Awesome Medical AI

Key papers

• An AI system to help scientists write expert-level empirical software (2025)
  Eser Ayg\"un et al.
  12.64
• BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology (2025)
  Ludovico Mitchener et al.
  10.71
• SmileyLlama: Modifying Large Language Models for Directed Chemical Space Exploration (2024)
  Joseph M. Cavanagh et al.
  9.86
• Towards an AI co-scientist (2025)
  Juraj Gottweis et al.
  9.77
• Accurate RNA 3D structure prediction using a language model-based deep learning approach (2022)
  Tao Shen et al.
  9.35
• Graph Neural Networks in Modern AI-aided Drug Discovery (2025)
  Odin Zhang et al.
  8.75
• Artificial Intelligence and Deep Learning Algorithms for Epigenetic Sequence Analysis: A Review for Epigeneticists and AI Experts (2025)
  Muhammad Tahir et al.
  8.64
• 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
  8.56
• MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research (2025)
  James Burgess et al.
  8.49
• PharmAgents: Building a Virtual Pharma with Large Language Model Agents (2025)
  Bowen Gao et al.
  8.07
• AI-Powered Prediction of Nanoparticle Pharmacokinetics: A Multi-View Learning Approach (2025)
  Amirhossein Khakpour et al.
  7.82
• HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data (2025)
  Hiren Madhu et al.
  7.70
• RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks (2024)
  Rafael Josip Peni\'c et al.
  7.62
• Physics-informed graph neural networks for flow field estimation in carotid arteries (2024)
  Julian Suk et al.
  7.55
• SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation (2025)
  Fanglei Xue et al.
  7.50
• Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization (2025)
  Jiajun Yu et al.
  7.40
• drGT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network (2024)
  Yoshitaka Inoue et al.
  7.38
• Unified modeling of 3D molecular generation via atomic interactions with PocketXMol. (2026)
  Xingang Peng et al.
  7.24
• Multi-view biomedical foundation models for molecule-target and property prediction (2024)
  Parthasarathy Suryanarayanan et al.
  7.23
• Contextualizing biological perturbation experiments through language (2025)
  Menghua Wu et al.
  7.19
• Representation Meets Optimization: Training PINNs and PIKANs for Gray-Box Discovery in Systems Pharmacology (2025)
  Nazanin Ahmadi Daryakenari et al.
  7.13
• FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction (2024)
  Alex Morehead and Jianlin Cheng
  7.08
• 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.
  6.86
• Physics-informed deep learning for infectious disease forecasting (2025)
  Ying Qian et al.
  6.78
• BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery (2024)
  Peter St. John et al.
  6.67
• SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction (2024)
  Bohao Xu et al.
  6.61
• QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials (2025)
  Francesc Saban\'es Zariquiey et al.
  6.58
• 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.
  6.47
• POLO: Preference-Guided Multi-Turn Reinforcement Learning for Lead Optimization (2025)
  Ziqing Wang et al.
  6.29
• Robust Inference-Time Steering of Protein Diffusion Models via Embedding Optimization (2026)
  Minhuan Li et al.
  6.29
• Machine Learning Enhanced Calculation of Quantum-Classical Binding Free Energies (2025)
  Moritz Bensberg et al.
  6.23
• Molecular-driven Foundation Model for Oncologic Pathology (2025)
  Anurag Vaidya et al.
  6.12
• Multi-Exit Kolmogorov-Arnold Networks: enhancing accuracy and parsimony (2025)
  James Bagrow and Josh Bongard
  6.12
• VALID-Mol: a Systematic Framework for Validated LLM-Assisted Molecular Design (2025)
  Malikussaid et al.
  6.12
• scDrugMap: Benchmarking Large Foundation Models for Drug Response Prediction (2025)
  Qing Wang et al.
  6.07
• Machine Learning Methods for Gene Regulatory Network Inference (2025)
  Akshata Hegde et al.
  6.01
• Interpretable Graph Kolmogorov-Arnold Networks for Multi-Cancer Classification and Biomarker Identification using Multi-Omics Data (2025)
  Fadi Alharbi et al.
  5.96
• CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction (2025)
  Jueon Park et al.
  5.93
• General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design (2024)
  Yue Jian et al.
  5.91
• Molecular Graph Contrastive Learning with Line Graph (2025)
  Xueyuan Chen et al.
  5.84
• AI-driven multi-omics integration for multi-scale predictive modeling of causal genotype-environment-phenotype relationships (2024)
  You Wu (1) et al.
  5.78
• GBDTSVM: Combined Support Vector Machine and Gradient Boosting Decision Tree Framework for efficient snoRNA-disease association prediction (2025)
  Ummay Maria Muna et al.
  5.76
• CellVerse: Do Large Language Models Really Understand Cell Biology? (2025)
  Fan Zhang et al.
  5.76
• Benchmarking AI scientists for omics data driven biological discovery (2025)
  Erpai Luo et al.
  5.76
• Robin: A multi-agent system for automating scientific discovery (2025)
  Ali Essam Ghareeb et al.
  5.76
• Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing (2025)
  Zijie Qiu et al.
  5.76
• Multi-modal AI for comprehensive breast cancer prognostication (2024)
  Jan Witowski et al.
  5.68
• TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools (2025)
  Shanghua Gao et al.
  5.65
• SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Models (2025)
  Kunyang Sun et al.
  5.65
• Democratizing AI scientists using ToolUniverse (2025)
  Shanghua Gao et al.
  5.63
• Protein Large Language Models: A Comprehensive Survey (2025)
  Yijia Xiao et al.
  5.59
• ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding (2024)
  Yijia Xiao et al.
  5.57
• ImageDDI: Image-enhanced Molecular Motif Sequence Representation for Drug-Drug Interaction Prediction (2025)
  Yuqin He et al.
  5.57
• Chemistry42: An AI-based platform for de novo molecular design (2021)
  Yan A. Ivanenkov et al.
  5.52
• Unraveling the Potential of Diffusion Models in Small Molecule Generation (2025)
  Peining Zhang et al.
  5.52
• ProtChatGPT: Towards Understanding Proteins with Large Language Models (2024)
  Chao Wang et al.
  5.51
• EHRNote-ChatQA: A Benchmark for Evidence-Grounded Multi-Turn Clinical Question Answering over Longitudinal Discharge Summaries (2026)
  Jiyoun Kim et al.
  5.49
• AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking (2025)
  Chunan Liu et al.
  5.46