Browse State-of-the-Art › Drug Discovery › Papers, page 7

Drug Discovery

Papers archive 2025-07-28

archive papers tagged: 1,337 · with a code link: 566 · where Syntology ran a sample: 182 (146 with a run with no instrument failure, 36 where every run was a failure of Syntology's instrument) Syntology

Show: all tagged papersonly where code ran (182 of 1,337 tagged: 146 with a run with no instrument failure, 36 where every run was a failure of Syntology's instrument)

Page 7 of 14: papers 601 to 700 of 1,337, in archive order: by repositories listed in the archive (most first), then newest first, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers that list no repository come after every paper that lists one.

Papers without a page here are shown as plain text. A Syntology line reads “N ran (of which C constructed an object rather than computing a result; K with no instrument failure: H honoured, V violated, P with no contract checked; I where Syntology's instrument failed) · U unverified”; the figure “where Syntology's instrument failed” counts failures of Syntology's instrument, not of the code. When the archive marks a repository official for the paper, the line starts with that repository's state (the archive's flag, not a verdict on who wrote the code); hover it for the repositories the samples that ran came from. Abstracts are on each paper's page.

• AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery
  17 May 2025 0 repositories listed
• MolTextNet: A Two-Million Molecule-Text Dataset for Multimodal Molecular Learning
  15 May 2025 0 repositories listed
• Pharmacophore-Conditioned Diffusion Model for Ligand-Based De Novo Drug Design
  15 May 2025 0 repositories listed
• In Silico Prediction and Validation of LmGt Inhibitors Using QSAR and Molecular Docking Approaches
  12 May 2025 0 repositories listed
• Multi-Modal Molecular Representation Learning via Structure Awareness
  9 May 2025 0 repositories listed
• AutoLoop: a novel autoregressive deep learning method for protein loop prediction with high accuracy
  6 May 2025 0 repositories listed
• Quantum QSAR for drug discovery
  6 May 2025 0 repositories listed
• Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning
  5 May 2025 0 repositories listed Syntology 0 ran · 1 unverified (of 1 harvested sample)
• Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks
  1 May 2025 0 repositories listed
• Multivariate Conformal Selection
  1 May 2025 0 repositories listed
• ProT-GFDM: A Generative Fractional Diffusion Model for Protein Generation
  29 Apr 2025 0 repositories listed
• Can AI Agents Design and Implement Drug Discovery Pipelines?
  28 Apr 2025 0 repositories listed
• Differential Privacy-Driven Framework for Enhancing Heart Disease Prediction
  25 Apr 2025 0 repositories listed
• Combining GCN Structural Learning with LLM Chemical Knowledge for or Enhanced Virtual Screening
  24 Apr 2025 0 repositories listed
• MetaMolGen: A Neural Graph Motif Generation Model for De Novo Molecular Design
  22 Apr 2025 0 repositories listed
• AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification
  15 Apr 2025 0 repositories listed
• Predicting Nanoparticle Effects on Small Biomolecule Functionalities Using the Capability of Scikit-learn and PyTorch: A Case Study on Inhibitors of the DNA Damage-Inducible Transcript 3 (CHOP)
  13 Apr 2025 0 repositories listed
• Scaling Laws of Graph Neural Networks for Atomistic Materials Modeling
  10 Apr 2025 0 repositories listed
• Mass Balance Approximation of Unfolding Improves Potential-Like Methods for Protein Stability Predictions
  9 Apr 2025 0 repositories listed
• De Novo Molecular Design Enabled by Direct Preference Optimization and Curriculum Learning
  2 Apr 2025 0 repositories listed
• Accelerating drug discovery with Artificial: a whole-lab orchestration and scheduling system for self-driving labs
  1 Apr 2025 0 repositories listed
• PharmAgents: Building a Virtual Pharma with Large Language Model Agents
  28 Mar 2025 0 repositories listed
• TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design
  26 Mar 2025 0 repositories listed
• Two for the Price of One: Integrating Large Language Models to Learn Biophysical Interactions
  26 Mar 2025 0 repositories listed
• Extracting Interpretable Logic Rules from Graph Neural Networks
  25 Mar 2025 0 repositories listed Syntology 6 ran (of which 0 constructed an object rather than computing a result; 0 with no instrument failure: 0 honoured, 0 violated, 0 with no contract checked; 6 where Syntology's instrument failed) · 1 unverified (of 7 harvested samples) · 7 pointer-only (licence)
• A Study on Neuro-Symbolic Artificial Intelligence: Healthcare Perspectives
  23 Mar 2025 0 repositories listed
• An Energy-Adaptive Elastic Equivariant Transformer Framework for Protein Structure Representation
  21 Mar 2025 0 repositories listed
• Preferential Multi-Objective Bayesian Optimization for Drug Discovery
  21 Mar 2025 0 repositories listed
• Advances in Protein Representation Learning: Methods, Applications, and Future Directions
  20 Mar 2025 0 repositories listed
• Chem42: a Family of chemical Language Models for Target-aware Ligand Generation
  20 Mar 2025 0 repositories listed
• Towards Unified Latent Space for 3D Molecular Latent Diffusion Modeling
  19 Mar 2025 0 repositories listed
• AI-Powered Prediction of Nanoparticle Pharmacokinetics: A Multi-View Learning Approach
  18 Mar 2025 0 repositories listed
• Linear to Neural Networks Regression: QSPR of Drugs via Degree-Distance Indices
  18 Mar 2025 0 repositories listed
• Sequence Analysis Using the Bezier Curve
  18 Mar 2025 0 repositories listed
• A Reinforcement Learning-Driven Transformer GAN for Molecular Generation
  17 Mar 2025 0 repositories listed
• Optimal compound downselection to promote diversity and parallel chemistry
  17 Mar 2025 0 repositories listed
• GenShin:geometry-enhanced structural graph embodies binding pose can better predicting compound-protein interaction affinity
  16 Mar 2025 0 repositories listed
• Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling
  13 Mar 2025 0 repositories listed
• POINT: a web-based platform for pharmacological investigation enhanced by multi-omics networks and knowledge graphs
  10 Mar 2025 0 repositories listed
• Backdoor Attacks on Discrete Graph Diffusion Models
  8 Mar 2025 0 repositories listed
• Hierarchical Functional Group Ranking via IUPAC Name Analysis for Drug Discovery: A Case Study on TDP1 Inhibitors
  7 Mar 2025 0 repositories listed
• Mol-CADiff: Causality-Aware Autoregressive Diffusion for Molecule Generation
  7 Mar 2025 0 repositories listed
• A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery
  6 Mar 2025 0 repositories listed
• A Morse Transform for Drug Discovery
  6 Mar 2025 0 repositories listed
• Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
  6 Mar 2025 0 repositories listed
• TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology
  5 Mar 2025 0 repositories listed
• Quantum Non-Linear Bandit Optimization
  4 Mar 2025 0 repositories listed
• Pushing the boundaries of Structure-Based Drug Design through Collaboration with Large Language Models
  3 Mar 2025 0 repositories listed
• Applying computational protein design to therapeutic antibody discovery -- current state and perspectives
  2 Mar 2025 0 repositories listed
• Performance Heterogeneity in Graph Neural Networks: Lessons for Architecture Design and Preprocessing
  1 Mar 2025 0 repositories listed
• ADAGE: Active Defenses Against GNN Extraction
  27 Feb 2025 0 repositories listed
• ChatMol: A Versatile Molecule Designer Based on the Numerically Enhanced Large Language Model
  27 Feb 2025 0 repositories listed
• KEDRec-LM: A Knowledge-distilled Explainable Drug Recommendation Large Language Model
  27 Feb 2025 0 repositories listed
• PhenoProfiler: Advancing Phenotypic Learning for Image-based Drug Discovery
  26 Feb 2025 0 repositories listed
• MuCoS: Efficient Drug-Target Prediction through Multi-Context-Aware Sampling
  25 Feb 2025 0 repositories listed
• Quantum Machine Learning in Precision Medicine and Drug Discovery -- A Game Changer for Tailored Treatments?
  25 Feb 2025 0 repositories listed
• Applications of Large Models in Medicine
  24 Feb 2025 0 repositories listed
• HybridLinker: Topology-Guided Posterior Sampling for Enhanced Diversity and Validity in 3D Molecular Linker Generation
  24 Feb 2025 0 repositories listed
• Auto-ADMET: An Effective and Interpretable AutoML Method for Chemical ADMET Property Prediction
  22 Feb 2025 0 repositories listed
• RAG-Enhanced Collaborative LLM Agents for Drug Discovery
  22 Feb 2025 0 repositories listed
• Drug-Target Interaction/Affinity Prediction: Deep Learning Models and Advances Review
  21 Feb 2025 0 repositories listed
• Multilevel classification framework for breast cancer cell selection and its integration with advanced disease models
  21 Feb 2025 0 repositories listed
• Predicting gene essentiality and drug response from perturbation screens in preclinical cancer models with LEAP: Layered Ensemble of Autoencoders and Predictors
  21 Feb 2025 0 repositories listed
• FragFM: Hierarchical Framework for Efficient Molecule Generation via Fragment-Level Discrete Flow Matching
  19 Feb 2025 0 repositories listed Syntology 8 ran (of which 0 constructed an object rather than computing a result; 8 with no instrument failure: 0 honoured, 0 violated, 8 with no contract checked; 0 where Syntology's instrument failed) · 6 unverified (of 14 harvested samples) · 2 pointer-only (licence)
• LIDDIA: Language-based Intelligent Drug Discovery Agent
  19 Feb 2025 0 repositories listed
• Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model
  19 Feb 2025 0 repositories listed
• E2CB2former: Effecitve and Explainable Transformer for CB2 Receptor Ligand Activity Prediction
  15 Feb 2025 0 repositories listed
• From large language models to multimodal AI: A scoping review on the potential of generative AI in medicine
  13 Feb 2025 0 repositories listed
• Graph-structured Small Molecule Drug Discovery Through Deep Learning: Progress, Challenges, and Opportunities
  13 Feb 2025 0 repositories listed
• DiffEx: Explaining a Classifier with Diffusion Models to Identify Microscopic Cellular Variations
  12 Feb 2025 0 repositories listed
• NatureLM: Deciphering the Language of Nature for Scientific Discovery
  11 Feb 2025 0 repositories listed
• DiffNMR2: NMR Guided Sampling Acquisition Through Diffusion Model Uncertainty
  6 Feb 2025 0 repositories listed
• Artificial Intelligence Approaches for Anti-Addiction Drug Discovery
  5 Feb 2025 0 repositories listed
• Docking-Aware Attention: Dynamic Protein Representations through Molecular Context Integration
  3 Feb 2025 0 repositories listed
• Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization
  31 Jan 2025 0 repositories listed
• From Data to Action: Charting A Data-Driven Path to Combat Antimicrobial Resistance
  30 Jan 2025 0 repositories listed
• MolGraph-xLSTM: A graph-based dual-level xLSTM framework with multi-head mixture-of-experts for enhanced molecular representation and interpretability
  30 Jan 2025 0 repositories listed
• Handling Missing Data in Downstream Tasks With Distribution-Preserving Guarantees
  23 Jan 2025 0 repositories listed
• Hallucinations Can Improve Large Language Models in Drug Discovery
  23 Jan 2025 0 repositories listed
• Biomedical Knowledge Graph: A Survey of Domains, Tasks, and Real-World Applications
  20 Jan 2025 0 repositories listed
• Computational Protein Science in the Era of Large Language Models (LLMs)
  17 Jan 2025 0 repositories listed
• Similarity-Quantized Relative Difference Learning for Improved Molecular Activity Prediction
  15 Jan 2025 0 repositories listed
• Decoding Interpretable Logic Rules from Neural Networks
  14 Jan 2025 0 repositories listed
• Symmetry-Aware Generative Modeling through Learned Canonicalization
  14 Jan 2025 0 repositories listed
• AlgoRxplorers | Precision in Mutation: Enhancing Drug Design with Advanced Protein Stability Prediction Tools
  13 Jan 2025 0 repositories listed
• GenMol: A Drug Discovery Generalist with Discrete Diffusion
  10 Jan 2025 0 repositories listed
• Large Language Models for Bioinformatics
  10 Jan 2025 0 repositories listed
• Prediction of Binding Affinity for ErbB Inhibitors Using Deep Neural Network Model with Morgan Fingerprints as Features
  9 Jan 2025 0 repositories listed
• On the Adversarial Robustness of Benjamini Hochberg
  6 Jan 2025 0 repositories listed
• From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering
  5 Jan 2025 0 repositories listed
• Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery
  1 Jan 2025 0 repositories listed
• A Deep Subgrouping Framework for Precision Drug Repurposing via Emulating Clinical Trials on Real-world Patient Data
  29 Dec 2024 0 repositories listed
• AI Model for Predicting Binding Affinity of Antidiabetic Compounds Targeting PPAR
  28 Dec 2024 0 repositories listed
• BioTD: an online database of biotoxins
  28 Dec 2024 0 repositories listed
• ViDTA: Enhanced Drug-Target Affinity Prediction via Virtual Graph Nodes and Attention-based Feature Fusion
  27 Dec 2024 0 repositories listed
• The Jungle of Generative Drug Discovery: Traps, Treasures, and Ways Out
  24 Dec 2024 0 repositories listed
• Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm
  19 Dec 2024 0 repositories listed
• Learning Disentangled Equivariant Representation for Explicitly Controllable 3D Molecule Generation
  19 Dec 2024 0 repositories listed
• Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction
  18 Dec 2024 0 repositories listed
• Decoding Drug Discovery: Exploring A-to-Z In silico Methods for Beginners
  15 Dec 2024 0 repositories listed

Syntology lines on 3 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced; each line links to that paper's sample list. Syntology's record for this page has not changed since 2026-09-28, the first build that kept a record date for it; when this build read Syntology's graph is in the build record. For agents: get_harvested_code_for_paper(arxiv_id) lists each paper's samples; how to connect.