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

Minsheng Hao, Nan Yan, Haiyang Bian, Yixin Chen, Jin Gu, Lei Wei, Xuegong Zhang; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:1-11

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF][Supplementary PDF]

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

[abs][Download PDF]

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

Jordi Abante, Caterina Fuses; Proceedings of the 20th Machine Learning in Computational Biology meeting, PMLR 311:128-147

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF][Supplementary PDF]

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

[abs][Download PDF][Supplementary PDF]

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

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF]

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

[abs][Download PDF][Supplementary PDF]

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

[abs][Download PDF]

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

[abs][Download PDF][Supplementary PDF]

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

[abs][Download PDF]

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

[abs][Download PDF][Supplementary PDF]