I built a semantic map that organizes research papers by analyzing their titles, abstracts, and keywords. This visualization highlights thematic clusters, hopefully making it easier to explore related research between domains. The themes that relate these papers are diverse, including biology, chemistry, problem domain or technical method.
To explore the papers interactively, select a paper that interests you and discover how it connects to others sharing similar themes within its cluster (toggle ‘Semantic Clusters’). Below is also a a table detailing all the papers, organized by cluster.
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A semantic map of AIDrugX Workshop papers
| Title | Authors | Type | Link |
|---|---|---|---|
| Cluster 1 | |||
| DiffER: Categorical Diffusion Models for Chemical Retrosynthesis | Sean Current ... srinivasan parthasarathy | Accept | Open Paper |
| Homomorphism Counts as Structural Encodings for Molecular Property Prediction | Linus Bao ... Matthias Lanzinger | Accept | Open Paper |
| SmileyLlama: Modifying Large Language Models \\for Directed Chemical Space Exploration | Joe Cavanagh ... Thomas D. Bannister | Accept | Open Paper |
| An Efficient Tokenization for Molecular Language Models | Seojin Kim ... Jinwoo Shin | Accept | Open Paper |
| Chain-of-thoughts for molecular understanding | Yunhui Jang ... Sungsoo Ahn | Accept | Open Paper |
| Cluster 2 | |||
| Deep Interactions for Multimodal Molecular Property Prediction | Patrick Soga ... Jundong Li | Accept | Open Paper |
| Geometry-text Multi-modal Foundation Model for Reactivity-oriented Molecule Editing | Haorui Li ... Anima Anandkumar | Accept | Open Paper |
| 3D Interaction Geometric Pre-training for Molecular Relational Learning | Namkyeong Lee ... Chanyoung Park | Accept | Open Paper |
| GFlowNet Pretraining with Inexpensive Rewards | Mohit Pandey ... Emmanuel Bengio | Accept | Open Paper |
| MolKD: Distilling Cross-Modal Knowledge in Chemical Reactions for Molecular Property Prediction | Liang Zeng | Accept | Open Paper |
| Molphenix: A Multimodal Foundation Model for PhenoMolecular Retrieval | Philip Fradkin ... Dominique Beaini | Accept | Open Paper |
| Learning Molecular Representation in a Cell | Gang Liu ... Shantanu Singh | Accept | Open Paper |
| Understanding the Sources of Performance in Deep Drug Response Models Reveals Insights and Improvements | Nikhil Branson ... Conrad Bessant | Accept | Open Paper |
| Reinforcement Learning for Enhanced Targeted Molecule Generation Via Language Models | Salma J. Ahmed, Emad A. Mohammed | Accept | Open Paper |
| SMORE-DRL: Scalable Multi-Objective Robust and Efficient Deep Reinforcement Learning for Molecular Optimization | Aws Al Jumaily ... Yifeng Li | Accept | Open Paper |
| Pharmacophore-based design by learning on voxel grids | Omar Mahmood ... Vishnu Sresht | Accept | Open Paper |
| MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning | Peter Eckmann ... Rose Yu | Accept | Open Paper |
| GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking | Yiliang Yuan, Mustafa Misir | Accept | Open Paper |
| Similarity-Quantized Relative Difference Learning for Improved Molecular Activity Prediction | Karina Zadorozhny ... Colin A Grambow | Accept | Open Paper |
| Cluster 3 | |||
| Improved Off-policy Reinforcement Learning in Biological Sequence Design | Hyeonah Kim ... Jinkyoo Park | Accept | Open Paper |
| Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design | Chenyu Wang ... Aviv Regev | Accept | Open Paper |
| Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding | Xiner Li ... Masatoshi Uehara | Accept | Open Paper |
| Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion | Anirban Sarkar ... Peter K Koo | Accept | Open Paper |
| Latent Diffusion Models for Controllable RNA Sequence Generation | Kaixuan Huang ... Mengdi Wang | Accept | Open Paper |
| Cluster 4 | |||
| Modeling Complex System Dynamics with Flow Matching Across Time and Conditions | Martin Rohbeck ... Romain Lopez | Accept | Open Paper |
| Correlational Lagrangian Schrodinger Bridge: Learning Dynamics with Population-Level Regularization | Yuning You ... Yang Shen | Accept | Open Paper |
| Cluster 5 | |||
| Training-Free Guidance with Applications to Protein Engineering | Lewis Cornwall ... Aaron Sim | Accept | Open Paper |
| ProtPainter: Draw or Drag Protein via Topology-guided Diffusion | Zhengxi Lu ... Min Zhang | Accept | Open Paper |
| TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation | Zongying Lin ... Yonghong Tian | Accept | Open Paper |
| Structure Language Models for Protein Conformation Generation | Jiarui Lu ... Jian Tang | Accept | Open Paper |
| MeMDLM: De Novo Membrane Protein Design with Masked Discrete Diffusion Protein Language Models | Shrey Goel ... Pranam Chatterjee | Accept | Open Paper |
| Improving Antibody Design with Force-Guided Sampling in Diffusion Models | Paulina Kulytė ... Pietro Lio | Accept | Open Paper |
| JAMUN: Transferable Molecular Conformational Ensemble Generation with Walk-Jump Sampling | Ameya Daigavane ... Joseph Kleinhenz | Accept | Open Paper |
| Learning Protocols for Non-Equilibrium Conformational Free-Energy Estimation Using Optimal Transport and Conditional Flow Matching | Lars Holdijk ... Max Welling | Accept | Open Paper |
| Generalized Flow Matching for Transition Dynamics Modeling | Haibo Wang ... Yuanqi Du | Accept | Open Paper |
| Cluster 6 | |||
| A Deep Generative Model for the Design of Synthesizable Ionizable Lipids | Yuxuan Ou ... José Miguel Hernández-Lobato | Accept | Open Paper |
| Generative Model for Synthesizing Ionizable Lipids: A Monte Carlo Tree Search Approach | Jingyi Zhao ... José Miguel Hernández-Lobato | Accept | Open Paper |
| Cluster 7 | |||
| Discrete Diffusion Schrödinger Bridge Matching for Graph Transformation | Jun Hyeong Kim ... Woo Youn Kim | Accept | Open Paper |
| Improving Molecular Graph Generation with Flow Matching and Optimal Transport | Xiaoyang Hou ... Shiwei Sun | Accept | Open Paper |
| Directly Optimizing for Synthesizability in Generative Molecular Design using Retrosynthesis Models | Jeff Guo, Philippe Schwaller | Spotlight | Open Paper |
| Generative Flows on Synthetic Pathway for Drug Design | Seonghwan Seo ... Woo Youn Kim | Accept | Open Paper |
| Molecular Generation with State Space Sequence Models | Anri Lombard ... Jan Buys | Accept | Open Paper |
| Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation | Jeff Guo, Philippe Schwaller | Accept | Open Paper |
| Best Practices for Multi-Fidelity Bayesian Optimization in Materials and Molecular Research | Victor Sabanza Gil ... Loïc Roch | Accept | Open Paper |
| MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks | Nayoung Kim ... Sungsoo Ahn | Accept | Open Paper |
| Improving Structural Plausibility in 3D Molecule Generation via Property-Conditioned Training with Distorted Molecules | Lucy Vost ... Charlotte Deane | Accept | Open Paper |
| Applications of Modular Co-Design for De Novo 3D Molecule Generation | Danny Reidenbach ... Saee Gopal Paliwal | Accept | Open Paper |
| Cluster 8 | |||
| Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+ | Ethan Weinberger ... Ryan Conrad | Accept | Open Paper |
| Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all | Ihab Bendidi ... Alisandra Kaye Denton | Accept | Open Paper |
| PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis | Yan Wu ... Thore Graepel | Spotlight | Open Paper |
| PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction | Aaron Wenteler ... César Miguel Valdez Córdova | Accept | Open Paper |
| Weighted Diversified Sampling for Efficient Data-Driven Single-Cell Gene-Gene Interaction Discovery | Yifan Wu ... Zhaozhuo Xu | Accept | Open Paper |
| Active learning for efficient discovery of optimal gene combinations in the combinatorial perturbation space | Jason Qin ... Yuhan Hao | Accept | Open Paper |
| CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer | Alexander Theus ... Valentina Boeva | Accept | Open Paper |
| Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics | Alejandro Velez-Arce ... Marinka Zitnik | Spotlight | Open Paper |
| Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states | Tianyu Liu ... Graham Heimberg | Accept | Open Paper |
| Scaling Dense Representations for Single Cell Gene Expression with Transcriptome-Scale Context | Nicholas Ho ... Eric P. Xing | Accept | Open Paper |
| Cell ontology guided transcriptome foundation model | Xinyu Yuan ... Jian Tang | Accept | Open Paper |
| Cluster 9 | |||
| Video Representation Learning of Cardiac MRI for Genetic Discovery | Matt Sooknah ... Jun Xu | Accept | Open Paper |
| Representation Learning based Target Discovery from UKBB MRI data | Sivaramakrishnan Sankarapandian ... Jun Xu | Accept | Open Paper |
| Cluster 10 | |||
| Foundational Model-aided Automatic High-throughput Drug Screening Using Self-controlled Cohort Study | Shenbo Xu ... Kenney Ng | Accept | Open Paper |
| TrialDura: Hierarchical Attention Transformer for Interpretable Clinical Trial Duration Prediction | Ling Yue ... Tianfan Fu | Accept | Open Paper |
| Interpretable Causal Representation Learning for Biological Data in the Pathway Space | Jesus de la Fuente Cedeño ... Mikel Hernaez | Accept | Open Paper |
| Learning to refine domain knowledge for biological network inference | Peiwen Li, Menghua Wu | Accept | Open Paper |
| FluxGAT: Integrating Flux Sampling with Graph Neural Networks for Unbiased Gene Essentiality Classification | Kieren Sharma ... Lucia Marucci | Accept | Open Paper |
| Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph | Kexin Huang ... Jure Leskovec | Accept | Open Paper |
| Leveraging Disease-Specific Topologies and Counterfactual Relationships in Knowledge Graphs for Inductive Reasoning in Drug Repurposing | Cerag Oguztuzun ... Rong Xu | Spotlight | Open Paper |
| A Foundational Multi-Modal Knowledge Graph for Pancreatic Cancer Drug Effects Prediction | Jingwen Hui ... Anima Anandkumar | Accept | Open Paper |
| Cluster 11 | |||
| TCRGenesis: Generation of SIINFEKL-specific T-cell receptor sequences using autoregressive Transformer | Yang An ... Benjamin Schubert | Accept | Open Paper |
| Modeling CAR Response at the Single-Cell Level Using Conditional OT | Alice Driessen ... Marianna Rapsomaniki | Accept | Open Paper |
| Disentangling the Peptide Space: A Contrastive Approach with Wasserstein Autoencoders | Mihir Agarwal, Progyan Das | Accept | Open Paper |
| Epitope Generation for Peptide-based Cancer Vaccine using Goal-directed Wasserstein Generative Adversarial Network with Gradient Penalty | Yen-Che Hsiao, Abhishek Dutta | Accept | Open Paper |
| Cluster 12 | |||
| LLMs are Highly-Constrained Biophysical Sequence Optimizers | Angelica Chen ... Nathan C. Frey | Spotlight | Open Paper |
| Language Models for Text-guided Protein Evolution | Zhanghan Ni ... Anima Anandkumar | Accept | Open Paper |
| Distilling Structural Representations into Protein Sequence Models | Jeffrey Ouyang-Zhang ... Daniel Jesus Diaz | Accept | Open Paper |
| LatentDE: Latent-based Directed Evolution accelerated by Gradient Ascent for Protein Sequence Design | Thanh V. T. Tran ... Truong Son Hy | Accept | Open Paper |
| PLMFit: Benchmarking Transfer Learning with Protein Language Models for Protein Engineering | Thomas Bikias ... Sai T. Reddy | Accept | Open Paper |
| Harnessing Preference Optimisation in Protein LMs for Hit Maturation in Cell Therapy | Katarzyna Janocha ... Nils Yannick Hammerla | Accept | Open Paper |
| Alignment-based and protein foundation models for viral evolution, vaccines and vectors | Sarah Gurev ... Debora Susan Marks | Spotlight | Open Paper |
| Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs | Talip Ucar ... Ferran Gonzalez | Accept | Open Paper |
| EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics | Chenqing Hua ... Shuangjia Zheng | Accept | Open Paper |
| Evaluating synergies among generative design models for multi-objective optimization of drug-like proteins | Jung-Eun Shin ... Ryan Peckner | Accept | Open Paper |
| Machine learning enables engineering of potent, specific, and therapeutically developable proteases | Jung-Eun Shin ... Ryan Peckner | Accept | Open Paper |
| IgBlend: Unifying 3D Structure and Sequence for Antibody LLMs | Cedric Malherbe, Talip Ucar | Spotlight | Open Paper |
| Antibody Library Design by Seeding Linear Programming with Inverse Folding and Protein Language Models | Conor F. Hayes ... Mikel Landajuela | Accept | Open Paper |
| Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences | Alan Nawzad Amin ... Andrew Gordon Wilson | Spotlight | Open Paper |
| Computational Antigen Optimization through Symbolic Optimization and Affinity Maturation Simulation | Jonathan G. Faris ... Felipe Leno da Silva | Spotlight | Open Paper |
| Cluster 13 | |||
| DeepADAR: A deep learning approach to model regulatory elements of ADAR-based RNA editing and its application to gRNA design | Andrew J Jung ... Brendan Frey | Spotlight | Open Paper |
| Detection of RNA Editing Sites by GPT Fine-tuning | Zohar Rosenwasser ... Gal Oren | Accept | Open Paper |
| Mixture of Experts Enable Efficient and Effective Protein Understanding and Design | Ning Sun ... Eric P. Xing | Spotlight | Open Paper |
| A Large-Scale Foundation Model for RNA Function and Structure Prediction | Shuxian Zou ... Eric P. Xing | Spotlight | Open Paper |
| Accurate and General DNA Representations Emerge from Genome Foundation Models at Scale | Caleb Ellington ... Le Song | Accept | Open Paper |
| Orthrus: Towards Evolutionary and Functional RNA Foundation Models | Philip Fradkin ... BO WANG | Spotlight | Open Paper |
| HELM: Hierarchical Encoding for mRNA Language Modeling | Mehdi Yazdani-Jahromi ... Rui Liao | Accept | Open Paper |
| Beyond Sequence: Impact of Geometric Context for RNA Property Prediction | Junjie Xu ... Rui Liao | Accept | Open Paper |
| ML-driven design of 3’ untranslated regions for mRNA stability | Alyssa Kramer Morrow ... Uri Laserson | Accept | Open Paper |
| Cluster 14 | |||
| AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactions | Wei Lu ... Shuangjia Zheng | Accept | Open Paper |
| BindingGYM: A Large-Scale Mutational Dataset Toward Deciphering Protein-Protein Interactions | Wei Lu ... Shuangjia Zheng | Accept | Open Paper |
| A Deep Learning Approach for RNA-Compound Interaction Prediction with Binding Site Interpretability | Haelee Bae, Hojung Nam | Spotlight | Open Paper |
| AptaBLE: A Deep Learning Platform for SELEX Optimization | Sawan Patel ... Sherwood Yao | Accept | Open Paper |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Jiaqing Xie ... Tianfan Fu | Spotlight | Open Paper |
| Understanding Protein-DNA Interactions by Paying Attention to Protein and Genomics Foundation Models | Dhruva Rajwade ... Anima Anandkumar | Accept | Open Paper |
| Cluster 15 | |||
| Bridging the Gap between Database Search and \emph{De Novo} Peptide Sequencing with SearchNovo | Jun Xia ... Stan Z. Li | Spotlight | Open Paper |
| Effective Protein-Protein Interaction Exploration with PPIretrieval | Chenqing Hua ... Shuangjia Zheng | Accept | Open Paper |
| PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models | Eli M Carrami, Sahand Sharifzadeh | Spotlight | Open Paper |
| GeneGench: Systematic Evaluation of Genomic Foundation Models and Beyond | Zicheng Liu ... Stan Z. Li | Accept | Open Paper |
| Diverse Genomic Embedding Benchmark for functional evaluation across the tree of life. | Jacob West-Roberts ... Yunha Hwang | Accept | Open Paper |
| MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model | Sumin Ha ... Sun Kim | Accept | Open Paper |
| Natural Language Prompts Guide the Design of Novel Functional Protein Sequences | Niksa Praljak ... Andrew Ferguson | Accept | Open Paper |
| Probing the Embedding Space of Protein Foundation Models through Intrinsic Dimension Analysis | Soojung Yang ... Rafael Gomez-Bombarelli | Accept | Open Paper |
| PepDoRA: A Unified Peptide Language Model via Weight-Decomposed Low-Rank Adaptation | Leyao Wang ... Pranam Chatterjee | Accept | Open Paper |
Methods
- Data pulled from the AIDrugX Workshop OpenReview portal here
- Find the workshop website here
- Semantic embeddings were generated using Sentence-BERT, using paper titles, abstracts, and keywords
- PCA was applied to reduce dimensionality for visualization
This is a cross post from my Behind BioML substack. Find the original here.