Browse State-of-the-Art › Drug Discovery › Papers, page 8
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 8 of 14: papers 701 to 800 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.
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From Bench to Bedside: A Review of Clinical Trials in Drug Discovery and Development12 Dec 2024 0 repositories listed
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Language model driven: a PROTAC generation pipeline with dual constraints of structure and property12 Dec 2024 0 repositories listed
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Intelligent System for Automated Molecular Patent Infringement Assessment10 Dec 2024 0 repositories listed
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Pharmacophore-guided de novo drug design with diffusion bridge10 Dec 2024 0 repositories listed
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Implicit Delta Learning of High Fidelity Neural Network Potentials8 Dec 2024 0 repositories listed
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Generalized Diffusion Model with Adjusted Offset Noise4 Dec 2024 0 repositories listed
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Offline Stochastic Optimization of Black-Box Objective Functions3 Dec 2024 0 repositories listed
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Graph-Based Biomarker Discovery and Interpretation for Alzheimer's Disease27 Nov 2024 0 repositories listed
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MADE: Graph Backdoor Defense with Masked Unlearning26 Nov 2024 0 repositories listed
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Enhancing Few-Shot Learning with Integrated Data and GAN Model Approaches25 Nov 2024 0 repositories listed
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DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration24 Nov 2024 0 repositories listed
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MIN: Multi-channel Interaction Network for Drug-Target Interaction with Protein Distillation23 Nov 2024 0 repositories listed
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Enhancing Molecular Design through Graph-based Topological Reinforcement Learning22 Nov 2024 0 repositories listed
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GeoScatt-GNN: A Geometric Scattering Transform-Based Graph Neural Network Model for Ames Mutagenicity Prediction22 Nov 2024 0 repositories listed
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Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction20 Nov 2024 0 repositories listed
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GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking19 Nov 2024 0 repositories listed
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A Modular Open Source Framework for Genomic Variant Calling18 Nov 2024 0 repositories listed
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Molecule Generation with Fragment Retrieval Augmentation18 Nov 2024 0 repositories listed
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BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery15 Nov 2024 0 repositories listed
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WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery Benchmarking14 Nov 2024 0 repositories listed
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Evaluating Molecule Synthesizability via Retrosynthetic Planning and Reaction Prediction13 Nov 2024 0 repositories listed
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A Comprehensive Guide to Enhancing Antibiotic Discovery Using Machine Learning Derived Bio-computation8 Nov 2024 0 repositories listed
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Character-level Tokenizations as Powerful Inductive Biases for RNA Foundational Models5 Nov 2024 0 repositories listed
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ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy4 Nov 2024 0 repositories listed
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GramSeq-DTA: A grammar-based drug-target affinity prediction approach fusing gene expression information3 Nov 2024 0 repositories listed
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Graph Fourier Neural ODEs: Modeling Spatial-temporal Multi-scales in Molecular Dynamics3 Nov 2024 0 repositories listed
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Pre-trained Molecular Language Models with Random Functional Group Masking3 Nov 2024 0 repositories listed
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Conditional Synthesis of 3D Molecules with Time Correction Sampler1 Nov 2024 0 repositories listed
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Lung tumor segmentation in MRI mice scans using 3D nnU-Net with minimum annotations1 Nov 2024 0 repositories listed
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Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling and Zero-Shot Transfer29 Oct 2024 0 repositories listed
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A Perspective for Adapting Generalist AI to Specialized Medical AI Applications and Their Challenges28 Oct 2024 0 repositories listed
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Contextual Representation Anchor Network to Alleviate Selection Bias in Few-Shot Drug Discovery28 Oct 2024 0 repositories listed
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E(3)-invariant diffusion model for pocket-aware peptide generation27 Oct 2024 0 repositories listed
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Efficient Biological Data Acquisition through Inference Set Design25 Oct 2024 0 repositories listed
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PatentAgent: Intelligent Agent for Automated Pharmaceutical Patent Analysis25 Oct 2024 0 repositories listed
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24 Oct 2024 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) · 3 unverified (of 11 harvested samples) · 11 pointer-only (licence)
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18 Oct 2024 0 repositories listed Syntology 1 ran (of which 1 constructed an object rather than computing a result; 1 with no instrument failure: 0 honoured, 0 violated, 1 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified; the one sample that ran constructed an object rather than computing a result (of 1 harvested sample)
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MultiOrg: A Multi-rater Organoid-detection Dataset18 Oct 2024 0 repositories listed
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Text-Guided Multi-Property Molecular Optimization with a Diffusion Language Model17 Oct 2024 0 repositories listed
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Utilizing Large Language Models in an iterative paradigm with domain feedback for zero-shot molecule optimization17 Oct 2024 0 repositories listed
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What Do LLMs Need to Understand Graphs: A Survey of Parametric Representation of Graphs16 Oct 2024 0 repositories listed
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Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks16 Oct 2024 0 repositories listed
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RapidDock: Unlocking Proteome-scale Molecular Docking16 Oct 2024 0 repositories listed
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KA-GNN: Kolmogorov-Arnold Graph Neural Networks for Molecular Property Prediction15 Oct 2024 0 repositories listed
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Systems-Structure-Based Drug Design14 Oct 2024 0 repositories listed
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UniGEM: A Unified Approach to Generation and Property Prediction for Molecules14 Oct 2024 0 repositories listed
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On Divergence Measures for Training GFlowNets12 Oct 2024 0 repositories listed
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CryoFM: A Flow-based Foundation Model for Cryo-EM Densities11 Oct 2024 0 repositories listed
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nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder11 Oct 2024 0 repositories listed
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InstructBioMol: Advancing Biomolecule Understanding and Design Following Human Instructions10 Oct 2024 0 repositories listed
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OWPCP: A Deep Learning Model to Predict Octanol-Water Partition Coefficient10 Oct 2024 0 repositories listed
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DLGNet: Hyperedge Classification through Directed Line Graphs for Chemical Reactions9 Oct 2024 0 repositories listed
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Pullback Flow Matching on Data Manifolds6 Oct 2024 0 repositories listed
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Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity4 Oct 2024 0 repositories listed
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Text-guided Diffusion Model for 3D Molecule Generation4 Oct 2024 0 repositories listed
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SynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design3 Oct 2024 0 repositories listed
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FARM: Functional Group-Aware Representations for Small Molecules2 Oct 2024 0 repositories listed
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Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches30 Sep 2024 0 repositories listed
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FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling29 Sep 2024 0 repositories listed
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Enhancing Robustness of Graph Neural Networks through p-Laplacian27 Sep 2024 0 repositories listed
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Optimistic Games for Combinatorial Bayesian Optimization with Application to Protein Design27 Sep 2024 0 repositories listed
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Quantum Machine Learning in Drug Discovery: Applications in Academia and Pharmaceutical Industries24 Sep 2024 0 repositories listed
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SwiftDossier: Tailored Automatic Dossier for Drug Discovery with LLMs and Agents24 Sep 2024 0 repositories listed
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23 Sep 2024 0 repositories listed
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GATher: Graph Attention Based Predictions of Gene-Disease Links23 Sep 2024 0 repositories listed
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Protein-Mamba: Biological Mamba Models for Protein Function Prediction22 Sep 2024 0 repositories listed
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FineMolTex: Towards Fine-grained Molecular Graph-Text Pre-training21 Sep 2024 0 repositories listed
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Discrimination vs. Generation: The Machine Learning Dichotomy for Dopaminergic Hit Discovery19 Sep 2024 0 repositories listed
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Natural Language Processing Methods for the Study of Protein-Ligand Interactions19 Sep 2024 0 repositories listed
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19 Sep 2024 0 repositories listed
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Quantum-inspired Reinforcement Learning for Synthesizable Drug Design13 Sep 2024 0 repositories listed
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Open Source Infrastructure for Automatic Cell Segmentation12 Sep 2024 0 repositories listed
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XMOL: Explainable Multi-property Optimization of Molecules12 Sep 2024 0 repositories listed
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A Perspective on AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems11 Sep 2024 0 repositories listed
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How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval10 Sep 2024 0 repositories listed
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PharmacoMatch: Efficient 3D Pharmacophore Screening via Neural Subgraph Matching10 Sep 2024 0 repositories listed
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Mapping Evolution of Molecules Across Biochemistry with Assembly Theory9 Sep 2024 0 repositories listed
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Machine Learning-Based Prediction of Key Genes Correlated to the Subretinal Lesion Severity in a Mouse Model of Age-Related Macular Degeneration8 Sep 2024 0 repositories listed
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Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries7 Sep 2024 0 repositories listed
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Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials6 Sep 2024 0 repositories listed
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MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs2 Sep 2024 0 repositories listed
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A Survey for Large Language Models in Biomedicine29 Aug 2024 0 repositories listed
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S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search27 Aug 2024 0 repositories listed
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HyperSBINN: A Hypernetwork-Enhanced Systems Biology-Informed Neural Network for Efficient Drug Cardiosafety Assessment26 Aug 2024 0 repositories listed
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Quantum-machine-assisted Drug Discovery: Survey and Perspective24 Aug 2024 0 repositories listed
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DrugAgent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction23 Aug 2024 0 repositories listed
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BatGPT-Chem: A Foundation Large Model For Retrosynthesis Prediction19 Aug 2024 0 repositories listed
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Learning Regularization for Graph Inverse Problems19 Aug 2024 0 repositories listed
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Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches18 Aug 2024 0 repositories listed
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Fragment-Masked Diffusion for Molecular Optimization17 Aug 2024 0 repositories listed
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Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding14 Aug 2024 0 repositories listed
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SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction11 Aug 2024 0 repositories listed
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Towards Evolutionary-based Automated Machine Learning for Small Molecule Pharmacokinetic Prediction1 Aug 2024 0 repositories listed
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Hashing based Contrastive Learning for Virtual Screening29 Jul 2024 0 repositories listed
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Quantum Long Short-Term Memory for Drug Discovery29 Jul 2024 0 repositories listed
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Generative artificial intelligence in dentistry: Current approaches and future challenges24 Jul 2024 0 repositories listed
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Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors21 Jul 2024 0 repositories listed
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A Hitchhiker's Guide to Deep Chemical Language Processing for Bioactivity Prediction16 Jul 2024 0 repositories listed
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Boosting drug-disease association prediction for drug repositioning via dual-feature extraction and cross-dual-domain decoding16 Jul 2024 0 repositories listed
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Repurformer: Transformers for Repurposing-Aware Molecule Generation16 Jul 2024 0 repositories listed
Syntology lines on 2 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 , 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.