Key papers

• An AI system to help scientists write expert-level empirical software (2025)
  Eser Ayg\"un et al.
  12.53
• Towards an AI co-scientist (2025)
  Juraj Gottweis et al.
  10.78
• BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology (2025)
  Ludovico Mitchener et al.
  10.60
• DrugGen 2: A disease-aware language model for enhancing drug discovery (2026)
  Ali Motahharynia et al.
  10.47
• DeepScientist: Advancing Frontier-Pushing Scientific Findings Progressively (2025)
  Yixuan Weng et al.
  9.44
• Graph Neural Networks in Modern AI-aided Drug Discovery (2025)
  Odin Zhang et al.
  8.64
• Artificial Intelligence and Deep Learning Algorithms for Epigenetic Sequence Analysis: A Review for Epigeneticists and AI Experts (2025)
  Muhammad Tahir et al.
  8.52
• Combining physics-based and data-driven models: advancing the frontiers of research with Scientific Machine Learning (2025)
  Alfio Quarteroni and Paola Gervasio and Francesco Regazzoni
  8.45
• MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research (2025)
  James Burgess et al.
  8.38
• Unified modeling of 3D molecular generation via atomic interactions with PocketXMol. (2026)
  Xingang Peng et al.
  8.23
• PharmAgents: Building a Virtual Pharma with Large Language Model Agents (2025)
  Bowen Gao et al.
  7.96
• ClinFusion: A Vision-Centric Multimodal LLM System for Holistic Medical Understanding (2026)
  Hangjie Yuan et al.
  7.92
• AI-Powered Prediction of Nanoparticle Pharmacokinetics: A Multi-View Learning Approach (2025)
  Amirhossein Khakpour et al.
  7.71
• Machine Learning Methods for Gene Regulatory Network Inference (2025)
  Akshata Hegde et al.
  7.64
• HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data (2025)
  Hiren Madhu et al.
  7.59
• Physics-informed graph neural networks for flow field estimation in carotid arteries (2024)
  Julian Suk et al.
  7.55
• drGT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network (2024)
  Yoshitaka Inoue et al.
  7.38
• Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization (2025)
  Jiajun Yu et al.
  7.29
• Multi-view biomedical foundation models for molecule-target and property prediction (2024)
  Parthasarathy Suryanarayanan et al.
  7.23
• Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation (2025)
  Sophia Tang et al.
  7.13
• Contextualizing biological perturbation experiments through language (2025)
  Menghua Wu et al.
  7.08
• Representation Meets Optimization: Training PINNs and PIKANs for Gray-Box Discovery in Systems Pharmacology (2025)
  Nazanin Ahmadi Daryakenari et al.
  7.02
• BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments (2024)
  Yusuf Roohani et al.
  7.00
• Physics-Informed Machine Learning in Biomedical Science and Engineering (2025)
  Nazanin Ahmadi et al.
  6.75
• Physics-informed deep learning for infectious disease forecasting (2025)
  Ying Qian et al.
  6.67
• SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Models (2025)
  Kunyang Sun et al.
  6.58
• Machine Learning Methods for Small Data and Upstream Bioprocessing Applications: A Comprehensive Review (2025)
  Johnny Peng et al.
  6.53
• PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (2024)
  Yan Wu et al.
  6.50
• Multimodal AI predicts clinical outcomes of drug combinations from preclinical data (2025)
  Yepeng Huang et al.
  6.36
• Robin: A multi-agent system for automating scientific discovery (2025)
  Ali Essam Ghareeb et al.
  6.23
• Interpretable Graph Kolmogorov-Arnold Networks for Multi-Cancer Classification and Biomarker Identification using Multi-Omics Data (2025)
  Fadi Alharbi et al.
  6.12
• ImageDDI: Image-enhanced Molecular Motif Sequence Representation for Drug-Drug Interaction Prediction (2025)
  Yuqin He et al.
  6.12
• Molecular-driven Foundation Model for Oncologic Pathology (2025)
  Anurag Vaidya et al.
  6.01
• Multi-Exit Kolmogorov-Arnold Networks: enhancing accuracy and parsimony (2025)
  James Bagrow and Josh Bongard
  6.01
• scDrugMap: Benchmarking Large Foundation Models for Drug Response Prediction (2025)
  Qing Wang et al.
  5.96
• TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools (2025)
  Shanghua Gao et al.
  5.84
• CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction (2025)
  Jueon Park et al.
  5.82
• AI-driven multi-omics integration for multi-scale predictive modeling of causal genotype-environment-phenotype relationships (2024)
  You Wu (1) et al.
  5.78
• Molecular Graph Contrastive Learning with Line Graph (2025)
  Xueyuan Chen et al.
  5.73
• Multi-modal AI for comprehensive breast cancer prognostication (2024)
  Jan Witowski et al.
  5.68
• GBDTSVM: Combined Support Vector Machine and Gradient Boosting Decision Tree Framework for efficient snoRNA-disease association prediction (2025)
  Ummay Maria Muna et al.
  5.65
• CellVerse: Do Large Language Models Really Understand Cell Biology? (2025)
  Fan Zhang et al.
  5.65
• Benchmarking AI scientists for omics data driven biological discovery (2025)
  Erpai Luo et al.
  5.65
• DynamicDTA: Drug-Target Binding Affinity Prediction Using Dynamic Descriptors and Graph Representation (2025)
  Dan Luo et al.
  5.65
• Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing (2025)
  Zijie Qiu et al.
  5.65
• Towards Scientific Intelligence: A Survey of LLM-based Scientific Agents (2025)
  Shuo Ren et al.
  5.54
• Chemistry42: An AI-based platform for de novo molecular design (2021)
  Yan A. Ivanenkov et al.
  5.52
• ProtChatGPT: Towards Understanding Proteins with Large Language Models (2024)
  Chao Wang et al.
  5.51
• Protein Large Language Models: A Comprehensive Survey (2025)
  Yijia Xiao et al.
  5.48
• Proteomic Learning of Gamma-Aminobutyric Acid (GABA) Receptor-Mediated Anesthesia (2025)
  Jian Jiang et al.
  5.43
• Mechanics and Design of Metastructured Auxetic Patches with Bio-inspired Materials (2025)
  Yingbin Chen et al.
  5.43
• Unraveling the Potential of Diffusion Models in Small Molecule Generation (2025)
  Peining Zhang et al.
  5.40
• Hyperbolic Genome Embeddings (2025)
  Raiyan R. Khan et al.
  5.40
• MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language (2024)
  Yoel Shoshan et al.
  5.37
• AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking (2025)
  Chunan Liu et al.
  5.35
• Transformer-Based Representation Learning for Robust Gene Expression Modeling and Cancer Prognosis (2025)
  Shuai Jiang et al.
  5.24
• HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Language Model (2025)
  Mingqian Ma et al.
  5.13
• PhenoProfiler: Advancing Phenotypic Learning for Image-based Drug Discovery (2025)
  Bo Li et al.
  5.13
• Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge (2023)
  Gilchan Park et al.
  5.12
• FROGENT: An End-to-End Full-process Drug Design Multi-Agent System (2025)
  Qihua Pan et al.
  5.04