt learning therefore provides lower computational resource costs applicable to clinical settings, that can serve as an alternative to fine-tuning ever increasing in size PLMs. Complementary code to reproduce experiments presented in this work can be found at: https://github.com/NtaylorOX/Public_Clinical_Prompt.

Diffusion models have significantly advanced text-to-image generation, enabling the creation of highly realistic images conditioned on textual prompts and seeds. Given the considerable intellectual and economic value embedded in such prompts, prompt theft poses a critical security and privacy concern. In this paper, we investigate prompt-stealing attacks targeting diffusion models. We reveal that numerical optimization-based prompt recovery methods are fundamentally limited as they do not account for the initial random noise used during image generation. We identify and exploit a noise-generation vulnerability (CWE-339), prevalent in major image-generation frameworks, originating from PyTorch's restriction of seed values to a range of 2^{32} when generating the initial random noise on CPUs. Through a large-scale empirical analysis conducted on images shared via the popular platform CivitAI, we demonstrate that approximately 95% of these images' seed values can be effectively brute-forced in 140 minutes per seed using our seed-recovery tool, SeedSnitch. Leveraging the recovered seed, we propose PromptPirate, a genetic algorithm-based optimization method explicitly designed for prompt stealing. PromptPirate surpasses state-of-the-art methods, i.e., PromptStealer, P2HP, and CLIP-Interrogator, achieving an 8-11% improvement in LPIPS similarity. Furthermore, we introduce straightforward and effective countermeasures that render seed stealing, and thus optimization-based prompt stealing, ineffective. We have disclosed our findings responsibly and initiated coordinated mitigation efforts with the developers to address this critical vulnerability.

Mutation testing is an effective approach to evaluate and strengthen software test suites, but its adoption is currently limited by the mutants' execution computational cost. Several strategies have been proposed to reduce this cost (a.k.a. mutation cost reduction strategies), however none of them has proven to be effective for all scenarios since they often need an ad-hoc manual selection and configuration depending on the software under test (SUT). In this paper, we propose a novel multi-objective evolutionary hyper-heuristic approach, dubbed Sentinel, to automate the generation of optimal cost reduction strategies for every new SUT. We evaluate Sentinel by carrying out a thorough empirical study involving 40 releases of 10 open-source real-world software systems and both baseline and state-of-the-art strategies as a benchmark. We execute a total of 4,800 experiments, and evaluate their results with both quality indicators and statistical significance tests, following the most recent best practice in the literature. The results show that strategies generated by Sentinel outperform the baseline strategies in 95% of the cases always with large effect sizes. They also obtain statistically significantly better results than state-of-the-art strategies in 88% of the cases, with large effect sizes for 95% of them. Also, our study reveals that the mutation strategies generated by Sentinel for a given software version can be used without any loss in quality for subsequently developed versions in 95% of the cases. These results show that Sentinel is able to automatically generate mutation strategies that reduce mutation testing cost without affecting its testing effectiveness (i.e. mutation score), thus taking off from the tester's shoulders the burden of manually selecting and configuring strategies for each SUT.

We introduce a novel framework that transforms the resource-intensive (adversarial) prompt optimization problem into an efficient, amortized inference task. Our core insight is that pretrained, non-autoregressive generative LLMs, such as Diffusion LLMs, which model the joint distribution over prompt-response pairs, can serve as powerful surrogates for prompt search. This approach enables the direct conditional generation of prompts, effectively replacing costly, per-instance discrete optimization with a small number of parallelizable samples. We provide a probabilistic analysis demonstrating that under mild fidelity assumptions, only a few conditional samples are required to recover high-reward (harmful) prompts. Empirically, we find that the generated prompts are low-perplexity, diverse jailbreaks that exhibit strong transferability to a wide range of black-box target models, including robustly trained and proprietary LLMs. Beyond adversarial prompting, our framework opens new directions for red teaming, automated prompt optimization, and leveraging emerging Flow- and Diffusion-based LLMs.

The rapid evolution of modern malware presents significant challenges to the development of effective defense mechanisms. Traditional cyber deception techniques often rely on static or manually configured parameters, limiting their adaptability to dynamic and sophisticated threats. This study leverages Generative AI (GenAI) models to automate the creation of adaptive cyber deception ploys, focusing on structured prompt engineering (PE) to enhance relevance, actionability, and deployability. We introduce a systematic framework (SPADE) to address inherent challenges large language models (LLMs) pose to adaptive deceptions, including generalized outputs, ambiguity, under-utilization of contextual information, and scalability constraints. Evaluations across diverse malware scenarios using metrics such as Recall, Exact Match (EM), BLEU Score, and expert quality assessments identified ChatGPT-4o as the top performer. Additionally, it achieved high engagement (93%) and accuracy (96%) with minimal refinements. Gemini and ChatGPT-4o Mini demonstrated competitive performance, with Llama3.2 showing promise despite requiring further optimization. These findings highlight the transformative potential of GenAI in automating scalable, adaptive deception strategies and underscore the critical role of structured PE in advancing real-world cybersecurity applications.

Vision-language foundation models (VLMs) show promise for diverse imaging tasks but often underperform on medical benchmarks. Prior efforts to improve performance include model finetuning, which requires large domain-specific datasets and significant compute, or manual prompt engineering, which is hard to generalize and often inaccessible to medical institutions seeking to deploy these tools. These challenges motivate interest in approaches that draw on a model's embedded knowledge while abstracting away dependence on human-designed prompts to enable scalable, weight-agnostic performance improvements. To explore this, we adapt the Declarative Self-improving Python (DSPy) framework for structured automated prompt optimization in medical vision-language systems through a comprehensive, formal evaluation. We implement prompting pipelines for five medical imaging tasks across radiology, gastroenterology, and dermatology, evaluating 10 open-source VLMs with four prompt optimization techniques. Optimized pipelines achieved a median relative improvement of 53% over zero-shot prompting baselines, with the largest gains ranging from 300% to 3,400% on tasks where zero-shot performance is low. These results highlight the substantial potential of applying automated prompt optimization to medical AI systems, demonstrating significant gains for vision-based applications requiring accurate clinical image interpretation. By reducing dependence on prompt design to elicit intended outputs, these techniques allow clinicians to focus on patient care and clinical decision-making. Furthermore, our experiments offer scalability and preserve data privacy, demonstrating performance improvement on open-source VLMs. We publicly release our evaluation pipelines to support reproducible research on specialized medical tasks, available at https://github.com/DaneshjouLab/prompt-triage-lab.

Prompt engineering for LLMs remains complex, with existing frameworks either hiding complexity behind restrictive APIs or providing inflexible canned patterns that resist customization -- making sophisticated agentic programming challenging. We present the Prompt Declaration Language (PDL), a novel approach to prompt representation that tackles this fundamental complexity by bringing prompts to the forefront, enabling manual and automatic prompt tuning while capturing the composition of LLM calls together with rule-based code and external tools. By abstracting away the plumbing for such compositions, PDL aims at improving programmer productivity while providing a declarative representation that is amenable to optimization. This paper demonstrates PDL's utility through a real-world case study of a compliance agent. Tuning the prompting pattern of this agent yielded up to 4x performance improvement compared to using a canned agent and prompt pattern.

Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

Pretrained visual-language models have demonstrated impressive zero-shot abilities in image captioning, when accompanied by hand-crafted prompts. Meanwhile, hand-crafted prompts utilize human prior knowledge to guide the model. However, due to the diversity between different domains, such hand-crafted prompt that provide invariant prior knowledge may result in mode collapse for some domains. Some researches attempted to incorporate expert knowledge and instruction datasets, but the results were costly and led to hallucinations. In this paper, we propose an unsupervised prompt learning method to improve Generalization of Image Captioning (GeneIC), which learns a domain-specific prompt vector for the target domain without requiring annotated data. GeneIC aligns visual and language modalities with a pre-trained Contrastive Language-Image Pre-Training (CLIP) model, thus optimizing the domain-specific prompt vector from two aspects: attribute and semantic consistency. Specifically, GeneIC first generates attribute-transferred images with differing attributes, while retaining semantic similarity with original images. Then, GeneIC uses CLIP to measure the similarity between the images and the generated sentences. By exploring the variable and invariant features in the original images and attribute-transferred images, attribute consistency constrains the attribute change direction of both images and sentences to learn domain-specific knowledge. The semantic consistency directly measures the similarity between the generated sentences and images to ensure the accuracy and comprehensiveness of the generated sentences. Consequently, GeneIC only optimizes the prompt vectors, which effectively retains the knowledge in the large model and introduces domain-specific knowledge.

Recent advancements in prompt engineering strategies, such as Chain-of-Thought (CoT) and Self-Discover, have demonstrated significant potential in improving the reasoning abilities of Large Language Models (LLMs). However, these state-of-the-art (SOTA) prompting strategies rely on single or fixed set of static seed reasoning modules like "think step by step" or "break down this problem" intended to simulate human approach to problem-solving. This constraint limits the flexibility of models in tackling diverse problems effectively. In this paper, we introduce Auto-Evolve, a novel framework that enables LLMs to self-create dynamic reasoning modules and downstream action plan, resulting in significant improvements over current SOTA methods. We evaluate Auto-Evolve on the challenging BigBench-Hard (BBH) dataset with Claude 2.0, Claude 3 Sonnet, Mistral Large, and GPT 4, where it consistently outperforms the SOTA prompt strategies. Auto-Evolve outperforms CoT by up to 10.4% and on an average by 7% across these four models. Our framework introduces two innovations: a) Auto-Evolve dynamically generates reasoning modules for each task while aligning with human reasoning paradigm, thus eliminating the need for predefined templates. b) We introduce an iterative refinement component, that incrementally refines instruction guidance for LLMs and helps boost performance by average 2.8% compared to doing it in a single step.

This paper is an opinion paper that looks at the future of computing in the age of Generative \& Agentic AI. Current software systems are static and inflexible, leading to significant challenges in translating human goals into computational actions. "Living software systems" powered by generative AI offer a solution to this fundamental problem in computing. Traditional software development involves multiple layers of imperfect translation, from business requirements to code, resulting in rigid systems that struggle to adapt to changing user needs and contexts. Generative AI, particularly large language models, can serve as a universal translator between human intent and computer operations. This approach enables the creation of more flexible, context-aware systems that can dynamically evolve to meet user goals. Two pathways for implementing living software systems are explored: using generative AI to accelerate traditional software development, and leveraging agentic AI to create truly adaptive systems. New skills like Prompt Engineering are necessary. By reimagining software as a living, adaptable entity, we can create computing interfaces that are more intuitive, powerful, and responsive to human needs.

Automated code generation can be a powerful technique for software development, significantly reducing developers' efforts and time required to create new code by generating it automatically based on requirements. Recently, OpenAI's language model ChatGPT has emerged as a powerful tool for generating human-like responses to a wide range of textual inputs (i.e., prompts), including those related to code generation. However, the effectiveness of ChatGPT for code generation is not well understood, and the generation performance could be heavily influenced by the choice of prompt. To answer these questions, we conducted experiments using the CodeXGlue dataset to evaluate ChatGPT's capabilities for two code generation tasks, including text-to-code and code-to-code generation. We designed prompts by leveraging the chain-of-thought strategy with multi-step optimizations. Our results showed that by carefully designing prompts to guide ChatGPT, the generation performance can be improved substantially. We also analyzed the factors that influenced the prompt design and provided insights that could guide future research.

This paper presents the second ChatGPT4PCG competition at the 2024 IEEE Conference on Games. In this edition of the competition, we follow the first edition, but make several improvements and changes. We introduce a new evaluation metric along with allowing a more flexible format for participants' submissions and making several improvements to the evaluation pipeline. Continuing from the first edition, we aim to foster and explore the realm of prompt engineering (PE) for procedural content generation (PCG). While the first competition saw success, it was hindered by various limitations; we aim to mitigate these limitations in this edition. We introduce diversity as a new metric to discourage submissions aimed at producing repetitive structures. Furthermore, we allow submission of a Python program instead of a prompt text file for greater flexibility in implementing advanced PE approaches, which may require control flow, including conditions and iterations. We also make several improvements to the evaluation pipeline with a better classifier for similarity evaluation and better-performing function signatures. We thoroughly evaluate the effectiveness of the new metric and the improved classifier. Additionally, we perform an ablation study to select a function signature to instruct ChatGPT for level generation. Finally, we provide implementation examples of various PE techniques in Python and evaluate their preliminary performance. We hope this competition serves as a resource and platform for learning about PE and PCG in general.

Generative AI (GenAI) holds significant promise for automating everyday image editing tasks, especially following the recent release of GPT-4o on March 25, 2025. However, what subjects do people most often want edited? What kinds of editing actions do they want to perform (e.g., removing or stylizing the subject)? Do people prefer precise edits with predictable outcomes or highly creative ones? By understanding the characteristics of real-world requests and the corresponding edits made by freelance photo-editing wizards, can we draw lessons for improving AI-based editors and determine which types of requests can currently be handled successfully by AI editors? In this paper, we present a unique study addressing these questions by analyzing 83k requests from the past 12 years (2013-2025) on the Reddit community, which collected 305k PSR-wizard edits. According to human ratings, approximately only 33% of requests can be fulfilled by the best AI editors (including GPT-4o, Gemini-2.0-Flash, SeedEdit). Interestingly, AI editors perform worse on low-creativity requests that require precise editing than on more open-ended tasks. They often struggle to preserve the identity of people and animals, and frequently make non-requested touch-ups. On the other side of the table, VLM judges (e.g., o1) perform differently from human judges and may prefer AI edits more than human edits. Code and qualitative examples are available at: https://psrdataset.github.io

Comprehending genomic information is essential for biomedical research, yet extracting data from complex distributed databases remains challenging. Large language models (LLMs) offer potential for genomic Question Answering (QA) but face limitations due to restricted access to domain-specific databases. GeneGPT is the current state-of-the-art system that enhances LLMs by utilizing specialized API calls, though it is constrained by rigid API dependencies and limited adaptability. We replicate GeneGPT and propose GenomAgent, a multi-agent framework that efficiently coordinates specialized agents for complex genomics queries. Evaluated on nine tasks from the GeneTuring benchmark, GenomAgent outperforms GeneGPT by 12% on average, and its flexible architecture extends beyond genomics to various scientific domains needing expert knowledge extraction.

Large Language Models, particularly decoder-only generative models such as GPT, are increasingly used to automate Software Engineering tasks. These models are primarily guided through natural language prompts, making prompt engineering a critical factor in system performance and behavior. Despite their growing role in SE research, prompt-related decisions are rarely documented in a systematic or transparent manner, hindering reproducibility and comparability across studies. To address this gap, we conducted a two-phase empirical study. First, we analyzed nearly 300 papers published at the top-3 SE conferences since 2022 to assess how prompt design, testing, and optimization are currently reported. Second, we surveyed 105 program committee members from these conferences to capture their expectations for prompt reporting in LLM-driven research. Based on the findings, we derived a structured guideline that distinguishes essential, desirable, and exceptional reporting elements. Our results reveal significant misalignment between current practices and reviewer expectations, particularly regarding version disclosure, prompt justification, and threats to validity. We present our guideline as a step toward improving transparency, reproducibility, and methodological rigor in LLM-based SE research.

Generative models (e.g., GANs, diffusion models) learn the underlying data distribution in an unsupervised manner. However, many applications of interest require sampling from a particular region of the output space or sampling evenly over a range of characteristics. For efficient sampling in these scenarios, we propose Generative Visual Prompt (PromptGen), a framework for distributional control over pre-trained generative models by incorporating knowledge of other off-the-shelf models. PromptGen defines control as energy-based models (EBMs) and samples images in a feed-forward manner by approximating the EBM with invertible neural networks, avoiding optimization at inference. Our experiments demonstrate how PromptGen can efficiently sample from several unconditional generative models (e.g., StyleGAN2, StyleNeRF, diffusion autoencoder, NVAE) in a controlled or/and de-biased manner using various off-the-shelf models: (1) with the CLIP model as control, PromptGen can sample images guided by text, (2) with image classifiers as control, PromptGen can de-bias generative models across a set of attributes or attribute combinations, and (3) with inverse graphics models as control, PromptGen can sample images of the same identity in different poses. (4) Finally, PromptGen reveals that the CLIP model shows a "reporting bias" when used as control, and PromptGen can further de-bias this controlled distribution in an iterative manner. The code is available at https://github.com/ChenWu98/Generative-Visual-Prompt.

Automatic prompt optimization (APO) has emerged as a powerful paradigm for improving LLM performance without manual prompt engineering. Reflective APO methods such as GEPA iteratively refine prompts by diagnosing failure cases, but the optimization process remains black-box and label-free, leading to uninterpretable trajectories and systematic failure. We identify and empirically demonstrate four limitations: on GSM8K with a defective seed, GEPA degrades accuracy from 23.81% to 13.50%. We propose VISTA, a multi-agent APO framework that decouples hypothesis generation from prompt rewriting, enabling semantically labeled hypotheses, parallel minibatch verification, and interpretable optimization trace. A two-layer explore-exploit mechanism combining random restart and epsilon-greedy sampling further escapes local optima. VISTA recovers accuracy to 87.57% on the same defective seed and consistently outperforms baselines across all conditions on GSM8K and AIME2025.

This paper presents a study of using large language models (LLMs) in modifying existing code. While LLMs for generating code have been widely studied, their role in code modification remains less understood. Although "prompting" serves as the primary interface for developers to communicate intents to LLMs, constructing effective prompts for code modification introduces challenges different from generation. Prior work suggests that natural language summaries may help scaffold this process, yet such approaches have been validated primarily in narrow domains like SQL rewriting. This study investigates two prompting strategies for LLM-assisted code modification: Direct Instruction Prompting, where developers describe changes explicitly in free-form language, and Summary-Mediated Prompting, where changes are made by editing the generated summaries of the code. We conducted an exploratory study with 15 developers who completed modification tasks using both techniques across multiple scenarios. Our findings suggest that developers followed an iterative workflow: understanding the code, localizing the edit, and validating outputs through execution or semantic reasoning. Each prompting strategy presented trade-offs: direct instruction prompting was more flexible and easier to specify, while summary-mediated prompting supported comprehension, prompt scaffolding, and control. Developers' choice of strategy was shaped by task goals and context, including urgency, maintainability, learning intent, and code familiarity. These findings highlight the need for more usable prompt interactions, including adjustable summary granularity, reliable summary-code traceability, and consistency in generated summaries.

We present a genetic algorithm framework for automatically discovering deep learning optimization algorithms. Our approach encodes optimizers as genomes that specify combinations of primitive update terms (gradient, momentum, RMS normalization, Adam-style adaptive terms, and sign-based updates) along with hyperparameters and scheduling options. Through evolutionary search over 50 generations with a population of 50 individuals, evaluated across multiple vision tasks, we discover an evolved optimizer that outperforms Adam by 2.6% in aggregate fitness and achieves a 7.7% relative improvement on CIFAR-10. The evolved optimizer combines sign-based gradient terms with adaptive moment estimation, uses lower momentum coefficients than Adam (β_1=0.86, β_2=0.94), and notably disables bias correction while enabling learning rate warmup and cosine decay. Our results demonstrate that evolutionary search can discover competitive optimization algorithms and reveal design principles that differ from hand-crafted optimizers. Code is available at https://github.com/mmarfinetz/evo-optimizer.

Large language models (LLMs) are increasingly adapted to downstream tasks via reinforcement learning (RL) methods like Group Relative Policy Optimization (GRPO), which often require thousands of rollouts to learn new tasks. We argue that the interpretable nature of language can often provide a much richer learning medium for LLMs, compared with policy gradients derived from sparse, scalar rewards. To test this, we introduce GEPA (Genetic-Pareto), a prompt optimizer that thoroughly incorporates natural language reflection to learn high-level rules from trial and error. Given any AI system containing one or more LLM prompts, GEPA samples system-level trajectories (e.g., reasoning, tool calls, and tool outputs) and reflects on them in natural language to diagnose problems, propose and test prompt updates, and combine complementary lessons from the Pareto frontier of its own attempts. As a result of GEPA's design, it can often turn even just a few rollouts into a large quality gain. Across four tasks, GEPA outperforms GRPO by 10% on average and by up to 20%, while using up to 35x fewer rollouts. GEPA also outperforms the leading prompt optimizer, MIPROv2, by over 10% across two LLMs, and demonstrates promising results as an inference-time search strategy for code optimization.

Current approaches to program synthesis with Large Language Models (LLMs) exhibit a "near miss syndrome": they tend to generate programs that semantically resemble the correct answer (as measured by text similarity metrics or human evaluation), but achieve a low or even zero accuracy as measured by unit tests due to small imperfections, such as the wrong input or output format. This calls for an approach known as Synthesize, Execute, Debug (SED), whereby a draft of the solution is generated first, followed by a program repair phase addressing the failed tests. To effectively apply this approach to instruction-driven LLMs, one needs to determine which prompts perform best as instructions for LLMs, as well as strike a balance between repairing unsuccessful programs and replacing them with newly generated ones. We explore these trade-offs empirically, comparing replace-focused, repair-focused, and hybrid debug strategies, as well as different template-based and model-based prompt-generation techniques. We use OpenAI Codex as the LLM and Program Synthesis Benchmark 2 as a database of problem descriptions and tests for evaluation. The resulting framework outperforms both conventional usage of Codex without the repair phase and traditional genetic programming approaches.

This paper presents a reinforced genetic approach to a defined d-resource system optimization problem. The classical evolution schema was ineffective due to a very strict feasibility function in the studied problem. Hence, the presented strategy has introduced several modifications and adaptations to standard genetic routines, e.g.: a migration operator which is an analogy to the biological random genetic drift.

Enabling large language models (LLMs) to perform tasks in zero-shot has been an appealing goal owing to its labor-saving (i.e., requiring no task-specific annotations); as such, zero-shot prompting approaches also enjoy better task generalizability. To improve LLMs' zero-shot performance, prior work has focused on devising more effective task instructions (e.g., ``let's think step by step'' ). However, we argue that, in order for an LLM to solve them correctly in zero-shot, individual test instances need more carefully designed and customized instructions. To this end, we propose PRoMPTd, an approach that rewrites the task prompt for each individual test input to be more specific, unambiguous, and complete, so as to provide better guidance to the task LLM. We evaluated PRoMPTd on eight datasets covering tasks including arithmetics, logical reasoning, and code generation, using GPT-4 as the task LLM. Notably, PRoMPTd achieves an absolute improvement of around 10% on the complex MATH dataset and 5% on the code generation task on HumanEval, outperforming conventional zero-shot methods. In addition, we also showed that the rewritten prompt can provide better interpretability of how the LLM resolves each test instance, which can potentially be leveraged as a defense mechanism against adversarial prompting. The source code and dataset can be obtained from https://github.com/salokr/PRoMPTd

Text entry is an essential task in our day-to-day digital interactions. Numerous intelligent features have been developed to streamline this process, making text entry more effective, efficient, and fluid. These improvements include sentence prediction and user personalization. However, as deep learning-based language models become the norm for these advanced features, the necessity for data collection and model fine-tuning increases. These challenges can be mitigated by harnessing the in-context learning capability of large language models such as GPT-3.5. This unique feature allows the language model to acquire new skills through prompts, eliminating the need for data collection and fine-tuning. Consequently, large language models can learn various text prediction techniques. We initially showed that, for a sentence prediction task, merely prompting GPT-3.5 surpassed a GPT-2 backed system and is comparable with a fine-tuned GPT-3.5 model, with the latter two methods requiring costly data collection, fine-tuning and post-processing. However, the task of prompting large language models to specialize in specific text prediction tasks can be challenging, particularly for designers without expertise in prompt engineering. To address this, we introduce Promptor, a conversational prompt generation agent designed to engage proactively with designers. Promptor can automatically generate complex prompts tailored to meet specific needs, thus offering a solution to this challenge. We conducted a user study involving 24 participants creating prompts for three intelligent text entry tasks, half of the participants used Promptor while the other half designed prompts themselves. The results show that Promptor-designed prompts result in a 35% increase in similarity and 22% in coherence over those by designers.

We propose CURE, a novel reinforcement learning framework with a dedicated reward design that co-evolves coding and unit test generation capabilities based on their interaction outcomes, without any ground-truth code as supervision. This approach enables flexible and scalable training and allows the unit tester to learn directly from the coder's mistakes. Our derived ReasonFlux-Coder-7B and 14B models improve code generation accuracy by 5.3% and Best-of-N accuracy by 9.0% after optimization on Qwen2.5-Instruct models, outperforming similarly sized Qwen-Coder, DeepSeek-Coder, and Seed-Coder. They naturally extend to downstream tasks such as test-time scaling and agentic coding-achieving a 8.1% improvement over the base model. For the long-CoT model, our ReasonFlux-Coder-4B consistently outperforms Qwen3-4B while achieving 64.8% inference efficiency in unit test generation. Notably, we also find that our model can serve as an effective reward model for reinforcement learning on base models. Project: https://github.com/Gen-Verse/CURE

The principles of automation and innovation serve as foundational elements for advancement in contemporary science and technology. Here, we introduce Pygen, an automation platform designed to empower researchers, technologists, and hobbyists to bring abstract ideas to life as core, usable software tools written in Python. Pygen leverages the immense power of autoregressive large language models to augment human creativity during the ideation, iteration, and innovation process. By combining state-of-the-art language models with open-source code generation technologies, Pygen has significantly reduced the manual overhead of tool development. From a user prompt, Pygen automatically generates Python packages for a complete workflow from concept to package generation and documentation. The findings of our work show that Pygen considerably enhances the researcher's productivity by enabling the creation of resilient, modular, and well-documented packages for various specialized purposes. We employ a prompt enhancement approach to distill the user's package description into increasingly specific and actionable. While being inherently an open-ended task, we have evaluated the generated packages and the documentation using Human Evaluation, LLM-based evaluation, and CodeBLEU, with detailed results in the results section. Furthermore, we documented our results, analyzed the limitations, and suggested strategies to alleviate them. Pygen is our vision of ethical automation, a framework that promotes inclusivity, accessibility, and collaborative development. This project marks the beginning of a large-scale effort towards creating tools where intelligent agents collaborate with humans to improve scientific and technological development substantially. Our code and generated examples are open-sourced at [https://github.com/GitsSaikat/Pygen]

Achieving precise alignment between user intent and generated visuals remains a central challenge in text-to-visual generation, as a single attempt often fails to produce the desired output. To handle this, prior approaches mainly scale the visual generation process (e.g., increasing sampling steps or seeds), but this quickly leads to a quality plateau. This limitation arises because the prompt, crucial for guiding generation, is kept fixed. To address this, we propose Prompt Redesign for Inference-time Scaling, coined PRIS, a framework that adaptively revises the prompt during inference in response to the scaled visual generations. The core idea of PRIS is to review the generated visuals, identify recurring failure patterns across visuals, and redesign the prompt accordingly before regenerating the visuals with the revised prompt. To provide precise alignment feedback for prompt revision, we introduce a new verifier, element-level factual correction, which evaluates the alignment between prompt attributes and generated visuals at a fine-grained level, achieving more accurate and interpretable assessments than holistic measures. Extensive experiments on both text-to-image and text-to-video benchmarks demonstrate the effectiveness of our approach, including a 15% gain on VBench 2.0. These results highlight that jointly scaling prompts and visuals is key to fully leveraging scaling laws at inference-time. Visualizations are available at the website: https://subin-kim-cv.github.io/PRIS.

Jailbreak attacks aim to exploit large language models (LLMs) by inducing them to generate harmful content, thereby revealing their vulnerabilities. Understanding and addressing these attacks is crucial for advancing the field of LLM safety. Previous jailbreak approaches have mainly focused on direct manipulations of harmful intent, with limited attention to the impact of persona prompts. In this study, we systematically explore the efficacy of persona prompts in compromising LLM defenses. We propose a genetic algorithm-based method that automatically crafts persona prompts to bypass LLM's safety mechanisms. Our experiments reveal that: (1) our evolved persona prompts reduce refusal rates by 50-70% across multiple LLMs, and (2) these prompts demonstrate synergistic effects when combined with existing attack methods, increasing success rates by 10-20%. Our code and data are available at https://github.com/CjangCjengh/Generic_Persona.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

Recent soft prompt research has tried to improve reasoning by inserting trained vectors into LLM inputs, yet whether the gain comes from the learned content or from the act of injection itself has not been carefully separated. We study Random Soft Prompts (RSPs), which drop the training step entirely and append a freshly drawn sequence of random embedding vectors to the input. Each RSP vector is sampled from an isotropic Gaussian fitted to the entrywise mean and variance of the pretrained embedding table; the sequence carries no learned content, and yet reaches accuracy comparable to optimized soft prompts on math reasoning benchmarks in several settings. The mechanism unfolds in two stages: because attention has to absorb a never-seen-before random position, the distribution over the first few generated tokens flattens and reasoning trajectories branch, and as generation continues this influence dilutes naturally so the response commits to a single completion. We show that during inference RSPs lift early-stage token diversity and, combined with temperature sampling, widen Pass@N, the probability that at least one out of N attempts is correct. Beyond inference, we carry the same effect into DAPO training and demonstrate practical gains. Our contributions are: (i) RSP isolates the simplest form of soft prompt -- training-free, freshly resampled -- providing a unified lens for the structural effect of injection that variants otherwise differing in training and form all share; (ii) a theoretical and empirical validation of the underlying mechanism; and (iii) an extension from inference to training.

LLMs have demonstrated commendable performance across diverse domains. Nevertheless, formulating high-quality prompts to assist them in their work poses a challenge for non-AI experts. Existing research in prompt engineering suggests somewhat scattered optimization principles and designs empirically dependent prompt optimizers. Unfortunately, these endeavors lack a structural design, incurring high learning costs and it is not conducive to the iterative updating of prompts, especially for non-AI experts. Inspired by structured reusable programming languages, we propose LangGPT, a structural prompt design framework. Furthermore, we introduce Minstrel, a multi-generative agent system with reflection to automate the generation of structural prompts. Experiments and the case study illustrate that structural prompts generated by Minstrel or written manually significantly enhance the performance of LLMs. Furthermore, we analyze the ease of use of structural prompts through a user survey in our online community.

The alignment of large language models (LLMs) with human values is critical as these models become increasingly integrated into various societal and decision-making processes. Traditional methods, such as reinforcement learning from human feedback (RLHF), achieve alignment by fine-tuning model parameters, but these approaches are often computationally expensive and impractical when models are frozen or inaccessible for parameter modification. In contrast, prompt optimization is a viable alternative to RLHF for LLM alignment. While the existing literature has shown empirical promise of prompt optimization, its theoretical underpinning remains under-explored. We address this gap by formulating prompt optimization as an optimization problem and try to provide theoretical insights into the optimality of such a framework. To analyze the performance of the prompt optimization, we study theoretical suboptimality bounds and provide insights in terms of how prompt optimization depends upon the given prompter and target model. We also provide empirical validation through experiments on various datasets, demonstrating that prompt optimization can effectively align LLMs, even when parameter fine-tuning is not feasible.

Recently, large pre-trained vision-language models have shown remarkable performance in zero-shot anomaly detection (ZSAD). With fine-tuning on a single auxiliary dataset, the model enables cross-category anomaly detection on diverse datasets covering industrial defects and medical lesions. Compared to manually designed prompts, prompt learning eliminates the need for expert knowledge and trial-and-error. However, it still faces the following challenges: (i) static learnable tokens struggle to capture the continuous and diverse patterns of normal and anomalous states, limiting generalization to unseen categories; (ii) fixed textual labels provide overly sparse category information, making the model prone to overfitting to a specific semantic subspace. To address these issues, we propose Conditional Prompt Synthesis (CoPS), a novel framework that synthesizes dynamic prompts conditioned on visual features to enhance ZSAD performance. Specifically, we extract representative normal and anomaly prototypes from fine-grained patch features and explicitly inject them into prompts, enabling adaptive state modeling. Given the sparsity of class labels, we leverage a variational autoencoder to model semantic image features and implicitly fuse varied class tokens into prompts. Additionally, integrated with our spatially-aware alignment mechanism, extensive experiments demonstrate that CoPS surpasses state-of-the-art methods by 2.5% AUROC in both classification and segmentation across 13 industrial and medical datasets. Code will be available at https://github.com/cqylunlun/CoPS.

The adaptation of large-scale vision-language models (VLMs) to downstream tasks with limited labeled data remains a significant challenge. While parameter-efficient prompt learning methods offer a promising path, they often suffer from catastrophic forgetting of pre-trained knowledge. Toward addressing this limitation, our work is grounded in the insight that governing the evolutionary path of prompts is essential for forgetting-free adaptation. To this end, we propose EvoPrompt, a novel framework designed to explicitly steer the prompt trajectory for stable, knowledge-preserving fine-tuning. Specifically, our approach employs a Modality-Shared Prompt Projector (MPP) to generate hierarchical prompts from a unified embedding space. Critically, an evolutionary training strategy decouples low-rank updates into directional and magnitude components, preserving early-learned semantic directions while only adapting their magnitude, thus enabling prompts to evolve without discarding foundational knowledge. This process is further stabilized by Feature Geometric Regularization (FGR), which enforces feature decorrelation to prevent representation collapse. Extensive experiments demonstrate that EvoPrompt achieves state-of-the-art performance in few-shot learning while robustly preserving the original zero-shot capabilities of pre-trained VLMs.

Motivation: Phenotype concept recognition (CR) is a fundamental task in biomedical text mining. However, existing methods either require ontology-specific training, making them struggle to generalize across diverse text styles and evolving biomedical terminology, or depend on general-purpose large language models (LLMs) that lack necessary domain knowledge. Results: To address these limitations, we propose AutoPCR, a prompt-based phenotype CR method designed to automatically generalize to new ontologies and unseen data without ontology-specific training. To further boost performance, we also introduce an optional self-supervised training strategy. Experiments show that AutoPCR achieves the best average and most robust performance across datasets. Further ablation and transfer studies demonstrate its inductive capability and generalizability to new ontologies. Availability and Implementation: Our code is available at https://github.com/yctao7/AutoPCR. Contact: drjieliu@umich.edu

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

Prompt engineering is a challenging and important task due to the high sensitivity of Large Language Models (LLMs) to the given prompt and the inherent ambiguity of a textual task instruction. Automatic prompt engineering is essential to achieve optimized performance from LLMs. Recent studies have demonstrated the capabilities of LLMs to automatically conduct prompt engineering by employing a meta-prompt that incorporates the outcomes of the last trials and proposes an improved prompt. However, this requires a high-quality benchmark to compare different prompts, which is difficult and expensive to acquire in many real-world use cases. In this work, we introduce a new method for automatic prompt engineering, using a calibration process that iteratively refines the prompt to the user intent. During the optimization process, the system jointly generates synthetic data of boundary use cases and optimizes the prompt according to the generated dataset. We demonstrate the effectiveness of our method with respect to strong proprietary models on real-world tasks such as moderation and generation. Our method outperforms state-of-the-art methods with a limited number of annotated samples. Furthermore, we validate the advantages of each one of the system's key components. Our system is built in a modular way, facilitating easy adaptation to other tasks. The code is available https://github.com/Eladlev/AutoPrompt{here}.

Despite advances in generation quality, current text-to-image (T2I) models often lack diversity, generating homogeneous outputs. This work introduces a framework to address the need for robust diversity evaluation in T2I models. Our framework systematically assesses diversity by evaluating individual concepts and their relevant factors of variation. Key contributions include: (1) a novel human evaluation template for nuanced diversity assessment; (2) a curated prompt set covering diverse concepts with their identified factors of variation (e.g. prompt: An image of an apple, factor of variation: color); and (3) a methodology for comparing models in terms of human annotations via binomial tests. Furthermore, we rigorously compare various image embeddings for diversity measurement. Notably, our principled approach enables ranking of T2I models by diversity, identifying categories where they particularly struggle. This research offers a robust methodology and insights, paving the way for improvements in T2I model diversity and metric development.

Recently, there has been an increasing interest in automated prompt optimization based on reinforcement learning (RL). This approach offers important advantages, such as generating interpretable prompts and being compatible with black-box foundation models. However, the substantial prompt space size poses challenges for RL-based methods, often leading to suboptimal policy convergence. This paper introduces MultiPrompter, a new framework that views prompt optimization as a cooperative game between prompters which take turns composing a prompt together. Our cooperative prompt optimization effectively reduces the problem size and helps prompters learn optimal prompts. We test our method on the text-to-image task and show its ability to generate higher-quality images than baselines.

LLMs have gained immense popularity among researchers and the general public for its impressive capabilities on a variety of tasks. Notably, the efficacy of LLMs remains significantly dependent on the quality and structure of the input prompts, making prompt design a critical factor for their performance. Recent advancements in automated prompt optimization have introduced diverse techniques that automatically enhance prompts to better align model outputs with user expectations. However, these methods often suffer from the lack of standardization and compatibility across different techniques, limited flexibility in customization, inconsistent performance across model scales, and they often exclusively rely on expensive proprietary LLM APIs. To fill in this gap, we introduce GREATERPROMPT, a novel framework that democratizes prompt optimization by unifying diverse methods under a unified, customizable API while delivering highly effective prompts for different tasks. Our framework flexibly accommodates various model scales by leveraging both text feedback-based optimization for larger LLMs and internal gradient-based optimization for smaller models to achieve powerful and precise prompt improvements. Moreover, we provide a user-friendly Web UI that ensures accessibility for non-expert users, enabling broader adoption and enhanced performance across various user groups and application scenarios. GREATERPROMPT is available at https://github.com/psunlpgroup/GreaterPrompt via GitHub, PyPI, and web user interfaces.

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. In this paper, we introduce BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function as in Bayesian optimization. Moreover, BioDiscoveryAgent, using Claude 3.5 Sonnet, achieves an average of 21% improvement in predicting relevant genetic perturbations across six datasets, and a 46% improvement in the harder task of non-essential gene perturbation, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb more than twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' efficacy.

One of the most profound challenges of modern machine learning is performing well on the long-tail of rare and underrepresented features. Large general-purpose models are trained for many tasks, but work best on high-frequency use cases. After training, it is hard to adapt a model to perform well on specific use cases underrepresented in the training corpus. Relying on prompt engineering or few-shot examples to maximize the output quality on a particular test case can be frustrating, as models can be highly sensitive to small changes, react in unpredicted ways or rely on a fixed system prompt for maintaining performance. In this work, we ask: "Can we optimize our training protocols to both improve controllability and performance on underrepresented use cases at inference time?" We revisit the divide between training and inference techniques to improve long-tail performance while providing users with a set of control levers the model is trained to be responsive to. We create a detailed taxonomy of data characteristics and task provenance to explicitly control generation attributes and implicitly condition generations at inference time. We fine-tune a base model to infer these markers automatically, which makes them optional at inference time. This principled and flexible approach yields pronounced improvements in performance, especially on examples from the long tail of the training distribution. While we observe an average lift of 5.7% win rates in open-ended generation quality with our markers, we see over 9.1% gains in underrepresented domains. We also observe relative lifts of up to 14.1% on underrepresented tasks like CodeRepair and absolute improvements of 35.3% on length instruction following evaluations.

Automatic Prompt Optimization (APO) has emerged as a critical technique for enhancing Large Language Model (LLM) performance, yet current state-of-the-art methods typically rely on large, labeled gold-standard development sets to compute fitness scores for evolutionary or Reinforcement Learning (RL) approaches. In real-world software engineering, however, such curated datasets are rarely available during the initial cold start of agent development, where engineers instead face messy production logs and evolving failure modes. We present ROAD (Reflective Optimization via Automated Debugging), a novel framework that bypasses the need for refined datasets by treating optimization as a dynamic debugging investigation rather than a stochastic search. Unlike traditional mutation strategies, ROAD utilizes a specialized multi-agent architecture, comprising an Analyzer for root-cause analysis, an Optimizer for pattern aggregation, and a Coach for strategy integration, to convert unstructured failure logs into robust, structured Decision Tree Protocols. We evaluated ROAD across both a standardized academic benchmark and a live production Knowledge Management engine. Experimental results demonstrate that ROAD is highly sample-efficient, achieving a 5.6 percent increase in success rate (73.6 percent to 79.2 percent) and a 3.8 percent increase in search accuracy within just three automated iterations. Furthermore, on complex reasoning tasks in the retail domain, ROAD improved agent performance by approximately 19 percent relative to the baseline. These findings suggest that mimicking the human engineering loop of failure analysis and patching offers a viable, data-efficient alternative to resource-intensive RL training for deploying reliable LLM agents.

Soft prompts have emerged as a powerful alternative to adapters in parameter-efficient fine-tuning (PEFT), enabling large language models (LLMs) to adapt to downstream tasks without architectural changes or parameter updates. While prior work has focused on stabilizing training via parameter interaction in small neural prompt encoders, their broader potential for transfer across languages remains unexplored. In this paper, we demonstrate that a prompt encoder can play a central role in improving performance on low-performing languages-those that achieve poor accuracy even under full-model fine-tuning. We introduce the Cross-Prompt Encoder (XPE), which combines a lightweight encoding architecture with multi-source training on typologically diverse languages - a design that enables the model to capture abstract and transferable patterns across languages. To complement XPE, we propose a Dual Soft Prompt mechanism that combines an encoder-based prompt with a directly trained standard soft prompt. This hybrid design proves especially effective for target languages that benefit from both broadly shared structure and language-specific alignment. Experiments on the SIB-200 benchmark reveal a consistent trade-off: XPE is most effective for low-performing languages, while hybrid variants offer broader adaptability across multilingual settings.

In computational cognitive modeling, capturing the full spectrum of human judgment and decision-making processes, beyond just optimal behaviors, is a significant challenge. This study explores whether Large Language Models (LLMs) can emulate the breadth of human reasoning by predicting both intuitive, fast System 1 and deliberate, slow System 2 processes. We investigate the potential of AI to mimic diverse reasoning behaviors across a human population, addressing what we call the "full reasoning spectrum problem". We designed reasoning tasks using a novel generalization of the Natural Language Inference (NLI) format to evaluate LLMs' ability to replicate human reasoning. The questions were crafted to elicit both System 1 and System 2 responses. Human responses were collected through crowd-sourcing and the entire distribution was modeled, rather than just the majority of the answers. We used personality-based prompting inspired by the Big Five personality model to elicit AI responses reflecting specific personality traits, capturing the diversity of human reasoning, and exploring how personality traits influence LLM outputs. Combined with genetic algorithms to optimize the weighting of these prompts, this method was tested alongside traditional machine learning models. The results show that LLMs can mimic human response distributions, with open-source models like Llama and Mistral outperforming proprietary GPT models. Personality-based prompting, especially when optimized with genetic algorithms, significantly enhanced LLMs' ability to predict human response distributions, suggesting that capturing suboptimal, naturalistic reasoning may require modeling techniques incorporating diverse reasoning styles and psychological profiles. The study concludes that personality-based prompting combined with genetic algorithms is promising for enhancing AI's 'human-ness' in reasoning.