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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
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
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
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
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
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
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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