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Proceedings of Machine Learning Research

Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research Proceedings of Machine Learning Research
Proceedings of Machine Learning Research
PMLR · 2026-06-02 · via Proceedings of Machine Learning Research

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Volume 311: Machine Learning in Computational Biology, 10-11 September 2025, New York, NY, USA

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Editors: David A Knowles, Peter K Koo

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GeST: Towards Building A Generative Pretrained Transformer for Learning Cellular Spatial Context

; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:1-11

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TCR-ECHO: Evolutionary Cross-attention with Physicochemical Bias for Hierarchical TCR-Peptide Binding Prediction

Tapanmitra Ravi, Irene M Ong; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:12-27

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Unsupervised Evolutionary Cell Type Matching via Entropy-Minimized Optimal Transport

Mu Qiao; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:28-43

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PerTurboAgent: An LLM-based Agent for Designing Iterative Perturb-Seq Experiments

Minsheng Hao, yongju lee, Hanchen Wang, Gabriele Scalia, Aviv Regev; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:44-64

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CN-SBM: Categorical Block Modelling For Primary and Residual Copy Number Variation

Kevin Lam, William Daniels, Maxwell Douglas, Daniel Lai, Samuel Aparicio, Benjamin Bloem-Reddy, Yongjin Park; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:65-80

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Can sparse autoencoders make sense of gene expression latent variable models?

Viktoria Schuster; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:81-94

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A Genomic Language Model for Zero-Shot Prediction of Promoter Indel Effects

Courtney Shearer, Rose Orenbuch, Felix Teufel, Christian Steinmetz, Daniel Ritter, Erik Xie, Artem Gazizov, Aviv Spinner, Mafalda Dias, Jonathan Frazer, Pascal Notin, Debora Marks; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:95-127

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Context-Dependent Genetic Modifiers of Huntington’s Disease Revealed Through Multimodal Machine Learning

Caterina Fuses, Georgia Zavou, Berta Ros, Josep M Canals, Jordi Abante; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:128-147

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GOLF: A Generative AI Framework for Pathogenicity Prediction of Myocilin OLF Variants

Thomas Walton, Darin Tsui, Amirali Aghazadeh, Raquel Lieberman, Lauren Fogel, Rafael Chagas, Dustin Huard; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:148-161

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Representation Learning Methods for Single-Cell Microscopy are Confounded by Background Cells

Arushi Gupta, Alan Moses, Alex Lu; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:162-177

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Automated Seizure Detection in Animal EEG Signals

Shreyan Ganguly, Zhanhong Jiang, Nyzil Massey, Nikhil Sanjay Rao, Thimmasettappa Thippeswamy, Soumik Sarkar; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:178-188

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Harnessing DNA Foundation Models for Cross-Species Transcription Factor Binding Site Prediction in Plant Genomes

Maryam Haghani, Krishna vamsi Dhulipalla, Song Li; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:189-198

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AI-based histopathology phenotyping reveals germline loci shaping breast cancer morphology

Shubham Chaudhary, Almut Voigts, Sergey Vilov, Matthias Heinig, Francesco Paolo Casale; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:199-212

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Variational Graph Auto-encoder for Denoising Single-cell Hi-C Data

Neda Shokraneh Kenari, Maxwell Libbrecht; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:213-229

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Addressing the Cold-Start Problem for Personalized Combination Drug Screening

Antoine de Mathelin, Christopher Tosh, Wesley Tansey; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:230-239

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Somatic Hypermutation Informed Vocabulary Encoder Representations

Chiho Im, Artem Mikelov, Ryan Zhao, Anshul Kundaje, Scott Boyd; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:240-250

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Self-Contemplating In-Context Learning Enhances T Cell Receptor Generation for Novel Epitopes

Pengfei Zhang, Sonal Prabhu, Gloria Grama, Seojin Bang, Heewook Lee; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:251-269

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BIRDccNEST: Interpretable single cell characterization with inferred directed cell networks

Gizem Cicekli, Adrita Samanta, Hao Zhu, Donna Slonim; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:270-279

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Towards functional annotation with latent protein language model features

Jacob Silberg, Elana Simon, James Zou; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:280-293

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Augmenting DNABERT Embeddings with Multimodal DNA Features for Improved Regulatory Sequence Interpretation

Nimisha Papineni, Pratik Dutta, Max Chao, Orbin Acanto, Rekha Sathian, Pallavi Surana, Ramana Davuluri; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:294-303

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Continued domain-specific pre-training of protein language models for pMHC-I binding prediction

Sergio Mares, Ariel Espinoza, Nilah Ioannidis; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:304-325

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F-MoDA: Efficient Fourier-based motif discovery in attribution maps

Ofir Yaish, Yaron Orenstein; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:326-335

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STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics

Joao F. Rocha, Ke Xu, Xingzhi Sun, Ananya Krishna, Dhananjay Bhaskar, Blanche Mongeon, Morgan Craig, Mark Gerstein, Smita Krishnaswamy; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:336-346

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