| Self-Supervised Learning of Phenotypic Representations from Cell Images with Weak Labels (Paper) |
Jan Oscar Cross-Zamirski, Guy Williams, Elizabeth Mouchet, Carola-Bibiane Schönlieb, Riku Turkki, Yinhai Wang |
| Biological Neurons vs Deep Reinforcement Learning: Sample efficiency in a simulated game-world (Paper) |
Forough Habibollahi, Moein Khajehnejad, Amitesh Gaurav, Brett Joseph Kagan |
| Learning More Effective Cell Representations Efficiently (Poster) |
Jason Xiaotian Dou, Minxue Jia, Nika Zaslavsky, Mark Ebeid, Runxue Bao, Shiyi Zhang, Ke Ni, Paul Pu Liang, Haiyi Mao, Zhi-Hong Mao |
| What cleaves? Is proteasomal cleavage prediction reaching a ceiling? (Paper) |
Ingo Ziegler, Bolei Ma, Ercong Nie, Bernd Bischl, David Rügamer, Benjamin Schubert, Emilio Dorigatti |
| CoSpar identifies early cell fate biases from single cell transcriptomic and lineage information (Poster) |
Shou-Wen Wang, Michael J Herriges, Kilian Hurley, Darrell N. Kotton |
| Network-Based Clustering of Pan-Cancer Data Accounting for Clinical Covariates (Paper) |
Fritz Bayer, Giusi Moffa, Niko Beerenwinkel, Jack Kuipers |
| Designing and Evolving Neuron-Specific Proteases (Paper) |
Han Spinner, Colin Hemez, Julia McCreary, David Ruchien Liu, Debora Susan Marks |
| Multimodal deep transfer learning for the analysis of optical coherence tomography scans and retinal fundus photographs (Paper) |
Zoi Tsangalidou, Edwin Fong, Josefine Vilsbøll Sundgaard, Trine Julie Abrahamsen, Kajsa Kvist |
| Spatially-aware dimension reduction of transcriptomics data (Paper) |
Lauren Okamoto, Andrew Jones, Archit Verma, Barbara E. Engelhardt |
| Benchmarking Graph Neural Network-based Imputation Methods on Single-Cell Transcriptomics Data (Paper) |
Han-Bo Li, Ramon Viñas Torné, Pietro Lio |
| Unsupervised language models for disease variant prediction (Paper) |
Allan Zhou, Nicholas Charles Landolfi, Dan O'Neill |
| Box Prediction Rebalancing for Training Single-Stage Object Detectors with Partially Labeled Data (Paper) |
Shafin Haque, R. Austin McEver |
| Utilizing Mutations to Evaluate Interpretability of Neural Networks on Genomic Data (Paper) |
Utku Ozbulak, Solha Kang, Jasper Zuallaert, Stephen Depuydt, Joris Vankerschaver |
| scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data (Paper) |
Tessa Durakis Green, Stefan Peidli, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Jake P. Taylor-King, Debora Susan Marks, Augustin Luna, Nils Blüthgen, Chris Sander |
| Representation Learning to Integrate and Interpret Omics Data (Paper) |
Sara Masarone |
| Kernelized Stein Discrepancies for Biological Sequences (Paper) |
Alan Nawzad Amin, Eli N Weinstein, Debora Susan Marks |
| 3D single-cell shape analysis of cancer cells using geometric deep learning (Paper) |
Matt De Vries, Lucas G Dent, Nathan Curry, Leo Rowe-Brown, Adam Tyson, Chris Dunsby, Chris Bakal |
| Using hierarchical variational autoencoders to incorporate conditional independent priors for paired single-cell multi-omics data integration (Paper) |
Ping-Han Hsieh, Ru-Xiu Hsiao, Tatiana Belova, Katalin Ferenc, Anthony Mathelier, Rebekka Burkholz, Chien-Yu Chen, Geir Kjetil Sandve, Marieke Lydia Kuijjer |
| Translating L-peptides into non-canonical linear and macrocyclic peptides (Paper) |
Somesh Mohapatra |
| Protein Language Model Predicts Mutation Pathogenicity and Clinical Prognosis (Paper) |
Xiangling Liu, Xinyu Yang, Linkun Ouyang, Guibing Guo, Jin Su, Ruibin Xi, Ke Yuan, Fajie Yuan |
| Fitness Inference for Drug Discovery with Directed Evolution (removed from public release at the request of the authors) (Paper) |
Nathaniel Lee Diamant, Ziqing Lu, Christina Helmling, Kangway V Chuang, Christian Cunningham, Tommaso Biancalani, Gabriele Scalia, Max W Shen |
| Data-driven subgroup identification for linear regression (Paper) |
Zachary Izzo, Ruishan Liu, James Zou |
| LANTERN-RD: Enabling Deep Learning for Mitigation of the Invasive Spotted Lanternfly (Poster) |
Srivatsa R Kundurthy |
| Generative model for Pseudomonad genomes (Poster) |
Manasa Kesapragada, R Shane Canon, Sean P Jungbluth, Marcin P Joachimiak, Adam P Arkin, Paramvir S Dehal |
| Learning relationships between histone modifications in single cells (Paper) |
Jake Yeung, Maria Florescu, Peter Zeller, Buys Anton de Barbanson, Max D Wellenstein, Alexander van Oudenaarden |
| Seeded iterative clustering for histology region identification (Paper) |
Eduard Chelebian, Francesco Ciompi, Carolina Wahlby |
| Fuzzy Logic for Biological Networks as ML Regression: Scaling to Single-Cell Datasets With Autograd (Poster) |
Constance LE GAC, Alice Driessen, Nicolas Deutschmann, Maria Rodriguez Martinez |
| Conditional Neural Processes for Molecules (Paper) |
Miguel Garcia Ortegon, Andreas Bender, Sergio Bacallado |
| MatchCLOT: Single-Cell Modality Matching with Contrastive Learning and Optimal Transport (Paper) |
Federico Gossi, Pushpak Pati, Adriano Martinelli, Marianna Rapsomaniki |
| Transformer Model for Genome Sequence Analysis (Paper) |
Noah Hurmer, Xiao-Yin To, Martin Binder, Hüseyin Anil Gündüz, Philipp C. Münch, René Mreches, Alice C McHardy, Bernd Bischl, Mina Rezaei |
| decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods (Paper) |
Camila Duitama González, Riccardo Vicedomini, Teo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi |
| Double trouble: Predicting new variant counts across two heterogeneous populations (Paper) |
Yunyi Shen, Lorenzo Masoero, Joshua Schraiber, Tamara Broderick |
| Forecasting labels under distribution-shift for machine-guided sequence design (Paper) |
Lauren Berk Wheelock, Stephen Malina, Jeffrey Gerold, Sam Sinai |
| Learning representations of cell populations for image-based profiling using contrastive learning (Poster) |
Robert Van Dijk, John Arevalo, Shantanu Singh, Anne E Carpenter |
| MolE: a molecular foundation model for drug discovery (Paper) |
Oscar Mendez-Lucio, Christos A Nicolaou, Berton Earnshaw |
| Is brightfield all you need for MoA prediction? (Poster) |
Ankit Gupta, Philip John Harrison, Håkan Wieslander, Jonne Rietdijk, Jordi Carreras Puigvert, Polina Georgiev, Carolina Wahlby, Ola Spjuth, Ida-Maria Sintorn |
| meTCRs - Learning a metric for T-cell receptors (Paper) |
Felix Drost, Lennard Schiefelbein, Benjamin Schubert |
| Knowledge distillation for fast and accurate DNA sequence correction (Paper) |
Anastasiya Belyaeva, Joel Shor, Daniel E Cook, Kishwar Shafin, Daniel Liu, Armin Töpfer, Aaron M Wenger, William J Rowell, Howard Yang, Alexey Kolesnikov, Cory Y McLean, Maria Nattestad, Andrew Carroll, Pi-Chuan Chang |
| CP2Image: generating high-quality single-cell images using CellProfiler representations (Paper) |
Yanni Ji, Marie Cutiongco, Bjørn Sand Jensen, Ke Yuan |
| A Modelling Framework for Catalysing Progress in the Rod-Shaped Bacterial Cell Growth Discourse (Paper) |
Shashi Nagarajan, Fredrik Lindsten |
| Standards, tooling and benchmarks to probe representation learning on proteins (Poster) |
Joaquin Gomez Sanchez, Sebastian Franz, Michael Heinzinger, Burkhard Rost, Christian Dallago |
| A single-cell gene expression language model (Paper) |
William Connell, Umair Khan, Michael Keiser |
| Improving Protein Subcellular Localization Prediction with Structural Prediction & Graph Neural Networks (Paper) |
Geoffroy Dubourg-Felonneau, Arash Abbasi, Eyal Akiva, Lawrence Lee |
| ChromFormer: A transformer-based model for 3D genome structure prediction (Paper) |
Henry Valeyre, Pushpak Pati, Federico Gossi, Vignesh Ram Somnath, Adriano Martinelli, Marianna Rapsomaniki |
| Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings (Paper) |
Frederike Lübeck, Charlotte Bunne, Gabriele Gut, Jacobo Sarabia del Castillo, Lucas Pelkmans, David Alvarez-Melis |
| TranceptEVE: Combining Family-specific and Family-agnostic Models of Protein Sequences for Improved Fitness Prediction (Paper) |
Pascal Notin, Lood Van Niekerk, Aaron W Kollasch, Daniel Ritter, Yarin Gal, Debora Susan Marks |
| Find your microenvironments faster with Neural Spatial LDA (Paper) |
Sivaramakrishnan Sankarapandian, Jun Xu, Zhenghao Chen |
| Continuous cell-state density inference and applications for single-cell data (Poster) |
Dominik Jenz Otto, Manu Setty, Brennan Dury |
| Multimodal Cell-Free DNA Embeddings are Informative for Early Cancer Detection (Paper) |
Felix Jackson |
| EpiAttend: A transformer model of gene regulation combining single cell epigenomes with DNA sequence (Poster) |
Russell Li, Heng Xu, Eran A Mukamel |
| An Empirical Study of ML-based Phenotyping and Denoising for Improved Genomic Discovery (Paper) |
Bo Yuan, Cory Y McLean, Farhad I Hormozdiari, Justin Cosentino |
| Machine Learning enabled Pooled Optical Screening in Human Lung Cancer Cells (Paper) |
Srinivasan Sivanandan, Max Salick, Bobby Leitmann, Kara Marie Liu, Mohammad Sultan, Navpreet Ranu, Cynthia Vivian Hao, Owen Chen, John Bisognano, Eric Lubeck, Ajamete Kaykas, Eilon Sharon, Ci Chu |
| Interpretable visualization of single cell data using Janus autoencoders (Paper) |
Gokul Gowri, Philippa Anne Richter, Xiaokang Lun, Peng Yin |
| Joint Protein Sequence-Structure Co-Design via Equivariant Diffusion (Paper) |
Ria Vinod, Kevin K. Yang, Lorin Crawford |
| Designing active and thermostable enzymes with sequence-only predictive models (Paper) |
Clara Fannjiang, Micah Olivas, Eric R. Greene, Craig J. Markin, Bram Wallace, Ben Krause, Margaux M. Pinney, James Fraser, Polly M Fordyce, Ali Madani, Nikhil Naik |
| SPOT: Spatial Optimal Transport for Analyzing Cellular Microenvironments (Paper) |
Shouvik Mani, Doron Haviv, Russell Z. Kunes, Dana Pe'er |
| Regression-Based Elastic Metric Learning on Shape Spaces of Cell Curves (Paper) |
Adele Myers, Nina Miolane |
| Protein language model rescue mutations highlight variant effects and structure in clinically relevant genes (Paper) |
Onuralp Soylemez, Pablo Cordero |
| Biological Cartography: Building and Benchmarking Representations of Life (Paper) |
Safiye Celik, Jan-Christian Huetter, Sandra Melo, Nathan Lazar, Rahul Mohan, Conor Tillinghast, Tommaso Biancalani, Marta Fay, Berton Earnshaw, Imran S Haque |
| Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps (Paper) |
Luca Eyring, Dominik Klein, Giovanni Palla, Sören Becker, Philipp Weiler, Niki Kilbertus, Fabian J Theis |
| Energy-based Modelling for Single-cell Data Annotation (Paper) |
Tianyi Liu, Philip Fradkin, Lazar Atanackovic, Leo J Lee |
| A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction (Paper) |
Krzysztof Koras, Marcin Możejko, Paulina Szymczak, Adam Izdebski, Eike Staub, Ewa Maria Szczurek |
| Using co-localization priors and microenvironment statistics to reconstruct tissue organization from single-cell data (Paper) |
Yitzchak Vaknin, Noa Moriel, Mor Nitzan |
| Designing Proteins using Sparse Data (Poster) |
Ada Shaw, Jung-Eun Shin, Nicole Nisha Thadani, Alan Nawzad Amin, Debora Susan Marks |
| Simultaneous alignment of cells and features of unpaired single-cell multi-omics datasets with co-optimal transport (Paper) |
Pinar Demetci, Quang Huy TRAN, Ievgen Redko, Ritambhara Singh |
| Personalised drug recommendation from augmented gene expression data - the right drug(s) for the right patient (Poster) |
Manuela Salvucci, Davy Suvee, Deniz Pirincci, Dimitrius Raphael, Eryk Kropiwnicki, Giovanni Dall’olio, James O’Reilly, Katie Sanford, Marika Catapano, Marta Sarrico, Xenia Galkina, Francesca Mulas |