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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 6 of 14: papers 501 to 600 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.

• Physics-Constrained Predictive Molecular Latent Space Discovery with Graph Scattering Variational Autoencoder
  29 Sep 2020 1 repository listed
• About Graph Degeneracy, Representation Learning and Scalability
  4 Sep 2020 1 repository listed
• PIGNet: A physics-informed deep learning model toward generalized drug-target interaction predictions
  22 Aug 2020 1 repository listed
• A Systematic Assessment of Deep Learning Models for Molecule Generation
  20 Aug 2020 1 repository listed
• Deep Inverse Reinforcement Learning for Structural Evolution of Small Molecules
  24 Jul 2020 1 repository listed
• Few-shot link prediction via graph neural networks for Covid-19 drug-repurposing
  20 Jul 2020 1 repository listed
• Visualizing Deep Graph Generative Models for Drug Discovery
  20 Jul 2020 1 repository listed
• Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing
  13 Jul 2020 1 repository listed
• Efficient Conformal Prediction via Cascaded Inference with Expanded Admission
  6 Jul 2020 1 repository listed Syntology official (archive's flag): 2 ran · 2 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 1 honoured, 0 violated, 0 with no contract checked; 1 where Syntology's instrument failed) · 0 unverified (of 2 harvested samples) · 2 pointer-only (licence)
• We Should at Least Be Able to Design Molecules That Dock Well
  20 Jun 2020 1 repository listed Syntology official (archive's flag): 8 ran · 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) · 1 unverified (of 9 harvested samples)
• DeepGG: a Deep Graph Generator
  7 Jun 2020 1 repository listed
• Causal Network Models of SARS-CoV-2 Expression and Aging to Identify Candidates for Drug Repurposing
  5 Jun 2020 1 repository listed
• Drug–target affinity prediction using graph neural network and contact maps
  1 Jun 2020 1 repository listed
• PaccMannᴿᴸ on SARS-CoV-2: Designing antiviral candidates with conditional generative models
  27 May 2020 1 repository listed
• Uncertainty Quantification Using Neural Networks for Molecular Property Prediction
  20 May 2020 1 repository listed Syntology official (archive's flag): 4 ran · 4 ran (of which 0 constructed an object rather than computing a result; 4 with no instrument failure: 0 honoured, 0 violated, 4 with no contract checked; 0 where Syntology's instrument failed) · 2 unverified (of 6 harvested samples)
• Improved Protein-ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference
  17 May 2020 1 repository listed Syntology official (archive's flag): 3 ran · 3 ran (of which 0 constructed an object rather than computing a result; 1 with no instrument failure: 1 honoured, 0 violated, 0 with no contract checked; 2 where Syntology's instrument failed) · 0 unverified (of 3 harvested samples)
• Multi-View Self-Attention for Interpretable Drug-Target Interaction Prediction
  1 May 2020 1 repository listed
• Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning
  26 Apr 2020 1 repository listed
• MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction
  23 Apr 2020 1 repository listed
• DeepPurpose: a Deep Learning Library for Drug-Target Interaction Prediction
  19 Apr 2020 1 repository listed
• DeepSIBA: Chemical Structure-based Inference of Biological Alterations
  1 Apr 2020 1 repository listed
• DeepGS: Deep Representation Learning of Graphs and Sequences for Drug-Target Binding Affinity Prediction
  31 Mar 2020 1 repository listed
• Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors using deep neural networks
  25 Mar 2020 1 repository listed
• Meta-Learning Initializations for Low-Resource Drug Discovery
  12 Mar 2020 1 repository listed Syntology official (archive's flag): 1 ran · 1 ran (of which 0 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 (of 1 harvested sample)
• ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning
  23 Feb 2020 1 repository listed Syntology 1 ran (of which 0 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) · 1 unverified (of 2 harvested samples)
• The Synthesizability of Molecules Proposed by Generative Models
  17 Feb 2020 1 repository listed
• AGATHA: Automatic Graph-mining And Transformer based Hypothesis generation Approach
  13 Feb 2020 1 repository listed
• GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation
  26 Jan 2020 1 repository listed
• DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations
  8 Jan 2020 1 repository listed
• Learning to Navigate in Synthetically Accessible Chemical Space Using Reinforcement Learning
  1 Jan 2020 1 repository listed
• TF3P: Three-dimensional Force Fields Fingerprint Learned by Deep Capsular Network
  24 Dec 2019 1 repository listed Syntology official (archive's flag): 1 ran · 1 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; 1 where Syntology's instrument failed) · 0 unverified (of 1 harvested sample) · 1 pointer-only (licence)
• JAX, M.D.: A Framework for Differentiable Physics
  9 Dec 2019 1 repository listed Syntology official (archive's flag): 5 ran · 5 ran (of which 0 constructed an object rather than computing a result; 5 with no instrument failure: 0 honoured, 0 violated, 5 with no contract checked; 0 where Syntology's instrument failed) · 0 unverified (of 5 harvested samples)
• Drug-Target Indication Prediction by Integrating End-to-End Learning and Fingerprints
  3 Dec 2019 1 repository listed
• DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction
  1 Dec 2019 1 repository listed
• Chemical-protein Interaction Extraction via Gaussian Probability Distribution and External Biomedical Knowledge
  21 Nov 2019 1 repository listed
• SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery
  12 Nov 2019 1 repository listed Syntology official (archive's flag): 3 ran · 3 ran (of which 0 constructed an object rather than computing a result; 3 with no instrument failure: 0 honoured, 0 violated, 3 with no contract checked; 0 where Syntology's instrument failed) · 1 unverified (of 4 harvested samples)
• Coverage Guided Testing for Recurrent Neural Networks
  5 Nov 2019 1 repository listed
• Study of Deep Generative Models for Inorganic Chemical Compositions
  25 Oct 2019 1 repository listed
• Achieving Robustness to Aleatoric Uncertainty with Heteroscedastic Bayesian Optimisation
  17 Oct 2019 1 repository listed
• Oblique Decision Trees from Derivatives of ReLU Networks
  30 Sep 2019 1 repository listed
• Data-Driven Approach to Encoding and Decoding 3-D Crystal Structures
  3 Sep 2019 1 repository listed Syntology 1 ran (of which 0 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) · 2 unverified (of 3 harvested samples)
• Molecule Property Prediction Based on Spatial Graph Embedding
  22 Aug 2019 1 repository listed
• ChemBO: Bayesian Optimization of Small Organic Molecules with Synthesizable Recommendations
  5 Aug 2019 1 repository listed Syntology 4 ran (of which 0 constructed an object rather than computing a result; 4 with no instrument failure: 0 honoured, 0 violated, 4 with no contract checked; 0 where Syntology's instrument failed) · 2 unverified (of 6 harvested samples)
• GraphDTA: prediction of drug–target binding affinity using graph convolutional networks
  2 Jul 2019 1 repository listed
• Sequential Experimental Design for Transductive Linear Bandits
  20 Jun 2019 1 repository listed
• Attention-based Multi-Input Deep Learning Architecture for Biological Activity Prediction: An Application in EGFR Inhibitors
  12 Jun 2019 1 repository listed
• Hierarchical Graph-to-Graph Translation for Molecules
  11 Jun 2019 1 repository listed
• A Bayesian Model of Dose-Response for Cancer Drug Studies
  10 Jun 2019 1 repository listed
• Scaffold-based molecular design using graph generative model
  31 May 2019 1 repository listed
• Adversarial Learned Molecular Graph Inference and Generation
  24 May 2019 1 repository listed
• Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples
  21 May 2019 1 repository listed
• Improving detection of protein-ligand binding sites with 3D segmentation
  13 Apr 2019 1 repository listed
• DeeplyTough: Learning Structural Comparison of Protein Binding Sites
  5 Apr 2019 1 repository listed
• Interpretable Deep Learning in Drug Discovery
  7 Mar 2019 1 repository listed
• WideDTA: prediction of drug-target binding affinity
  4 Feb 2019 1 repository listed
• Drug cell line interaction prediction
  28 Dec 2018 1 repository listed
• KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images
  22 Nov 2018 1 repository listed
• Semi-supervised Ensemble Learning with Weak Supervision for Biomedical Relationship Extraction
  17 Nov 2018 1 repository listed
• ChemBoost: A chemical language based approach for protein-ligand binding affinity prediction
  2 Nov 2018 1 repository listed
• Independent Vector Analysis for Data Fusion Prior to Molecular Property Prediction with Machine Learning
  1 Nov 2018 1 repository listed
• Deeply learning molecular structure-property relationships using attention- and gate-augmented graph convolutional network
  28 May 2018 1 repository listed
• Ligand Pose Optimization with Atomic Grid-Based Convolutional Neural Networks
  20 Oct 2017 1 repository listed
• A generalized method toward drug-target interaction prediction via low-rank matrix projection
  6 Jun 2017 1 repository listed
• Therapeutic target discovery using Boolean network attractors: improvements of kali
  10 Nov 2016 1 repository listed
• Heter-LP: A heterogeneous label propagation algorithm and its application in drug repositioning
  8 Nov 2016 1 repository listed
• Massively Multitask Networks for Drug Discovery
  6 Feb 2015 1 repository listed
• A Graph-in-Graph Learning Framework for Drug-Target Interaction Prediction
  15 Jul 2025 0 repositories listed
• Graph Learning
  8 Jul 2025 0 repositories listed
• Exploring Modularity of Agentic Systems for Drug Discovery
  27 Jun 2025 0 repositories listed
• Diverse Mini-Batch Selection in Reinforcement Learning for Efficient Chemical Exploration in de novo Drug Design
  26 Jun 2025 0 repositories listed
• Large Language Model Agent for Modular Task Execution in Drug Discovery
  26 Jun 2025 0 repositories listed
• A standard transformer and attention with linear biases for molecular conformer generation
  24 Jun 2025 0 repositories listed
• Context-Aware Scientific Knowledge Extraction on Linked Open Data using Large Language Models
  21 Jun 2025 0 repositories listed
• Active Learning-Guided Seq2Seq Variational Autoencoder for Multi-target Inhibitor Generation
  18 Jun 2025 0 repositories listed
• Exploring Non-contrastive Self-supervised Representation Learning for Image-based Profiling
  17 Jun 2025 0 repositories listed
• Q2SAR: A Quantum Multiple Kernel Learning Approach for Drug Discovery
  17 Jun 2025 0 repositories listed
• Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion
  17 Jun 2025 0 repositories listed
• Bures-Wasserstein Flow Matching for Graph Generation
  16 Jun 2025 0 repositories listed
• Learning Causality for Modern Machine Learning
  13 Jun 2025 0 repositories listed
• CaliciBoost: Performance-Driven Evaluation of Molecular Representations for Caco-2 Permeability Prediction
  9 Jun 2025 0 repositories listed
• Generalization Analysis for Bayesian Optimal Experiment Design under Model Misspecification
  9 Jun 2025 0 repositories listed
• Graph Neural Networks in Modern AI-aided Drug Discovery
  7 Jun 2025 0 repositories listed
• AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation
  6 Jun 2025 0 repositories listed Syntology 7 ran (of which 0 constructed an object rather than computing a result; 6 with no instrument failure: 0 honoured, 0 violated, 6 with no contract checked; 1 where Syntology's instrument failed) · 5 unverified (of 12 harvested samples) · 1 pointer-only (licence)
• AUTOCT: Automating Interpretable Clinical Trial Prediction with LLM Agents
  4 Jun 2025 0 repositories listed
• STELLA: Towards Protein Function Prediction with Multimodal LLMs Integrating Sequence-Structure Representations
  4 Jun 2025 0 repositories listed
• Recent Developments in GNNs for Drug Discovery
  2 Jun 2025 0 repositories listed
• Aligning Protein Conformation Ensemble Generation with Physical Feedback
  30 May 2025 0 repositories listed
• Enhancing Drug Discovery: Autoencoder-Based Latent Space Augmentation for Improved Molecular Solubility Prediction using LatMixSol
  30 May 2025 0 repositories listed
• A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly
  27 May 2025 0 repositories listed
• Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction
  26 May 2025 0 repositories listed
• Transformers in Protein: A Survey
  26 May 2025 0 repositories listed
• Chemical classification program synthesis using generative artificial intelligence
  24 May 2025 0 repositories listed
• Conformal Prediction for Uncertainty Estimation in Drug-Target Interaction Prediction
  24 May 2025 0 repositories listed
• Applications of Modular Co-Design for De Novo 3D Molecule Generation
  23 May 2025 0 repositories listed
• Beyond Correlation: Towards Causal Large Language Model Agents in Biomedicine
  22 May 2025 0 repositories listed
• Can Large Language Models Design Biological Weapons? Evaluating Moremi Bio
  22 May 2025 0 repositories listed
• Multi-omic Causal Discovery using Genotypes and Gene Expression
  21 May 2025 0 repositories listed
• Virtual Cells: Predict, Explain, Discover
  20 May 2025 0 repositories listed
• A Comprehensive Benchmarking Platform for Deep Generative Models in Molecular Design
  19 May 2025 0 repositories listed
• Active Learning on Synthons for Molecular Design
  19 May 2025 0 repositories listed

Syntology lines on 12 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.