Drug Discovery

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7 papers in the last four weeks, up 75% on the four weeks before. 0.1% of all new papers.

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Scientific Discovery under Validation Congestion via Multi-Fidelity Pairwise Rankings
Oct 1, 2026Kevin Tirta Wijaya, Alston Lo, Michael Sun +2Drug Discovery Scientific Discovery
University of Bonn · Fraunhofer SCAI · Massachusetts Institute of Technology
RetroGEF: Dynamic Graph Edit Flow for Single-Step Retrosynthesis
Sep 29, 2026Xiaozhuang Song, Xuemin Chen, Xinjian Zhao +2Drug Discovery Generative Flow Networks
The Chinese University of Hong Kong, Shenzhen · Shanghai AI Laboratory
RIDE: Reference-Anchored Inference-Time Diffusion Editing for Scaffold Hopping
Sep 28, 2026Ruoxi Gao, Frazier N. Baker, Trieu Nguyen +1Drug Discovery Diffusion Dynamics
Department of Computer Science and Engineering, The Ohio State University · Department of Biomedical Informatics, The Ohio State University · Translational Data Analytics Institute, The Ohio State University +1
TopU-LBVS: A Realistic Multi Target Benchmark for Ligand Based Virtual Screening
Sep 24, 2026Surbhi Kumar, Yuhe Zhou, Varun Shiralkar +2Drug Discovery Screening
UT Dallas, Mathematical Sciences Richardson, TX, USA
Adapting Boltz-2 with limited experimental activity data improves early enrichment in virtual screening
Sep 21, 2026Kairi Furui, Masahito OhueScreening Drug Discovery
Department of Computer Science, School of Computing, Institute of Science Tokyo, Yokohama 226-8501, Japan
Pretrained Medical Representations for the Practical Screening of Drug Repositioning Candidates
Sep 17, 2026Yuhei Fujioka, Daitaro Misawa, Shingo FukumaMedical World Model Electronic Health Records
Cancerscan Inc., Tokyo, Japan · Kyoto University, Graduate School of Medicine, Kyoto, Japan · Hiroshima University, Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens
Sep 12, 2026Carl Edwards, Edward De Brouwer, Xiner Li +5Screening Drug Discovery
Genentech, South San Francisco, CA, USA
Coupled Tensor-Tensor Completion Method with Applications in Drug Repurposing
Sep 2, 2026Maryam Bagherian, Albert Hung, Ivo Dinov +1Tensor Completion Biomedical
Department of Mathematics & Statistics, Idaho State University, Physical Science Complex — 921 S. 8th Ave., Stop 8085 — Pocatello, ID 83209 · Computer Science & Artificial Intelligence Laboratory, Massachusetts Institute of Technology · Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor +2
Mol-JEPA: A multimodal Joint Embedding Predictive Architecture for Molecules
Aug 23, 2026Florian Rottach, Sebastian Schieferdecker, William Rudman +2Molecular Representation Learning Molecules
University of Tübingen · 2Boehringer Ingelheim · 3The University of Texas at Austin +1
Designing a Robust LLM-Based Evaluation System for Agentic AI in Drug Discovery Through Human Alignment
Aug 21, 2026Emma Granqvist, Rocío Mercado, Samuel GenhedenLlm-As-A-Judge Drug Discovery
Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden · Department of Computer Science and Engineering, Section for Data Science and AI, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden · Science for Life Laboratory (SciLifeLab), Gothenburg, Sweden
A Modular Agentic Framework for Synthetically Constrained Multi-Objective Hit-to-Lead Optimization
Aug 11, 2026Kelvin P. Idanwekhai, Enes Kelestemur, Benjamin Strickland +6Drug Discovery Molecular Optimization
Department of Chemistry, UNC Chapel Hill, Chapel Hill, NC, USA · Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy at UNC, Chapel Hill, NC, USA · Department of Applied Physical Sciences, UNC Chapel Hill, NC, USA +1
MolBioKG: Grounding Out-of-Graph Molecules in Biomedical Knowledge Graphs via Multi-Resolution Structural Anchoring
Aug 7, 2026Yiming Zhang, Hikaru Shindo, Shuan Chen +5Biomedical Knowledge Graph Drug Discovery
1The University of Tokyo · 2SB Intuitions · Department of AI Systems Medicine, Institute of Science Tokyo
Hit Selection Using SSMD-Based Machine Learning Performance Metrics in High-Throughput Screening Assays
Aug 6, 2026Xiaohua Douglas ZhangScreening Receiver Operating Characteristic Area Under The Curve
Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY40536, USA
EpiBench: Can LLMs Understand Epitopes for Antibody Drug Discovery?
Aug 6, 2026Zirui Wang, Jiaqi Wang, Qinghan Wang +4Epitope Prediction Antibody
1Valhalla Technology · 2Zhejiang University
LLM-Guided Retrieval for Prediction of Molecular Perturbation Responses
Aug 3, 2026Betty Xiong, Jan-Christian Huetter, Gabriele Scalia +2Single-Cell Perturbation Prediction Transcriptomics
Department of Biomedical Data Science Stanford University Stanford, CA 94305, USA · Biology Research & AI Development, Genentech DNA Way, South San Francisco, CA 94080, USA
From Cellular Responses to Pharmacological Domains: Multimodal Zero-Shot Drug Representation Learning
Jul 28, 2026Jintao Huang, Lu Leng, Ziyuan YangDrug Discovery Pharmacokinetics
Nanchang Hangkong University, Nanchang, Jiangxi, China · Sichuan University, Chengdu, Sichuan, China
MEGA-CL: A Molecular Foundation Model for Generalizable ADMET Prediction through Graph External Attention and Contrastive Learning
Jul 27, 2026Tinghui Jin, Kedu Jin, Ying Li +8Absorption, Distribution, Metabolism, And Excretion Drug Discovery
School of Science, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China · 2Sir Run Run Hospital, Nanjing Medical University, Nanjing, China · 3Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
Do AI-Native Biotechs Need Departments? Benchmarking Company World Models for AI-Driven Drug Development
Jul 21, 2026Yinan WangAi-Native Drug Discovery
Noah AI Research
ChemHyperMag: Physics-informed magnetic hypergraph learning improves molecular ADMET prediction
Jul 19, 2026Hexiao Ding, Hongzhao Chen, Jing Lan +12Absorption, Distribution, Metabolism, And Excretion Drug Discovery
Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China · University of Liverpool, Liverpool, United Kingdom · Shanghai Jiao Tong University, Shanghai, China +1
Automatic Ordinary Differential Equations Discovery For Biological Systems Using Large Language Model Powered Agentic System
Jul 15, 2026David Krongauz, Arad Zulti, Eran Segal +1Model Discovery Ordinary Differential Equations
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel · Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel · Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, United Arab Emirates +2
HEDGEHOG: Hierarchical Evaluation of Drug Generators Through Rigorous Filtration
Jul 14, 2026Daria A. Ryabchenko, Pavel Gurevich, Shamil Kadyrov +5Molecular Generation Drug Discovery
Ligand Pro, Moscow, Russia · Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia · 1Ligand Pro, Moscow, Russia +1
$\mathtt{Q^2SAR}$ : overcoming classical bottlenecks in drug discovery via quantum multiple kernel learning
Jul 13, 2026Mariano Caruso, Daniel Ruiz, Alejandro Giraldo +1Quantum Kernels Drug Discovery
UGR, Granada, Spain · UNIR, La Rioja, Spain · FIDESOL, Granada, Spain +4
Advancing Optimal Subset Oracle via Learning Relaxation of Neural Set Functions
Jul 13, 2026Yongquan Shi, Zijing Ou, Shiping Wang +1Variational Inference Surrogate Gradient
Fuzhou University · Imperial College London · National University of Singapore
Vilya-1: An all-atom foundation model for macrocycle structure prediction and design
Jul 10, 2026Vilya Research, :, Pascal Sturmfels +8Drug Discovery Chemical Structures
Vilya Research
DrugGen 2: A disease-aware language model for enhancing drug discovery
Jul 9, 2026Ali Motahharynia, Mohammadreza Ghaffarzadeh-Esfahani, Mahsa Sheikholeslami +4Drug Design Drug Discovery
Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran · Isfahan Neuroscience Research Center, Isfahan University of Medical Sciences, Isfahan, Iran · Department of Medicinal Chemistry, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran +3
A Quiet Failure in Calibrated Virtual Screening: Marginal Conformal Prediction Under-Covers the Minority Class, and a Class-Conditional Fix Recovers It
Jul 7, 2026Muhammadjon Tursunbadalov, Mustafojon TursunbadalovOnline Conformal Prediction Minority
School of Science and Technology, Champions College Prep, United States
URSA: Chemistry-Aware Benchmark for Utilitarian Retrosynthesis Assessment
Jul 6, 2026Bogdan Zagribelnyy, Ivan Ilin, Nikita Bondarev +7Chemistry Drug Discovery
Insilico Medicine AI Limited, Masdar City, Abu Dhabi, UAE · Independent researcher · Insilico Medicine Canada Inc., Montreal, Quebec, Canada +1
Folding, Reasoning, and Scaling with Open-source Drug Discovery Engine
Jul 4, 2026Aureka AI OpenDDE projectDrug Discovery
OpenDDE Project, Aureka AI Research
A Precedent-Guided Co-Scientist for Side-Effect-Aware Drug Redesign
Jul 3, 2026Yujin Kim, Charmgil HongDrug Discovery Pharmacokinetics
Department of Computer Science and Electrical Engineering, Handong Global University, Pohang, Republic of Korea.
An Additive MLP-GNN Framework for Characterizing Chemical and Structural Contributions to Aqueous Solubility
Jul 2, 2026Sampreeti Bhattacharya, Arkaprava RoyTransferable Implicit Solvent Machine Learning Potential Molecular Property Prediction
Bridging the NISQ and Fault-Tolerant Regimes: Generative-ML-Assisted Quantum Selected CI for Molecular Simulations
Jun 29, 2026Anurag K. S. V., Ashish Kumar Patra, Manas Mukherjee +4Hybrid Quantum-Classical Pipeline Quantum Chemistry
Qclairvoyance Quantum Labs, Secunderabad, TG 500094, India · Centre for Quantum Technologies, National University of Singapore, SG 117543, Singapore · The University of Arizona, Tucson, AZ 85721, USA +1
Beyond Drug Discovery: The Nanotechnology Molecular Optimization (NMO) Benchmark
Jun 29, 2026Matthias Blaschke, Daniel Kienzle, Zsuzsanna Koczor-Benda +3Molecular Optimization Drug Discovery
University of Augsburg · CAAPS† · Germany +2
Multi-Objective Molecular Generation with Frequency-Controlled Evolutionary Dynamics
Jun 25, 2026Elia Colleoni, Paolo Guida, Didier Barradas-Bautista +1Molecular Generation Drug Discovery
Clean Energy Research Center (CERP) Physical Science and Engineering (PSE) Division King Abdullah University of Science and Technology Thuwal, Saudi Arabia 23955 · Kaust Visualization Lab (KVL) Core Lab Division King Abdullah University of Science and Technology Thuwal, Saudi Arabia 23955
Substitution-Based Analysis of Structural Novelty for Generative Models of Materials
Jun 22, 2026Masahiro Negishi, Aron WalshCrystal Structure Crystal
Department of Materials, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, London, United Kingdom.
JEDEL: Zero-Shot DNA-Encoded Library Design for Early-Stage Drug Discovery
Jun 21, 2026Zygimantas Jocys, Zhanxing Zhu, Henriette M. G. Willems +1Drug Design Drug Discovery
School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, United Kingdom. · The ALBORADA Drug Discovery Institute, University of Cambridge,2026 Hills Road, Cambridge, CB2 0AH, United Kingdom.
DeepRoot: A KG-Coordinated Multi-Agent System for Therapeutic Reasoning over Historical Medical Texts
Jun 14, 2026Zijian Carl Ma, Sean J. Wang, Sijbren Kramer +1Biomedical Knowledge Graph Clinical Reasoning Training
Department of Bioengineering · Stanford University · Amazon AWS AI
Where Black-box Drug-Target Interaction Prediction Models Look: Cross-Method Explainability
Jun 12, 2026Ali Vefghi, Zahed Rahmati, Mohammad AkbariAbsorption, Distribution, Metabolism, And Excretion Explainability
Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran
APCyc: Property-Informed Design of Cyclic Peptides via Automated Cyclization
Jun 11, 2026Yifan Zhao, Lang Qin, Jintai ChenDrug Discovery
AI Thrust The Hong Kong University of Science and Technology (Guangzhou) Guangzhou, China · AI-Peptide Drug Design Joint Laboratory The Hong Kong University of Science and Technology (Guangzhou) Guangzhou, China
Physics-Aware Auxiliary Losses Improve Out-of-Distribution Generalization of a GNN Synthesizability Filter
Jun 10, 2026Riya Bisht, Dhruv AgarwalOut-Of-Distribution Graph Neural Networks
Probabilistic Contrastive Pretraining for Multi-task ADME Property Prediction
Jun 9, 2026Yifan Xue, Srimukh Prasad Veccham, Saee Paliwal +2Absorption, Distribution, Metabolism, And Excretion Drug Discovery
NVIDIA Santa Clara, CA 95051
ShallowBench: Benchmarking Generative Drug Design Models on Shallow-Pocket Targets
Jun 4, 2026Saket Reddy, Shiwei LiuDrug Design Drug Discovery
University of Illinois - Urbana-Champaign
CP-Agent: Context-Aware Multimodal Reasoning for Cellular Morphological Profiling under Chemical Perturbations
Jun 2, 2026Yuxin Zhang, Yiyao Li, Ping Shu Ho +3Drug Discovery Multimodal Agents
Department of Electrical and Computer Engineering, The University of Hong Kong · School of Computing and Data Science, The University of Hong Kong · Nvidia AI Technology Center +2
Fairness Definitions and Metrics in Deep Reinforcement Learning for Drug Discovery in Healthcare: A Rapid Evidence Review
Jun 1, 2026Esmaeil Shakeri, Ronnie de Souza Santos, Behrouz FarDrug Discovery Algorithmic Fairness
Department of Electrical and Software Engineering, Schulich School of Engineering, University of Calgary, Canada
Genotype-Conditioned Molecular Generation via Evidence-Grounded Multi-Objective Latent Perturbation in Diffusion Models
May 31, 2026Brenda Nogueira, Gisela A. Gonzalez-Montiel, Nitesh V. Chawla +1Drug Discovery Molecular Generation
Department of Computer Science and Engineering University of Notre Dame Notre Dame, IN, 46556 · Department of Chemistry and Biochemistry University of Notre Dame Notre Dame, IN, 46556 · Lucy Family Institute for Data & Society University of Notre Dame Notre Dame, IN, 46556
UniD $^3$ : A Knowledge Graph-Enhanced RAG Framework for Drug-Disease Discovery and Reasoning
May 31, 2026Qing Wang, Tianshi Liu, Minghao Zhou +5Biomedical Knowledge Graph Drug-Drug Interactions
Department of Health Outcomes and Biomedical Informatics, University of Florida, Florida, USA · Department of Hematology, H. Lee Moffitt Cancer Center and Research Institute, Florida, USA · Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, USA +2
LLM-AutoSciLab: Closed-Loop Scientific Discovery via Active Experimentation with LLMs
May 21, 2026Sanchit Kabra, Nikhil Abhyankar, Saaketh Desai +2Scientific Discovery Drug Discovery
1Virginia Tech · 2Sandia National Laboratories
Molecular Lead Optimization via Agentic Tool Planning
May 21, 2026Lingxiao Li, Haobo Zhang, Ruohao Fan +2Molecular Optimization Drug Discovery
University of Michigan Ann Arbor, Michigan, USA · Department of Biochemistry and Molecular Medicine University of California, Davis Davis, California, USA · Department of Pharmacology and Toxicology Michigan State University East Lansing, Michigan, USA
SMDD-Bench: Can LLMs Solve Real-World Small Molecule Drug Design Tasks?
May 20, 2026Kevin Han, Renfei Zhang, Kathy Wei +3Drug Discovery Large Language Model Agents
Carnegie Mellon University · Stealth · Pennsylvania State University
Fine-tuning Pocket-Aware Diffusion Models via Denoising Policy Optimization
May 17, 2026Yuan Xue, Daniel Kudenko, Megha KhoslaDrug Design Molecular Optimization
L3S Research Center, Hanover, Germany · Delft University of Technology, Delft, Netherlands
DrugSAGE:Self-evolving Agent Experience for Efficient State-of-the-Art Drug Discovery
May 14, 2026Yikun Zhang, Xiwei Cheng, Tianyu Liu +2Drug Discovery Agentic Discovery
1Northeastern University · 2Broad Institute of MIT and Harvard · 3Yale University +1
Learning to Select Source Domains: Proxy-Rewarded Policy Optimization for Molecular OOD Generalization
May 13, 2026Zhuohao Lin, Kun Li, Jiameng Chen +4Drug Discovery Out-Of-Distribution
School of Computer Science Wuhan University Wuhan, China · College of Computer Science and Technology, Zhejiang University Hangzhou, China · School of Life Sciences and Technology, Tongji University Shanghai, 200092, China +1
A Non-Destructive Methodological Framework for Modernizing Legacy Clinical Reporting Systems for AI-Driven Pharmacoinformatics: A SAS Case Study
May 13, 2026Jaime YanMedical Report Generation Drug-Drug Interactions
Harrisburg University of Science and Technology, Harrisburg, PA, USA
Digital Twins as Synthetic Controls in Single-Arm Trials
May 12, 2026Daniele Bertolini, Franklin Fuller, Aaron M. Smith +2Digital Twins Controlled Study
Unlearn.AI, Inc., San Francisco, CA
ToolMol: Evolutionary Agentic Framework for Multi-objective Drug Discovery
May 12, 2026Andrew Y. Zhou, Sharvaree Vadgama, Sumanth Varambally +3Drug Design Drug Discovery
Department of Computer Science and Engineering, UC San Diego, La Jolla, California, United States · Department of Computer Science, Stanford University, Stanford, California · Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California
AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
May 11, 2026Edward De Brouwer, Carl Edwards, Alexander Wu +9Phenotypes Virtual Cell
Genentech
On Improving Graph Neural Networks for QSAR by Pre-training on Extended-Connectivity Fingerprints
May 11, 2026Sam Money-Kyrle, Markus Dablander, Thierry Hanser +3Graph Neural Networks Molecular Representation Learning
Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford, OX1 3LB, United Kingdom. · Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford, OX2 6GG, United Kingdom. · Molecular Informatics and AI, Lhasa Limited, Granary Wharf House,May 2 Canal Wharf, Leeds, LS11 5PS, United Kingdom.
Many Needles in a Haystack: Active Hit Discovery for Perturbation Experiments
May 11, 2026Andrea Rubbi, Arpit Merchant, Samuel Ogden +4Bayesian Experimental Design Bayesian Optimization
Department of Computer Science and Technology, University of Cambridge, Cambridge, UK · Cambridge Center for AI in Medicine, University of Cambridge, Cambridge, UK · MediaTek Research, Cambridge, UK +1
MolWorld: Molecule World Models for Actionable Molecular Optimization
May 9, 2026Yang Qiao, Bo Pan, Hao-Wei Pang +3Molecular Optimization Molecules
Emory University · Atlanta, GA, USA · Merck & Co., Inc. +1
From Holo Pockets to Electron Density: GPT-style Drug Design with Density
May 9, 2026Jiahao Chen, Letian Gao, Yanhao Zhu +4Drug Design Molecular Generation
Gaoling School of Artificial Intelligence, Renmin University of China, Beijing, China · Beijing Key Laboratory of Research on Large Models and Intelligent Governance, Beijing, China · Engineering Research Center of Next Generation Intelligent Search and Recommendation, MOE, Beijing, China +3
Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scale
May 7, 2026Haydn Jones, Yimeng Zeng, Alden Rose +11Biomedical Drug Discovery
Department of Computer and Information Science, University of Pennsylvania · Department of Genetics, University of Pennsylvania · 3Departments of Bioengineering and Chemical and Biomolecular Engineering,2026 University of Pennsylvania

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Scientific Discovery under Validation Congestion via Multi-Fidelity Pairwise Rankings

Kevin Tirta Wijaya, Alston Lo, Michael Sun, Wojciech Matusik+1

University of Bonn · Fraunhofer SCAI · Massachusetts Institute of Technology

Drug Discovery Scientific Discovery Screening Data-Curation Validation Congestion

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Modern computational methods can now propose candidate molecules, materials, and other scientific designs at an unprecedented scale, creating a validation congestion where candidates are abundant, but experimental capacity to physically evaluate them remains scarce. Discovering novel scientific designs has therefore become increasingly dependent on curation: selecting a small set of promising designs for slow and costly experiments. Existing curation methods typically rely on data-driven regression models that predict absolute scores, but training these models requires substantial experimental data to begin with. Yet, useful curation signals do not have to take the form of absolute measurements, as scientific design discovery is often comparative in nature. Here, we propose that curation can instead be primarily driven by expert pairwise rankings, which are substantially easier to gather. The expertise can come from computational tools or human input of multiple levels of fidelity, ranging from empirical rules of thumb to agentic workflows and experienced scientists. We introduce PRISMS, a framework that uses pairwise rankings from one or more experts, potentially spanning multiple levels of expertise, to identify the most promising candidates without relying on data-hungry regressors. When experts differ in fidelity and cost, PRISMS escalates pairwise queries from lower- to higher-fidelity rankers based on a Fisher-information criterion. In iterative screening that selects designs from fixed drug discovery libraries, PRISMS achieves 50% top-10 discovery recall in ~42% fewer rounds than regression-only active learning, and in ~15% fewer rounds than the ranking-based method with no selective escalation. In optimization that generates new designs without restriction to a predefined library, PRISMS achieves ~18.8% higher hypervolume than the Bayesian optimization baseline.

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