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Dec 11

Endowing Protein Language Models with Structural Knowledge

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

  • 5 authors
·
Jan 26, 2024

Bioformer: an efficient transformer language model for biomedical text mining

Pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art performance in natural language processing (NLP) tasks. Recently, BERT has been adapted to the biomedical domain. Despite the effectiveness, these models have hundreds of millions of parameters and are computationally expensive when applied to large-scale NLP applications. We hypothesized that the number of parameters of the original BERT can be dramatically reduced with minor impact on performance. In this study, we present Bioformer, a compact BERT model for biomedical text mining. We pretrained two Bioformer models (named Bioformer8L and Bioformer16L) which reduced the model size by 60% compared to BERTBase. Bioformer uses a biomedical vocabulary and was pre-trained from scratch on PubMed abstracts and PubMed Central full-text articles. We thoroughly evaluated the performance of Bioformer as well as existing biomedical BERT models including BioBERT and PubMedBERT on 15 benchmark datasets of four different biomedical NLP tasks: named entity recognition, relation extraction, question answering and document classification. The results show that with 60% fewer parameters, Bioformer16L is only 0.1% less accurate than PubMedBERT while Bioformer8L is 0.9% less accurate than PubMedBERT. Both Bioformer16L and Bioformer8L outperformed BioBERTBase-v1.1. In addition, Bioformer16L and Bioformer8L are 2-3 fold as fast as PubMedBERT/BioBERTBase-v1.1. Bioformer has been successfully deployed to PubTator Central providing gene annotations over 35 million PubMed abstracts and 5 million PubMed Central full-text articles. We make Bioformer publicly available via https://github.com/WGLab/bioformer, including pre-trained models, datasets, and instructions for downstream use.

  • 5 authors
·
Feb 3, 2023

bert2BERT: Towards Reusable Pretrained Language Models

In recent years, researchers tend to pre-train ever-larger language models to explore the upper limit of deep models. However, large language model pre-training costs intensive computational resources and most of the models are trained from scratch without reusing the existing pre-trained models, which is wasteful. In this paper, we propose bert2BERT, which can effectively transfer the knowledge of an existing smaller pre-trained model (e.g., BERT_BASE) to a large model (e.g., BERT_LARGE) through parameter initialization and significantly improve the pre-training efficiency of the large model. Specifically, we extend the previous function-preserving on Transformer-based language model, and further improve it by proposing advanced knowledge for large model's initialization. In addition, a two-stage pre-training method is proposed to further accelerate the training process. We did extensive experiments on representative PLMs (e.g., BERT and GPT) and demonstrate that (1) our method can save a significant amount of training cost compared with baselines including learning from scratch, StackBERT and MSLT; (2) our method is generic and applicable to different types of pre-trained models. In particular, bert2BERT saves about 45% and 47% computational cost of pre-training BERT_BASE and GPT_BASE by reusing the models of almost their half sizes. The source code will be publicly available upon publication.

  • 10 authors
·
Oct 14, 2021

What Language Model Architecture and Pretraining Objective Work Best for Zero-Shot Generalization?

Large pretrained Transformer language models have been shown to exhibit zero-shot generalization, i.e. they can perform a wide variety of tasks that they were not explicitly trained on. However, the architectures and pretraining objectives used across state-of-the-art models differ significantly, and there has been limited systematic comparison of these factors. In this work, we present a large-scale evaluation of modeling choices and their impact on zero-shot generalization. In particular, we focus on text-to-text models and experiment with three model architectures (causal/non-causal decoder-only and encoder-decoder), trained with two different pretraining objectives (autoregressive and masked language modeling), and evaluated with and without multitask prompted finetuning. We train models with over 5 billion parameters for more than 170 billion tokens, thereby increasing the likelihood that our conclusions will transfer to even larger scales. Our experiments show that causal decoder-only models trained on an autoregressive language modeling objective exhibit the strongest zero-shot generalization after purely unsupervised pretraining. However, models with non-causal visibility on their input trained with a masked language modeling objective followed by multitask finetuning perform the best among our experiments. We therefore consider the adaptation of pretrained models across architectures and objectives. We find that pretrained non-causal decoder models can be adapted into performant generative causal decoder models, using autoregressive language modeling as a downstream task. Furthermore, we find that pretrained causal decoder models can be efficiently adapted into non-causal decoder models, ultimately achieving competitive performance after multitask finetuning. Code and checkpoints are available at https://github.com/bigscience-workshop/architecture-objective.

  • 8 authors
·
Apr 12, 2022

Efficient Transformer Knowledge Distillation: A Performance Review

As pretrained transformer language models continue to achieve state-of-the-art performance, the Natural Language Processing community has pushed for advances in model compression and efficient attention mechanisms to address high computational requirements and limited input sequence length. Despite these separate efforts, no investigation has been done into the intersection of these two fields. In this work, we provide an evaluation of model compression via knowledge distillation on efficient attention transformers. We provide cost-performance trade-offs for the compression of state-of-the-art efficient attention architectures and the gains made in performance in comparison to their full attention counterparts. Furthermore, we introduce a new long-context Named Entity Recognition dataset, GONERD, to train and test the performance of NER models on long sequences. We find that distilled efficient attention transformers can preserve a significant amount of original model performance, preserving up to 98.6% across short-context tasks (GLUE, SQUAD, CoNLL-2003), up to 94.6% across long-context Question-and-Answering tasks (HotpotQA, TriviaQA), and up to 98.8% on long-context Named Entity Recognition (GONERD), while decreasing inference times by up to 57.8%. We find that, for most models on most tasks, performing knowledge distillation is an effective method to yield high-performing efficient attention models with low costs.

  • 4 authors
·
Nov 22, 2023

ERNIE-Tiny : A Progressive Distillation Framework for Pretrained Transformer Compression

Pretrained language models (PLMs) such as BERT adopt a training paradigm which first pretrain the model in general data and then finetune the model on task-specific data, and have recently achieved great success. However, PLMs are notorious for their enormous parameters and hard to be deployed on real-life applications. Knowledge distillation has been prevailing to address this problem by transferring knowledge from a large teacher to a much smaller student over a set of data. We argue that the selection of thee three key components, namely teacher, training data, and learning objective, is crucial to the effectiveness of distillation. We, therefore, propose a four-stage progressive distillation framework ERNIE-Tiny to compress PLM, which varies the three components gradually from general level to task-specific level. Specifically, the first stage, General Distillation, performs distillation with guidance from pretrained teacher, gerenal data and latent distillation loss. Then, General-Enhanced Distillation changes teacher model from pretrained teacher to finetuned teacher. After that, Task-Adaptive Distillation shifts training data from general data to task-specific data. In the end, Task-Specific Distillation, adds two additional losses, namely Soft-Label and Hard-Label loss onto the last stage. Empirical results demonstrate the effectiveness of our framework and generalization gain brought by ERNIE-Tiny.In particular, experiments show that a 4-layer ERNIE-Tiny maintains over 98.0%performance of its 12-layer teacher BERT base on GLUE benchmark, surpassing state-of-the-art (SOTA) by 1.0% GLUE score with the same amount of parameters. Moreover, ERNIE-Tiny achieves a new compression SOTA on five Chinese NLP tasks, outperforming BERT base by 0.4% accuracy with 7.5x fewer parameters and9.4x faster inference speed.

  • 9 authors
·
Jun 4, 2021

LlamaFusion: Adapting Pretrained Language Models for Multimodal Generation

We present LlamaFusion, a framework for empowering pretrained text-only large language models (LLMs) with multimodal generative capabilities, enabling them to understand and generate both text and images in arbitrary sequences. LlamaFusion leverages existing Llama-3's weights for processing texts autoregressively while introducing additional and parallel transformer modules for processing images with diffusion. During training, the data from each modality is routed to its dedicated modules: modality-specific feedforward layers, query-key-value projections, and normalization layers process each modality independently, while the shared self-attention layers allow interactions across text and image features. By freezing the text-specific modules and only training the image-specific modules, LlamaFusion preserves the language capabilities of text-only LLMs while developing strong visual understanding and generation abilities. Compared to methods that pretrain multimodal generative models from scratch, our experiments demonstrate that, LlamaFusion improves image understanding by 20% and image generation by 3.6% using only 50% of the FLOPs while maintaining Llama-3's language capabilities. We also demonstrate that this framework can adapt existing vision-language models with multimodal generation ability. Overall, this framework not only leverages existing computational investments in text-only LLMs but also enables the parallel development of language and vision capabilities, presenting a promising direction for efficient multimodal model development.

  • 7 authors
·
Dec 19, 2024

Parameter-Efficient Fine-Tuning Methods for Pretrained Language Models: A Critical Review and Assessment

With the continuous growth in the number of parameters of transformer-based pretrained language models (PLMs), particularly the emergence of large language models (LLMs) with billions of parameters, many natural language processing (NLP) tasks have demonstrated remarkable success. However, the enormous size and computational demands of these models pose significant challenges for adapting them to specific downstream tasks, especially in environments with limited computational resources. Parameter Efficient Fine-Tuning (PEFT) offers an effective solution by reducing the number of fine-tuning parameters and memory usage while achieving comparable performance to full fine-tuning. The demands for fine-tuning PLMs, especially LLMs, have led to a surge in the development of PEFT methods, as depicted in Fig. 1. In this paper, we present a comprehensive and systematic review of PEFT methods for PLMs. We summarize these PEFT methods, discuss their applications, and outline future directions. Furthermore, we conduct experiments using several representative PEFT methods to better understand their effectiveness in parameter efficiency and memory efficiency. By offering insights into the latest advancements and practical applications, this survey serves as an invaluable resource for researchers and practitioners seeking to navigate the challenges and opportunities presented by PEFT in the context of PLMs.

  • 5 authors
·
Dec 19, 2023

Integrating Knowledge Graph embedding and pretrained Language Models in Hypercomplex Spaces

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

  • 7 authors
·
Aug 4, 2022

Benchmarking for Public Health Surveillance tasks on Social Media with a Domain-Specific Pretrained Language Model

A user-generated text on social media enables health workers to keep track of information, identify possible outbreaks, forecast disease trends, monitor emergency cases, and ascertain disease awareness and response to official health correspondence. This exchange of health information on social media has been regarded as an attempt to enhance public health surveillance (PHS). Despite its potential, the technology is still in its early stages and is not ready for widespread application. Advancements in pretrained language models (PLMs) have facilitated the development of several domain-specific PLMs and a variety of downstream applications. However, there are no PLMs for social media tasks involving PHS. We present and release PHS-BERT, a transformer-based PLM, to identify tasks related to public health surveillance on social media. We compared and benchmarked the performance of PHS-BERT on 25 datasets from different social medial platforms related to 7 different PHS tasks. Compared with existing PLMs that are mainly evaluated on limited tasks, PHS-BERT achieved state-of-the-art performance on all 25 tested datasets, showing that our PLM is robust and generalizable in the common PHS tasks. By making PHS-BERT available, we aim to facilitate the community to reduce the computational cost and introduce new baselines for future works across various PHS-related tasks.

  • 5 authors
·
Apr 9, 2022

From PEFT to DEFT: Parameter Efficient Finetuning for Reducing Activation Density in Transformers

Pretrained Language Models (PLMs) have become the de facto starting point for fine-tuning on downstream tasks. However, as model sizes continue to increase, traditional fine-tuning of all parameters becomes challenging. To address this, parameter-efficient fine-tuning (PEFT) methods have gained popularity as a means to adapt PLMs effectively. In parallel, recent studies have revealed the presence of activation sparsity within the intermediate outputs of the multilayer perception (MLP) blocks in transformers. Low activation density enables efficient model inference on sparsity-aware hardware. Building upon this insight, in this work, we propose a novel density loss that encourages higher activation sparsity (equivalently, lower activation density) in the pre-trained models. We demonstrate the effectiveness of our approach by utilizing mainstream PEFT techniques including QLoRA, LoRA, Adapter, Prompt/Prefix Tuning to facilitate efficient model adaptation across diverse downstream tasks. Experiments show that our proposed method DEFT, Density-Efficient Fine-Tuning, can reduce the activation density consistently and up to 50.72% on RoBERTa_Large, and 53.19% (encoder density) and 90.60% (decoder density) on Flan-T5_XXL (11B) compared to PEFT using GLUE and QA (SQuAD) benchmarks respectively while maintaining competitive performance on downstream tasks. We also showcase that DEFT works complementary with quantized and pruned models

  • 3 authors
·
Feb 2, 2024 1

Massively Multilingual Lexical Specialization of Multilingual Transformers

While pretrained language models (PLMs) primarily serve as general-purpose text encoders that can be fine-tuned for a wide variety of downstream tasks, recent work has shown that they can also be rewired to produce high-quality word representations (i.e., static word embeddings) and yield good performance in type-level lexical tasks. While existing work primarily focused on the lexical specialization of monolingual PLMs with immense quantities of monolingual constraints, in this work we expose massively multilingual transformers (MMTs, e.g., mBERT or XLM-R) to multilingual lexical knowledge at scale, leveraging BabelNet as the readily available rich source of multilingual and cross-lingual type-level lexical knowledge. Concretely, we use BabelNet's multilingual synsets to create synonym pairs (or synonym-gloss pairs) across 50 languages and then subject the MMTs (mBERT and XLM-R) to a lexical specialization procedure guided by a contrastive objective. We show that such massively multilingual lexical specialization brings substantial gains in two standard cross-lingual lexical tasks, bilingual lexicon induction and cross-lingual word similarity, as well as in cross-lingual sentence retrieval. Crucially, we observe gains for languages unseen in specialization, indicating that multilingual lexical specialization enables generalization to languages with no lexical constraints. In a series of subsequent controlled experiments, we show that the number of specialization constraints plays a much greater role than the set of languages from which they originate.

  • 3 authors
·
Aug 1, 2022

Calibrated Language Models Must Hallucinate

Recent language models have a mysterious tendency to generate false but plausible-sounding text. Such "hallucinations" are an obstacle to the usability of language-based AI systems and can harm people who rely upon their outputs. This work shows shows that there is an inherent statistical reason that pretrained language models hallucinate certain types of facts, having nothing to do with the transformer LM architecture or data quality. For "arbitrary" facts whose veracity cannot be determined from the training data, we show that hallucination is necessary for language models that satisfy a statistical calibration condition appropriate for generative language models. Specifically, if the maximum probability of any fact is bounded, we show that the probability of generating a hallucination is close to the fraction of facts that occur exactly once in the training data (a "Good-Turing" estimate), even assuming ideal training data without errors. One conclusion is that models pretrained to be sufficiently good predictors (i.e., calibrated) may require post-training to mitigate hallucinations on the type of arbitrary facts that tend to appear once in the training set. However, our analysis also suggests that there is no statistical reason that pretraining will lead to hallucination on facts that tend to appear more than once in the training data (like references to publications such as articles and books, whose hallucinations have been particularly notable and problematic) or on systematic facts (like arithmetic calculations). Therefore, different architectures and learning algorithms may mitigate these latter types of hallucinations.

  • 2 authors
·
Nov 24, 2023

A Survey of GPT-3 Family Large Language Models Including ChatGPT and GPT-4

Large language models (LLMs) are a special class of pretrained language models obtained by scaling model size, pretraining corpus and computation. LLMs, because of their large size and pretraining on large volumes of text data, exhibit special abilities which allow them to achieve remarkable performances without any task-specific training in many of the natural language processing tasks. The era of LLMs started with OpenAI GPT-3 model, and the popularity of LLMs is increasing exponentially after the introduction of models like ChatGPT and GPT4. We refer to GPT-3 and its successor OpenAI models, including ChatGPT and GPT4, as GPT-3 family large language models (GLLMs). With the ever-rising popularity of GLLMs, especially in the research community, there is a strong need for a comprehensive survey which summarizes the recent research progress in multiple dimensions and can guide the research community with insightful future research directions. We start the survey paper with foundation concepts like transformers, transfer learning, self-supervised learning, pretrained language models and large language models. We then present a brief overview of GLLMs and discuss the performances of GLLMs in various downstream tasks, specific domains and multiple languages. We also discuss the data labelling and data augmentation abilities of GLLMs, the robustness of GLLMs, the effectiveness of GLLMs as evaluators, and finally, conclude with multiple insightful future research directions. To summarize, this comprehensive survey paper will serve as a good resource for both academic and industry people to stay updated with the latest research related to GPT-3 family large language models.

  • 1 authors
·
Oct 4, 2023

Biomedical and Clinical Language Models for Spanish: On the Benefits of Domain-Specific Pretraining in a Mid-Resource Scenario

This work presents biomedical and clinical language models for Spanish by experimenting with different pretraining choices, such as masking at word and subword level, varying the vocabulary size and testing with domain data, looking for better language representations. Interestingly, in the absence of enough clinical data to train a model from scratch, we applied mixed-domain pretraining and cross-domain transfer approaches to generate a performant bio-clinical model suitable for real-world clinical data. We evaluated our models on Named Entity Recognition (NER) tasks for biomedical documents and challenging hospital discharge reports. When compared against the competitive mBERT and BETO models, we outperform them in all NER tasks by a significant margin. Finally, we studied the impact of the model's vocabulary on the NER performances by offering an interesting vocabulary-centric analysis. The results confirm that domain-specific pretraining is fundamental to achieving higher performances in downstream NER tasks, even within a mid-resource scenario. To the best of our knowledge, we provide the first biomedical and clinical transformer-based pretrained language models for Spanish, intending to boost native Spanish NLP applications in biomedicine. Our best models are freely available in the HuggingFace hub: https://huggingface.co/BSC-TeMU.

  • 7 authors
·
Sep 8, 2021

VLMT: Vision-Language Multimodal Transformer for Multimodal Multi-hop Question Answering

The increasing availability of multimodal data across text, tables, and images presents new challenges for developing models capable of complex cross-modal reasoning. Existing methods for Multimodal Multi-hop Question Answering (MMQA) often suffer from limited reasoning capabilities, reliance on modality conversion, and inadequate alignment between visual and textual representations. To address these limitations, this paper introduces Vision-Language Multimodal Transformer (VLMT), a unified architecture that integrates a transformer-based vision encoder with a sequence-to-sequence language model. VLMT employs a direct token-level injection mechanism to fuse visual and textual inputs within a shared embedding space, eliminating the need for intermediate projection layers. To enhance cross-modal alignment and reasoning, a three-stage pretraining strategy is proposed to progressively align vision-language representations and improve the model's capacity for multimodal understanding. Based on the pretrained backbone, two task-specific modules are instantiated to form a two-stage MMQA framework: a multimodal reranker that predicts document relevance scores and utilizes a relative threshold with top-k strategy for context retrieval, and a multimodal question answering model that generates contextually grounded answers based on the retrieved evidence. Comprehensive experiments on two benchmark datasets demonstrate the effectiveness of the proposed approach. On MultimodalQA validation set, VLMT-Large achieves 76.5% Exact Match and 80.1% F1, outperforming the previous state-of-the-art by +9.1% in Exact Match and +8.8% in F1. On WebQA, it attains a QA score of 47.6, surpassing prior models such as PERQA by +3.2. These results highlight VLMT's strong capabilities in multimodal reasoning and its potential to advance real-world information retrieval and question answering systems.

  • 4 authors
·
Apr 11

MLP Memory: Language Modeling with Retriever-pretrained External Memory

While modern decoder-only LLMs achieve superior performance across various domains, hallucinations have risen to be a common problem in their generated text, hindering their application in knowledge-intensive tasks. Retriever-augmented generation (RAG) offers a solution, but the non-parametric nature of the retriever hinders its deep interaction with LLM. In this work, we propose to decouple memorization from the LLM decoder using a pretrained, differentiable external memory. The external memory is an MLP pretrained by imitating the behavior of a retriever on the entire pretraining dataset. Our resulting architecture, which comprises a transformer decoder and an external MLP memory pretrained on language modeling and retriever imitation respectively, demonstrates strong perplexity and performance on downstream tasks. Experiments show our architecture exhibits steeper power-law scaling with model size, achieving 17.5% and 24.1% improvement on WikiText-103 and Web datasets compared to decoder-only models while benefiting from added training without overfitting. We demonstrate superior performance on three hallucination benchmarks and nine memory-intensive tasks. Additionally, our approach delivers 80times speedup over kNN-LM (500M tokens) and 1.3times faster inference than decoder-only models. Unlike kNN-LM, which impairs reasoning, our MLP memory improves StrategyQA performance. We will open-source our code and models in the future.

  • 7 authors
·
Aug 3

Efficient Language Model Training through Cross-Lingual and Progressive Transfer Learning

Most Transformer language models are primarily pretrained on English text, limiting their use for other languages. As the model sizes grow, the performance gap between English and other languages with fewer compute and data resources increases even further. Consequently, more resource-efficient training methods are needed to bridge the gap for languages with fewer resources available. To address this problem, we introduce a cross-lingual and progressive transfer learning approach, called CLP-Transfer, that transfers models from a source language, for which pretrained models are publicly available, like English, to a new target language. As opposed to prior work, which focused on the cross-lingual transfer between two languages, we extend the transfer to the model size. Given a pretrained model in a source language, we aim for a same-sized model in a target language. Instead of training a model from scratch, we exploit a smaller model that is in the target language but requires much fewer resources. Both small and source models are then used to initialize the token embeddings of the larger model based on the overlapping vocabulary of the source and target language. All remaining weights are reused from the model in the source language. This approach outperforms the sole cross-lingual transfer and can save up to 80% of the training steps compared to the random initialization.

  • 2 authors
·
Jan 23, 2023

LaTtE-Flow: Layerwise Timestep-Expert Flow-based Transformer

Recent advances in multimodal foundation models unifying image understanding and generation have opened exciting avenues for tackling a wide range of vision-language tasks within a single framework. Despite progress, existing unified models typically require extensive pretraining and struggle to achieve the same level of performance compared to models dedicated to each task. Additionally, many of these models suffer from slow image generation speeds, limiting their practical deployment in real-time or resource-constrained settings. In this work, we propose Layerwise Timestep-Expert Flow-based Transformer (LaTtE-Flow), a novel and efficient architecture that unifies image understanding and generation within a single multimodal model. LaTtE-Flow builds upon powerful pretrained Vision-Language Models (VLMs) to inherit strong multimodal understanding capabilities, and extends them with a novel Layerwise Timestep Experts flow-based architecture for efficient image generation. LaTtE-Flow distributes the flow-matching process across specialized groups of Transformer layers, each responsible for a distinct subset of timesteps. This design significantly improves sampling efficiency by activating only a small subset of layers at each sampling timestep. To further enhance performance, we propose a Timestep-Conditioned Residual Attention mechanism for efficient information reuse across layers. Experiments demonstrate that LaTtE-Flow achieves strong performance on multimodal understanding tasks, while achieving competitive image generation quality with around 6x faster inference speed compared to recent unified multimodal models.

  • 9 authors
·
Jun 7 2

Large-Scale Chemical Language Representations Capture Molecular Structure and Properties

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

  • 6 authors
·
Jun 17, 2021

A general language model for peptide identification

Advances in peptide identification are revolutionizing our ability to decipher protein functions and accelerate therapeutic discovery. We present PDeepPP, a deep learning framework that integrates pretrained protein language models with parallel transformer-CNN architectures, achieving state-of-the-art performance in peptide characterization tasks. The model's hybrid architecture demonstrates unique capabilities in capturing both local sequence motifs and global structural features, as evidenced by 29% improved cluster separation in UMAP visualizations compared to conventional approaches. Evaluated across 33 biological recognition tasks - including post-translational modification site prediction and bioactive peptide identification - PDeepPP outperformed existing methods in 25 tasks with average AUC improvements of 4.2%. Notably, it achieved 0.9726 accuracy with PR AUC 0.9977 in antimicrobial peptide detection while reducing false negatives by 37.5% in antimalarial recognition scenarios. This framework enables accurate large-scale peptide analysis, achieving 218* acceleration over sequence-alignment-based methods while maintaining 99.5% specificity in critical glycosylation site detection.PDeepPP establishes a new paradigm for computational peptide analysis through its synergistic architecture design, enabling rapid yet precise functional annotation that bridges molecular pattern recognition with translational biomedical applications.We have made our implementation, including code, data, and pretrained models, publicly available via GitHub (https://github.com/fondress/PDeepPP) and Hugging Face (https://huggingface.co/fondress/PDeppPP).

  • 8 authors
·
Feb 21

VLSM-Adapter: Finetuning Vision-Language Segmentation Efficiently with Lightweight Blocks

Foundation Vision-Language Models (VLMs) trained using large-scale open-domain images and text pairs have recently been adapted to develop Vision-Language Segmentation Models (VLSMs) that allow providing text prompts during inference to guide image segmentation. If robust and powerful VLSMs can be built for medical images, it could aid medical professionals in many clinical tasks where they must spend substantial time delineating the target structure of interest. VLSMs for medical images resort to fine-tuning base VLM or VLSM pretrained on open-domain natural image datasets due to fewer annotated medical image datasets; this fine-tuning is resource-consuming and expensive as it usually requires updating all or a significant fraction of the pretrained parameters. Recently, lightweight blocks called adapters have been proposed in VLMs that keep the pretrained model frozen and only train adapters during fine-tuning, substantially reducing the computing resources required. We introduce a novel adapter, VLSM-Adapter, that can fine-tune pretrained vision-language segmentation models using transformer encoders. Our experiments in widely used CLIP-based segmentation models show that with only 3 million trainable parameters, the VLSM-Adapter outperforms state-of-the-art and is comparable to the upper bound end-to-end fine-tuning. The source code is available at: https://github.com/naamiinepal/vlsm-adapter.

  • 4 authors
·
May 9, 2024

Understanding In-Context Learning in Transformers and LLMs by Learning to Learn Discrete Functions

In order to understand the in-context learning phenomenon, recent works have adopted a stylized experimental framework and demonstrated that Transformers can learn gradient-based learning algorithms for various classes of real-valued functions. However, the limitations of Transformers in implementing learning algorithms, and their ability to learn other forms of algorithms are not well understood. Additionally, the degree to which these capabilities are confined to attention-based models is unclear. Furthermore, it remains to be seen whether the insights derived from these stylized settings can be extrapolated to pretrained Large Language Models (LLMs). In this work, we take a step towards answering these questions by demonstrating the following: (a) On a test-bed with a variety of Boolean function classes, we find that Transformers can nearly match the optimal learning algorithm for 'simpler' tasks, while their performance deteriorates on more 'complex' tasks. Additionally, we find that certain attention-free models perform (almost) identically to Transformers on a range of tasks. (b) When provided a teaching sequence, i.e. a set of examples that uniquely identifies a function in a class, we show that Transformers learn more sample-efficiently. Interestingly, our results show that Transformers can learn to implement two distinct algorithms to solve a single task, and can adaptively select the more sample-efficient algorithm depending on the sequence of in-context examples. (c) Lastly, we show that extant LLMs, e.g. LLaMA-2, GPT-4, can compete with nearest-neighbor baselines on prediction tasks that are guaranteed to not be in their training set.

  • 4 authors
·
Oct 4, 2023

IconShop: Text-Guided Vector Icon Synthesis with Autoregressive Transformers

Scalable Vector Graphics (SVG) is a popular vector image format that offers good support for interactivity and animation. Despite its appealing characteristics, creating custom SVG content can be challenging for users due to the steep learning curve required to understand SVG grammars or get familiar with professional editing software. Recent advancements in text-to-image generation have inspired researchers to explore vector graphics synthesis using either image-based methods (i.e., text -> raster image -> vector graphics) combining text-to-image generation models with image vectorization, or language-based methods (i.e., text -> vector graphics script) through pretrained large language models. However, these methods still suffer from limitations in terms of generation quality, diversity, and flexibility. In this paper, we introduce IconShop, a text-guided vector icon synthesis method using autoregressive transformers. The key to success of our approach is to sequentialize and tokenize SVG paths (and textual descriptions as guidance) into a uniquely decodable token sequence. With that, we are able to fully exploit the sequence learning power of autoregressive transformers, while enabling both unconditional and text-conditioned icon synthesis. Through standard training to predict the next token on a large-scale vector icon dataset accompanied by textural descriptions, the proposed IconShop consistently exhibits better icon synthesis capability than existing image-based and language-based methods both quantitatively and qualitatively. Meanwhile, we observe a dramatic improvement in generation diversity, which is validated by the objective Uniqueness and Novelty measures. More importantly, we demonstrate the flexibility of IconShop with multiple novel icon synthesis tasks, including icon editing, icon interpolation, icon semantic combination, and icon design auto-suggestion.

  • 4 authors
·
Apr 27, 2023

BEAST: Efficient Tokenization of B-Splines Encoded Action Sequences for Imitation Learning

We present the B-spline Encoded Action Sequence Tokenizer (BEAST), a novel action tokenizer that encodes action sequences into compact discrete or continuous tokens using B-splines. In contrast to existing action tokenizers based on vector quantization or byte pair encoding, BEAST requires no separate tokenizer training and consistently produces tokens of uniform length, enabling fast action sequence generation via parallel decoding. Leveraging our B-spline formulation, BEAST inherently ensures generating smooth trajectories without discontinuities between adjacent segments. We extensively evaluate BEAST by integrating it with three distinct model architectures: a Variational Autoencoder (VAE) with continuous tokens, a decoder-only Transformer with discrete tokens, and Florence-2, a pretrained Vision-Language Model with an encoder-decoder architecture, demonstrating BEAST's compatibility and scalability with large pretrained models. We evaluate BEAST across three established benchmarks consisting of 166 simulated tasks and on three distinct robot settings with a total of 8 real-world tasks. Experimental results demonstrate that BEAST (i) significantly reduces both training and inference computational costs, and (ii) consistently generates smooth, high-frequency control signals suitable for continuous control tasks while (iii) reliably achieves competitive task success rates compared to state-of-the-art methods.

  • 14 authors
·
Jun 6

TunBERT: Pretrained Contextualized Text Representation for Tunisian Dialect

Pretrained contextualized text representation models learn an effective representation of a natural language to make it machine understandable. After the breakthrough of the attention mechanism, a new generation of pretrained models have been proposed achieving good performances since the introduction of the Transformer. Bidirectional Encoder Representations from Transformers (BERT) has become the state-of-the-art model for language understanding. Despite their success, most of the available models have been trained on Indo-European languages however similar research for under-represented languages and dialects remains sparse. In this paper, we investigate the feasibility of training monolingual Transformer-based language models for under represented languages, with a specific focus on the Tunisian dialect. We evaluate our language model on sentiment analysis task, dialect identification task and reading comprehension question-answering task. We show that the use of noisy web crawled data instead of structured data (Wikipedia, articles, etc.) is more convenient for such non-standardized language. Moreover, results indicate that a relatively small web crawled dataset leads to performances that are as good as those obtained using larger datasets. Finally, our best performing TunBERT model reaches or improves the state-of-the-art in all three downstream tasks. We release the TunBERT pretrained model and the datasets used for fine-tuning.

  • 9 authors
·
Nov 25, 2021

Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Novel Proteins

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

  • 1 authors
·
May 7, 2023

Revisiting the Hypothesis: Do pretrained Transformers Learn In-Context by Gradient Descent?

The emergence of In-Context Learning (ICL) in LLMs remains a significant phenomenon with little understanding. To explain ICL, recent studies try to theoretically connect it to Gradient Descent (GD). We ask, does this connection hold up in actual pre-trained models? We highlight the limiting assumptions in prior works that make their context considerably different from the practical context in which language models are trained. For example, the theoretical hand-constructed weights used in these studies have properties that don't match those of real LLMs. Furthermore, their experimental verification uses ICL objective (training models explicitly for ICL), which differs from the emergent ICL in the wild. We also look for evidence in real models. We observe that ICL and GD have different sensitivity to the order in which they observe demonstrations. Finally, we probe and compare the ICL vs. GD hypothesis in a natural setting. We conduct comprehensive empirical analyses on language models pre-trained on natural data (LLaMa-7B). Our comparisons of three performance metrics highlight the inconsistent behavior of ICL and GD as a function of various factors such as datasets, models, and the number of demonstrations. We observe that ICL and GD modify the output distribution of language models differently. These results indicate that the equivalence between ICL and GD remains an open hypothesis and calls for further studies.

  • 3 authors
·
Oct 12, 2023

Pretrained Transformers for Text Ranking: BERT and Beyond

The goal of text ranking is to generate an ordered list of texts retrieved from a corpus in response to a query. Although the most common formulation of text ranking is search, instances of the task can also be found in many natural language processing applications. This survey provides an overview of text ranking with neural network architectures known as transformers, of which BERT is the best-known example. The combination of transformers and self-supervised pretraining has been responsible for a paradigm shift in natural language processing (NLP), information retrieval (IR), and beyond. In this survey, we provide a synthesis of existing work as a single point of entry for practitioners who wish to gain a better understanding of how to apply transformers to text ranking problems and researchers who wish to pursue work in this area. We cover a wide range of modern techniques, grouped into two high-level categories: transformer models that perform reranking in multi-stage architectures and dense retrieval techniques that perform ranking directly. There are two themes that pervade our survey: techniques for handling long documents, beyond typical sentence-by-sentence processing in NLP, and techniques for addressing the tradeoff between effectiveness (i.e., result quality) and efficiency (e.g., query latency, model and index size). Although transformer architectures and pretraining techniques are recent innovations, many aspects of how they are applied to text ranking are relatively well understood and represent mature techniques. However, there remain many open research questions, and thus in addition to laying out the foundations of pretrained transformers for text ranking, this survey also attempts to prognosticate where the field is heading.

  • 3 authors
·
Oct 13, 2020

LifeGPT: Topology-Agnostic Generative Pretrained Transformer Model for Cellular Automata

The Game of Life (Life), a well known algorithm within the broader class of cellular automata (CA), exhibits complex emergent dynamics, with extreme sensitivity to initial conditions. Modeling and predicting such intricate behavior without explicit knowledge of the system's underlying topology presents a significant challenge, motivating the development of algorithms that can generalize across various grid configurations and boundary conditions. We develop a decoder-only generative pretrained transformer model to solve this problem, showing that our model can simulate Life on a toroidal grid with no prior knowledge on the size of the grid, or its periodic boundary conditions (LifeGPT). LifeGPT is topology-agnostic with respect to its training data and our results show that a GPT model is capable of capturing the deterministic rules of a Turing-complete system with near-perfect accuracy, given sufficiently diverse training data. We also introduce the idea of an `autoregressive autoregressor' to recursively implement Life using LifeGPT. Our results pave the path towards true universal computation within a large language model (LLM) framework, synthesizing of mathematical analysis with natural language processing, and probing AI systems for situational awareness about the evolution of such algorithms without ever having to compute them. Similar GPTs could potentially solve inverse problems in multicellular self-assembly by extracting CA-compatible rulesets from real-world biological systems to create new predictive models, which would have significant consequences for the fields of bioinspired materials, tissue engineering, and architected materials design.

  • 2 authors
·
Sep 3, 2024

Swin3D: A Pretrained Transformer Backbone for 3D Indoor Scene Understanding

The use of pretrained backbones with fine-tuning has been successful for 2D vision and natural language processing tasks, showing advantages over task-specific networks. In this work, we introduce a pretrained 3D backbone, called {\SST}, for 3D indoor scene understanding. We design a 3D Swin transformer as our backbone network, which enables efficient self-attention on sparse voxels with linear memory complexity, making the backbone scalable to large models and datasets. We also introduce a generalized contextual relative positional embedding scheme to capture various irregularities of point signals for improved network performance. We pretrained a large {\SST} model on a synthetic Structured3D dataset, which is an order of magnitude larger than the ScanNet dataset. Our model pretrained on the synthetic dataset not only generalizes well to downstream segmentation and detection on real 3D point datasets, but also outperforms state-of-the-art methods on downstream tasks with +2.3 mIoU and +2.2 mIoU on S3DIS Area5 and 6-fold semantic segmentation, +1.8 mIoU on ScanNet segmentation (val), +1.9 [email protected] on ScanNet detection, and +8.1 [email protected] on S3DIS detection. A series of extensive ablation studies further validate the scalability, generality, and superior performance enabled by our approach. The code and models are available at https://github.com/microsoft/Swin3D .

  • 8 authors
·
Apr 13, 2023 1

Memory Decoder: A Pretrained, Plug-and-Play Memory for Large Language Models

Large Language Models (LLMs) have shown strong abilities in general language tasks, yet adapting them to specific domains remains a challenge. Current method like Domain Adaptive Pretraining (DAPT) requires costly full-parameter training and suffers from catastrophic forgetting. Meanwhile, Retrieval-Augmented Generation (RAG) introduces substantial inference latency due to expensive nearest-neighbor searches and longer context. This paper introduces Memory Decoder, a plug-and-play pretrained memory that enables efficient domain adaptation without changing the original model's parameters. Memory Decoder employs a small transformer decoder that learns to imitate the behavior of an external non-parametric retriever. Once trained, Memory Decoder can be seamlessly integrated with any pretrained language model that shares the same tokenizer, requiring no model-specific modifications. Experimental results demonstrate that Memory Decoder enables effective adaptation of various Qwen and Llama models to three distinct specialized domains: biomedicine, finance, and law, reducing perplexity by an average of 6.17 points. Overall, Memory Decoder introduces a novel paradigm centered on a specially pretrained memory component designed for domain-specific adaptation. This memory architecture can be integrated in a plug-and-play manner, consistently enhancing performance across multiple models within the target domain.

  • 7 authors
·
Aug 13 2

Making the Most of your Model: Methods for Finetuning and Applying Pretrained Transformers

This thesis provides methods and analysis of models which make progress on this goal. The techniques outlined are task agnostic, and should provide benefit when used with nearly any transformer LM. We introduce two new finetuning methods which add new capabilities to the models they are used on. The first adds a recurrence mechanism, which removes the fixed-window sized constraint and improves the efficiency of a transformer decoder. The second allows masked language models (MLMs) to be used for initialization of both the encoder and decoder of a non-autoregressive sequence-to-sequence transformer, opening up generative applications of models which were previously only used for natural language understanding tasks. We also introduce two new techniques for improving the quality of predictions of any transformer decoder without additional finetuning. One, hidden state optimization, can be applied to any transformer decoder to improve the quality of predictions at inference time, especially for few-shot classification. The other, conditional beam search, allows practitioners to search for natural language generation (NLG) model outputs with high likelihood while conditioning on the event that the output is not degenerate (e.g. empty, repetitive, etc.). Finally, we provide theoretical and empirical insights on the divergence of model-likelihood and output quality which has widely been observed in prior work. These insights apply to any model which represents a distribution over text, and apply to language models which are not transformers or even autoregressive. We argue that the NLP community has, to some extent, misunderstood the implications of these findings, and encourage a point of view which has more nuance.

  • 1 authors
·
Aug 28, 2024

BudgetLongformer: Can we Cheaply Pretrain a SotA Legal Language Model From Scratch?

Pretrained transformer models have achieved state-of-the-art results in many tasks and benchmarks recently. Many state-of-the-art Language Models (LMs), however, do not scale well above the threshold of 512 input tokens. In specialized domains though (such as legal, scientific or biomedical), models often need to process very long text (sometimes well above 10000 tokens). Even though many efficient transformers have been proposed (such as Longformer, BigBird or FNet), so far, only very few such efficient models are available for specialized domains. Additionally, since the pretraining process is extremely costly in general - but even more so as the sequence length increases - it is often only in reach of large research labs. One way of making pretraining cheaper is the Replaced Token Detection (RTD) task, by providing more signal during training, since the loss can be computed over all tokens. In this work, we train Longformer models with the efficient RTD task on legal data to showcase that pretraining efficient LMs is possible using much less compute. We evaluate the trained models on challenging summarization tasks requiring the model to summarize long texts to show to what extent the models can achieve good performance on downstream tasks. We find that both the small and base models outperform their baselines on the in-domain BillSum and out-of-domain PubMed tasks in their respective parameter range. We publish our code and models for research purposes.

  • 2 authors
·
Nov 30, 2022

Efficient Long-Range Transformers: You Need to Attend More, but Not Necessarily at Every Layer

Pretrained transformer models have demonstrated remarkable performance across various natural language processing tasks. These models leverage the attention mechanism to capture long- and short-range dependencies in the sequence. However, the (full) attention mechanism incurs high computational cost - quadratic in the sequence length, which is not affordable in tasks with long sequences, e.g., inputs with 8k tokens. Although sparse attention can be used to improve computational efficiency, as suggested in existing work, it has limited modeling capacity and often fails to capture complicated dependencies in long sequences. To tackle this challenge, we propose MASFormer, an easy-to-implement transformer variant with Mixed Attention Spans. Specifically, MASFormer is equipped with full attention to capture long-range dependencies, but only at a small number of layers. For the remaining layers, MASformer only employs sparse attention to capture short-range dependencies. Our experiments on natural language modeling and generation tasks show that a decoder-only MASFormer model of 1.3B parameters can achieve competitive performance to vanilla transformers with full attention while significantly reducing computational cost (up to 75%). Additionally, we investigate the effectiveness of continual training with long sequence data and how sequence length impacts downstream generation performance, which may be of independent interest.

  • 5 authors
·
Oct 18, 2023 1

BiPFT: Binary Pre-trained Foundation Transformer with Low-rank Estimation of Binarization Residual Polynomials

Pretrained foundation models offer substantial benefits for a wide range of downstream tasks, which can be one of the most potential techniques to access artificial general intelligence. However, scaling up foundation transformers for maximal task-agnostic knowledge has brought about computational challenges, especially on resource-limited devices such as mobiles. This work proposes the first Binary Pretrained Foundation Transformer (BiPFT) for natural language understanding (NLU) tasks, which remarkably saves 56 times operations and 28 times memory. In contrast to previous task-specific binary transformers, BiPFT exhibits a substantial enhancement in the learning capabilities of binary neural networks (BNNs), promoting BNNs into the era of pre-training. Benefiting from extensive pretraining data, we further propose a data-driven binarization method. Specifically, we first analyze the binarization error in self-attention operations and derive the polynomials of binarization error. To simulate full-precision self-attention, we define binarization error as binarization residual polynomials, and then introduce low-rank estimators to model these polynomials. Extensive experiments validate the effectiveness of BiPFTs, surpassing task-specific baseline by 15.4% average performance on the GLUE benchmark. BiPFT also demonstrates improved robustness to hyperparameter changes, improved optimization efficiency, and reduced reliance on downstream distillation, which consequently generalize on various NLU tasks and simplify the downstream pipeline of BNNs. Our code and pretrained models are publicly available at https://github.com/Xingrun-Xing/BiPFT.

  • 7 authors
·
Dec 14, 2023

Paralinguistics-Enhanced Large Language Modeling of Spoken Dialogue

Large Language Models (LLMs) have demonstrated superior abilities in tasks such as chatting, reasoning, and question-answering. However, standard LLMs may ignore crucial paralinguistic information, such as sentiment, emotion, and speaking style, which are essential for achieving natural, human-like spoken conversation, especially when such information is conveyed by acoustic cues. We therefore propose Paralinguistics-enhanced Generative Pretrained Transformer (ParalinGPT), an LLM that utilizes text and speech modalities to better model the linguistic content and paralinguistic attributes of spoken dialogue. The model takes the conversational context of text, speech embeddings, and paralinguistic attributes as input prompts within a serialized multitasking multimodal framework. Specifically, our framework serializes tasks in the order of current paralinguistic attribute prediction, response paralinguistic attribute prediction, and response text generation with autoregressive conditioning. We utilize the Switchboard-1 corpus, including its sentiment labels as the paralinguistic attribute, as our spoken dialogue dataset. Experimental results indicate the proposed serialized multitasking method outperforms typical sequence classification techniques on current and response sentiment classification. Furthermore, leveraging conversational context and speech embeddings significantly improves both response text generation and sentiment prediction. Our proposed framework achieves relative improvements of 6.7%, 12.0%, and 3.5% in current sentiment accuracy, response sentiment accuracy, and response text BLEU score, respectively.

  • 9 authors
·
Dec 23, 2023