Abstract is missing.
- GeST: Towards Building A Generative Pretrained Transformer for Learning Cellular Spatial ContextMinsheng Hao, Nan Yan, Haiyang Bian, Yixin Chen, Jin Gu, Lei Wei 0009, Xuegong Zhang. 1-11 [doi]
- TCR-ECHO: Evolutionary Cross-attention with Physicochemical Bias for Hierarchical TCR-Peptide Binding PredictionTapanmitra Ravi, Irene M. Ong. 12-27 [doi]
- Unsupervised Evolutionary Cell Type Matching via Entropy-Minimized Optimal TransportMu Qiao. 28-43 [doi]
- PerTurboAgent: An LLM-based Agent for Designing Iterative Perturb-Seq ExperimentsMinsheng Hao, Yongju Lee, Hanchen Wang 0002, Gabriele Scalia, Aviv Regev. 44-64 [doi]
- CN-SBM: Categorical Block Modelling For Primary and Residual Copy Number VariationKevin Lam, William Daniels, J. Maxwell Douglas, Daniel Lai, Samuel Aparicio, Benjamin Bloem-Reddy, Yongjin Park. 65-80 [doi]
- Can sparse autoencoders make sense of gene expression latent variable models?Viktoria Schuster. 81-94 [doi]
- A Genomic Language Model for Zero-Shot Prediction of Promoter Indel EffectsCourtney Shearer, Rose Orenbuch, Felix Teufel, Christian Steinmetz, Daniel Ritter 0006, Erik Xie, Artem Gazizov, Aviv Spinner, Mafalda Dias, Jonathan Frazer, Pascal Notin, Debora S. Marks. 95-127 [doi]
- Context-Dependent Genetic Modifiers of Huntington’s Disease Revealed Through Multimodal Machine LearningCaterina Fuses, Georgia Zavou, Berta Ros, Josep M. Canals, Jordi Abante. 128-147 [doi]
- GOLF: A Generative AI Framework for Pathogenicity Prediction of Myocilin OLF VariantsThomas Walton, Darin Tsui, Amirali Aghazadeh, Raquel Lieberman, Lauren Fogel, Rafael Chagas, Dustin Huard. 148-161 [doi]
- Representation Learning Methods for Single-Cell Microscopy are Confounded by Background CellsArushi Gupta, Alan M. Moses, Alex Lu 0002. 162-177 [doi]
- Automated Seizure Detection in Animal EEG SignalsShreyan Ganguly, Zhanhong Jiang, Nyzil Massey, Nikhil Sanjay Rao, Thimmasettappa Thippeswamy, Soumik Sarkar. 178-188 [doi]
- Harnessing DNA Foundation Models for Cross-Species Transcription Factor Binding Site Prediction in Plant GenomesMaryam Haghani, Krishna Vamsi Dhulipalla, Song Li. 189-198 [doi]
- AI-based histopathology phenotyping reveals germline loci shaping breast cancer morphologyShubham Chaudhary, Almut Voigts, Sergey Vilov, Matthias Heinig, Francesco Paolo Casale. 199-212 [doi]
- Variational Graph Auto-encoder for Denoising Single-cell Hi-C DataNeda Shokraneh Kenari, Maxwell W. Libbrecht. 213-229 [doi]
- Addressing the Cold-Start Problem for Personalized Combination Drug ScreeningAntoine de Mathelin, Christopher Tosh, Wesley Tansey. 230-239 [doi]
- Somatic Hypermutation Informed Vocabulary Encoder RepresentationsChiho Im, Artem Mikelov, Ryan Zhao, Anshul Kundaje, Scott D. Boyd. 240-250 [doi]
- Self-Contemplating In-Context Learning Enhances T Cell Receptor Generation for Novel EpitopesPengfei Zhang, Sonal Prabhu, Gloria Grama, Seojin Bang, Heewook Lee. 251-269 [doi]
- BIRDccNEST: Interpretable single cell characterization with inferred directed cell networksGizem Cicekli, Adrita Samanta, Hao Zhu, Donna Slonim. 270-279 [doi]
- Towards functional annotation with latent protein language model featuresJacob Silberg, Elana Simon, James Zou 0001. 280-293 [doi]
- Augmenting DNABERT Embeddings with Multimodal DNA Features for Improved Regulatory Sequence InterpretationNimisha Papineni, Pratik Dutta, Max Chao, Orbin Acanto, Rekha Sathian, Pallavi Surana, Ramana V. Davuluri. 294-303 [doi]
- Continued domain-specific pre-training of protein language models for pMHC-I binding predictionSergio E. Mares, Ariel Espinoza Weinberger, Nilah M. Ioannidis. 304-325 [doi]
- F-MoDA: Efficient Fourier-based motif discovery in attribution mapsOfir Yaish, Yaron Orenstein. 326-335 [doi]
- STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction DynamicsJoão F. Rocha, Ke Xu 0010, Xingzhi Sun 0003, Ananya Krishna, Dhananjay Bhaskar, Blanche Mongeon, Morgan Craig, Mark Gerstein, Smita Krishnaswamy. 336-346 [doi]