---
tags:
- pearl
- molecular-property-prediction
---

# PEARL Benchmark -- Top-5 Models per Dataset

Parameter-Efficient Adaptation with Retrieval-Augmented Learning for Molecular Property Prediction. Each dataset folder below holds its top-5 best-performing methods, ranked by the dataset's primary metric.

Code: https://github.com/raghvendra5688/PEARL

## BACE (classification, ranked by MCC)

| Rank | Method | MCC | Configuration | Path |
|---|---|---|---|---|
| 1 | E2E LoRA -- Uni-Mol | 0.6234 | Weighted Loss | [BACE/rank1_e2e-lora-uni-mol](./BACE/rank1_e2e-lora-uni-mol) |
| 2 | E2E LoRA -- HF | 0.5660 | ibm__MoLFormer__XL__both__10pct, fl | [BACE/rank2_e2e-lora-hf](./BACE/rank2_e2e-lora-hf) |
| 3 | FT Embed | 0.5570 | MolFormer_Finetuned_FL | [BACE/rank3_ft-embed](./BACE/rank3_ft-embed) |
| 4 | RAFE | 0.5570 | MolFormer_Finetuned_FL | [BACE/rank4_rafe](./BACE/rank4_rafe) |
| 5 | FT Embed+PC | 0.5500 | Molformer_Finetuned_WL_embeddings | [BACE/rank5_ft-embed-pc](./BACE/rank5_ft-embed-pc) |

## BBBP (classification, ranked by MCC)

| Rank | Method | MCC | Configuration | Path |
|---|---|---|---|---|
| 1 | RAFE | 0.7980 | MolFormer_Finetuned_FL | [BBBP/rank1_rafe](./BBBP/rank1_rafe) |
| 2 | FT Embed+PC | 0.7890 | MolFormer_Finetuned_FL_embeddings | [BBBP/rank2_ft-embed-pc](./BBBP/rank2_ft-embed-pc) |
| 3 | FT Embed | 0.7870 | MolFormer_Finetuned_FL | [BBBP/rank3_ft-embed](./BBBP/rank3_ft-embed) |
| 4 | E2E LoRA -- Uni-Mol | 0.7740 | Weighted Loss | [BBBP/rank4_e2e-lora-uni-mol](./BBBP/rank4_e2e-lora-uni-mol) |
| 5 | E2E LoRA -- HF | 0.7670 | ibm__MoLFormer__XL__both__10pct, fl | [BBBP/rank5_e2e-lora-hf](./BBBP/rank5_e2e-lora-hf) |

## FLAVOR (classification, ranked by MCC)

| Rank | Method | MCC | Configuration | Path |
|---|---|---|---|---|
| 1 | Chemprop | 0.8090 | D-MPNN | [FLAVOR/rank1_chemprop](./FLAVOR/rank1_chemprop) |
| 2 | PC-only | 0.8080 | XGBoost | [FLAVOR/rank2_pc-only](./FLAVOR/rank2_pc-only) |
| 3 | E2E LoRA -- HF | 0.8020 | DeepChem__ChemBERTa__77M__MTR, wl | [FLAVOR/rank3_e2e-lora-hf](./FLAVOR/rank3_e2e-lora-hf) |
| 4 | FT Embed+PC | 0.8010 | Molformer_Finetuned_WL_embeddings | [FLAVOR/rank4_ft-embed-pc](./FLAVOR/rank4_ft-embed-pc) |
| 5 | RAFE | 0.8000 | ChemBERTa_77M_MTR_FL | [FLAVOR/rank5_rafe](./FLAVOR/rank5_rafe) |

## HERG (classification, ranked by MCC)

| Rank | Method | MCC | Configuration | Path |
|---|---|---|---|---|
| 1 | E2E LoRA -- Uni-Mol | 0.6093 | Weighted Loss | [HERG/rank1_e2e-lora-uni-mol](./HERG/rank1_e2e-lora-uni-mol) |
| 2 | PC-only | 0.6040 | XGBoost | [HERG/rank2_pc-only](./HERG/rank2_pc-only) |
| 3 | FT Embed+PC | 0.6015 | UniMol_FL | [HERG/rank3_ft-embed-pc](./HERG/rank3_ft-embed-pc) |
| 4 | RAFE | 0.5889 | UniMol_FL | [HERG/rank4_rafe](./HERG/rank4_rafe) |
| 5 | FT Embed | 0.5798 | UniMol_FL | [HERG/rank5_ft-embed](./HERG/rank5_ft-embed) |

## DILI (classification, ranked by MCC)

| Rank | Method | MCC | Configuration | Path |
|---|---|---|---|---|
| 1 | RAFE | 0.7897 | UniMol_FL | [DILI/rank1_rafe](./DILI/rank1_rafe) |
| 2 | E2E LoRA -- HF | 0.7704 | DeepChem__ChemBERTa__77M__MTR, wl | [DILI/rank2_e2e-lora-hf](./DILI/rank2_e2e-lora-hf) |
| 3 | PC-only | 0.7650 | CatBoost | [DILI/rank3_pc-only](./DILI/rank3_pc-only) |
| 4 | GCN | 0.7280 | GINConv | [DILI/rank4_gcn](./DILI/rank4_gcn) |
| 5 | E2E LoRA -- Uni-Mol | 0.7079 | Focal Loss | [DILI/rank5_e2e-lora-uni-mol](./DILI/rank5_e2e-lora-uni-mol) |

## CACO2 (regression, ranked by Spearman)

| Rank | Method | Spearman | Configuration | Path |
|---|---|---|---|---|
| 1 | PC-only | 0.8534 | CatBoost | [CACO2/rank1_pc-only](./CACO2/rank1_pc-only) |
| 2 | RAFE | 0.8347 | ChemBERTa_77M_MTR_Huber | [CACO2/rank2_rafe](./CACO2/rank2_rafe) |
| 3 | FT Embed+PC | 0.8271 | ChemBERTa_77M_MTR_Huber | [CACO2/rank3_ft-embed-pc](./CACO2/rank3_ft-embed-pc) |
| 4 | FT Embed | 0.8211 | ChemBERTa_77M_MTR_Huber | [CACO2/rank4_ft-embed](./CACO2/rank4_ft-embed) |
| 5 | Chemprop | 0.8022 | D-MPNN | [CACO2/rank5_chemprop](./CACO2/rank5_chemprop) |

## HALF_LIFE (regression, ranked by Spearman)

| Rank | Method | Spearman | Configuration | Path |
|---|---|---|---|---|
| 1 | FT Embed | 0.6226 | MolFormer_Finetuned_Huber | [HALF_LIFE/rank1_ft-embed](./HALF_LIFE/rank1_ft-embed) |
| 2 | FT Embed+PC | 0.5927 | MolFormer_Finetuned_Huber | [HALF_LIFE/rank2_ft-embed-pc](./HALF_LIFE/rank2_ft-embed-pc) |
| 3 | RAFE | 0.5684 | MolFormer_Finetuned_Huber | [HALF_LIFE/rank3_rafe](./HALF_LIFE/rank3_rafe) |
| 4 | E2E LoRA -- HF | 0.5406 | DeepChem__ChemBERTa__77M__MTR, huber | [HALF_LIFE/rank4_e2e-lora-hf](./HALF_LIFE/rank4_e2e-lora-hf) |
| 5 | PC-only | 0.5211 | CatBoost | [HALF_LIFE/rank5_pc-only](./HALF_LIFE/rank5_pc-only) |