A Masked Image Modeling Approach to CyCIF Panel Reduction and Marker Imputation

Zachary S. Sims, Young Hwan Chang; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:1-9

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Multitask-Guided Self-Supervised Tabular Learning for Patient-Specific Survival Prediction

You Wu, Omid Bazgir, Yongju Lee, Tommaso Biancalani, James Lu, Ehsan Hajiramezanali; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:10-22

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Open Biomedical Network Benchmark: A Python Toolkit for Benchmarking Datasets with Biomedical Networks

Renming Liu, Arjun Krishnan; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:23-59

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Disentangling shared and private latent factors in multimodal Variational Autoencoders

Kaspar Märtens, Christopher Yau; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:60-75

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Evaluating Tuning Strategies for Sequence Generation with Protein Language Models

Andrea Nathansen, Kevin Klein, Bernhard Renard, Melania Nowicka, Jakub M Bartoszewicz; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:76-89

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A Supervised Contrastive Framework for Learning Disentangled Representations of Cellular Perturbation Data

Xinming Tu, Jan-Christian Hütter, Zitong Jerry Wang, Takamasa Kudo, Aviv Regev, Romain Lopez; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:90-100

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A Transductive Approach to Survival Ranking for Cancer Risk Stratification

Ethar Alzaid, Muhammad Dawood, Fayyaz Minhas; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:101-109

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Towards creating longer genetic sequences with GANs: Generation in principal component space

Antoine Szatkownik, Cyril Furtlehner, Guillaume Charpiat, Burak Yelmen, Flora Jay; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:110-122

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On Modelability and Generalizability: Are Machine Learning Models for Drug Synergy Exploiting Artefacts and Biases in Available Data?

Arushi G. K. Majha, Ian Stott, Andreas Bender; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:123-134

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A Multi-Granularity Approach to Similarity Search in Multiplexed Immunofluorescence Images

Jennifer Yu, Zhenqin Wu, Aaron Mayer, Alexandro Trevino, James Zou; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:135-147

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ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings

Chenwei Zhang, Jordan Lovrod, Boyan Beronov, Khanh Dao Duc, Anne Condon; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:148-162

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Investigating RNA splicing as a source of cellular diversity using a binomial mixture model

Keren Isaev, David A. Knowles; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:163-175

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Model-based imputation enables improved resolution for identifying differential chromatin contacts in single-cell Hi-C data

Neda Shokraneh Kenari, Megan Andrews, Max Libbrecht; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:176-193

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TCR-BERT: learning the grammar of T-cell receptors for flexible antigen-binding analyses

Kevin E. Wu, Kathryn Yost, Bence Daniel, Julia Belk, Yu Xia, Takeshi Egawa, Ansuman Satpathy, Howard Chang, James Zou; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:194-229

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H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing

Gian Marco Visani, William Galvin, Michael Pun, Armita Nourmohammad; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:230-249

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GUANinE v1.0: Benchmark Datasets for Genomic AI Sequence-to-Function Models

eyes s. robson, Nilah Ioannidis; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:250-266

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Improving transformer secondary structure predictions with secondary structure ”fixing” task

Juneki Hong, Dezhong Deng, David A. Hendrix; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:267-278

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Characterizing uncertainty in predictions of genomic sequence-to-activity models

Ayesha Bajwa, Ruchir Rastogi, Pooja Kathail, Richard W. Shuai, Nilah Ioannidis; Proceedings of the 18th Machine Learning in Computational Biology meeting, PMLR 240:279-297

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