Workshop
Learning Meaningful Representations of Life
Elizabeth Wood · Adji Bousso Dieng · Aleksandrina Goeva · Alex X Lu · Anshul Kundaje · Chang Liu · Debora Marks · Ed Boyden · Eli N Weinstein · Lorin Crawford · Mor Nitzan · Rebecca Boiarsky · Romain Lopez · Tamara Broderick · Ray Jones · Wouter Boomsma · Yixin Wang · Stephen Ra
Virtual
Fri 9 Dec, 4:30 a.m. PST
All events will be in a non-NeurIPS Zoom and on Gather.Town, without embedded streaming. Links below.
Chat is not available.
Timezone: America/Los_Angeles
Schedule
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Fri 4:30 a.m. - 5:00 a.m.
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Poster Preview on Gather.Town ( Poster Session ) > link | 🔗 |
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Fri 5:00 a.m. - 6:00 a.m.
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Keynote - Rich Bonneau ( Talks ) > link | Richard Bonneau 🔗 |
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Fri 6:00 a.m. - 7:00 a.m.
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Contributed & Lightning talks
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Talks
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Fri 7:00 a.m. - 8:00 a.m.
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Poster Session
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Poster Session
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Fri 8:00 a.m. - 9:00 a.m.
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Keynote - Shantanu Singh ( Keynote ) > link | Shantanu Singh 🔗 |
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Fri 9:00 a.m. - 10:00 a.m.
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Contributed & Lightning talks
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Talks
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Fri 10:00 a.m. - 11:00 a.m.
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Keynote - Pulin Li ( Talks ) > link | 🔗 |
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Fri 11:00 a.m. - 12:00 p.m.
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Contributed & Lightning talks
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Talks
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Fri 12:00 p.m. - 1:00 p.m.
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Itai Yanai - "Night Science:" The creative side of the scientific process
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Talk
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Fri 1:00 p.m. - 2:00 p.m.
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Poster Session
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Poster Session
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Personalised drug recommendation from augmented gene expression data - the right drug(s) for the right patient ( Poster ) > link | Manuela Salvucci · Francesca Mulas · Marika Catapano 🔗 |
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Simultaneous alignment of cells and features of unpaired single-cell multi-omics datasets with co-optimal transport ( Poster ) > link | Pinar Demetci · Quang Huy TRAN · Ievgen Redko · Ritambhara Singh 🔗 |
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How can we use natural evolution and genetic experiments to design protein functions? ( Poster ) > link | Ada Shaw · June Shin · Debora Marks 🔗 |
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Using co-localization priors and microenvironment statistics to reconstruct tissue organization from single-cell data ( Poster ) > link | Yitzchak Vaknin · Noa Moriel · Mor Nitzan 🔗 |
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A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction ( Poster ) > link | Krzysztof Koras · Marcin Możejko · Paulina Szymczak · Adam Izdebski · Eike Staub · Ewa Szczurek 🔗 |
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Energy-based Modelling for Single-cell Data Annotation ( Poster ) > link | Tianyi Liu · Philip Fradkin · Lazar Atanackovic · Leo J Lee 🔗 |
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Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps ( Poster ) > link | Luca Eyring · Dominik Klein · Giovanni Palla · Sören Becker · Philipp Weiler · Niki Kilbertus · Fabian Theis 🔗 |
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Biological Cartography: Building and Benchmarking Representations of Life ( Poster ) > link | Safiye Celik · Jan-Christian Huetter · Sandra Melo · Nathan Lazar · Rahul Mohan · Conor Tillinghast · Tommaso Biancalani · Marta Fay · Berton Earnshaw · Imran Haque 🔗 |
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Protein language model rescue mutations highlight variant effects and structure in clinically relevant genes ( Poster ) > link | Onuralp Soylemez · Pablo Cordero 🔗 |
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Regression-Based Elastic Metric Learning on Shape Spaces of Cell Curves ( Poster ) > link | Adele Myers · Nina Miolane 🔗 |
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Learning Canonical Cellular Environments from Spatial Transcriptomic Data via Optimal Transport ( Poster ) > link | Shouvik Mani · Doron Haviv · Dana Peer 🔗 |
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Designing active and thermostable enzymes with sequence-only predictive models ( Poster ) > link |
11 presentersClara Fannjiang · Micah Olivas · Eric Greene · Craig Markin · Bram Wallace · Ben Krause · Margaux Pinney · James Fraser · Polly Fordyce · Ali Madani · Nikhil Naik |
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Joint Protein Sequence-Structure Co-Design via Equivariant Diffusion ( Poster ) > link | Ria Vinod 🔗 |
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Interpretable visualization of single cell data using Janus autoencoders ( Poster ) > link | Gokul Gowri · Phillipa Richter · Xiaokang Lun · Peng Yin 🔗 |
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Machine Learning enabled Pooled Optical Screening in Human Lung Cancer Cells ( Poster ) > link |
12 presentersSrinivasan Sivanandan · Max Salick · Bobby Leitmann · Kara Liu · Navpreet Ranu · Cynthia Hao · Owen Chen · John Bisognano · Eric Lubeck · Ajamete Kaykas · Eilon Sharon · Ci Chu |
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An Empirical Study of ML-based Phenotyping and Denoising for Improved Genomic Discovery ( Poster ) > link | Bo Yuan · Cory McLean · Farhad Hormozdiari · Justin Cosentino 🔗 |
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EpiAttend: A transformer model of gene regulation combining single cell epigenomes with DNA sequence ( Poster ) > link | Eran A Mukamel · Russell Li 🔗 |
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Multimodal Cell-Free DNA Embeddings are Informative for Early Cancer Detection ( Poster ) > link | Felix Jackson 🔗 |
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Continuous cell-state density inference and applications for single-cell data ( Poster ) > link | Dominik Otto · Manu Setty · Brennan Dury 🔗 |
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Find your microenvironments faster with Neural Spatial LDA ( Poster ) > link | Sivaramakrishnan Sankarapandian · Zhenghao Chen · Jun Xu 🔗 |
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TranceptEVE: Combining Family-specific and Family-agnostic Models of Protein Sequences for Improved Fitness Prediction ( Poster ) > link | Pascal Notin · Lodevicus van Niekerk · Aaron Kollasch · Daniel Ritter · Yarin Gal · Debora Marks 🔗 |
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Tuned Quadratic Landscapes for Benchmarking Model-Guided Protein Design ( Poster ) > link | Neil Thomas · Atish Agarwala · David Belanger · Yun Song · Lucy Colwell 🔗 |
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Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings ( Poster ) > link | Frederike Lübeck · Charlotte Bunne · Gabriele Gut · Jacobo Sarabia del Castillo · Lucas Pelkmans · David Alvarez-Melis 🔗 |
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ChromFormer: A transformer-based model for 3D genome structure prediction ( Poster ) > link | Henry Valeyre · Pushpak Pati · Federico Gossi · Vignesh Ram Somnath · Adriano Martinelli · Maria Anna Rapsomaniki 🔗 |
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Improving Protein Subcellular Localization Prediction with Structural Prediction & Graph Neural Networks ( Poster ) > link | Geoffroy Dubourg-Felonneau · Arash Abbasi · Eyal Akiva · Lawrence Lee 🔗 |
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A single-cell gene expression language model ( Poster ) > link | William Connell · Umair Khan · Michael Keiser 🔗 |
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Standards, tooling and benchmarks to probe representation learning on proteins ( Poster ) > link | Joaquin Gomez Sanchez · Sebastian Franz · Michael Heinzinger · Burkhard Rost · Christian Dallago 🔗 |
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A Modelling Framework for Catalysing Progress in the Rod-Shaped Bacterial Cell Growth Discourse ( Poster ) > link | Shashi Nagarajan · Fredrik Lindsten 🔗 |
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CP2Image: generating high-quality single-cell images using CellProfiler representations ( Poster ) > link | Yanni Ji · Marie Cutiongco · Bjørn S Jensen · Ke Yuan 🔗 |
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Knowledge distillation for fast and accurate DNA sequence correction ( Poster ) > link |
14 presentersAnastasiya Belyaeva · Joel Shor · Daniel Cook · Kishwar Shafin · Daniel Liu · Armin Töpfer · Aaron Wenger · William Rowell · Howard Yang · Alexey Kolesnikov · Cory McLean · Maria Nattestad · Andrew Carroll · Pi-Chuan Chang |
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meTCRs - Learning a metric for T-cell receptors ( Poster ) > link | Felix Drost · Lennard Schiefelbein · Benjamin Schubert 🔗 |
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Is brightfield all you need for MoA prediction? ( Poster ) > link | Ankit Gupta · Philip Harrison · Håkan Wieslander · Jonne Rietdijk · Jordi Puigvert · Polina Georgiev · Carolina Wählby · Ola Spjuth · Ida-Maria Sintorn 🔗 |
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MolE: a molecular foundation model for drug discovery ( Poster ) > link | Oscar Méndez-Lucio · Christos Nicolaou · Berton Earnshaw 🔗 |
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Learning representations of cell populations for image-based profiling using contrastive learning ( Poster ) > link | Robert van Dijk · John Arevalo · Shantanu Singh · Anne Carpenter 🔗 |
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Forecasting labels under distribution-shift for machine-guided sequence design ( Poster ) > link | Lauren B Wheelock · Stephen Malina · Jeffrey Gerold · Sam Sinai 🔗 |
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Double trouble: Predicting new variant counts across two heterogeneous populations ( Poster ) > link | Yunyi Shen · Tamara Broderick 🔗 |
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decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods ( Poster ) > link | Camila Duitama González · Riccardo Vicedomini · Teo Lemane · Nicolas Rascovan · Hugues Richard · Rayan Chikhi 🔗 |
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Transformer Model for Genome Sequence Analysis ( Poster ) > link | Noah Hurmer · Xiao-Yin To · Martin Binder · Hüseyin Anil Gündüz · Philipp Münch · René Mreches · Alice McHardy · Bernd Bischl · Mina Rezaei 🔗 |
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SCOOTR: Single-Cell Multimodal Data Integration with Contrastive Learning and Optimal Transport ( Poster ) > link | Federico Gossi · Pushpak Pati · Adriano Martinelli · Maria Anna Rapsomaniki 🔗 |
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Conditional Neural Processes for Molecules ( Poster ) > link | Miguel Garcia-Ortegon · Andreas Bender · Sergio Bacallado 🔗 |
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Fuzzy Logic for Biological Networks as ML Regression: Scaling to Single-Cell Datasets With Autograd ( Poster ) > link | Constance LE GAC · Alice Driessen · Nicolas Deutschmann · Maria Rodriguez Martinez 🔗 |
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Seeded iterative clustering for histology region identification ( Poster ) > link | Eduard Artur Chelebian Kocharyan · Francesco Ciompi · Carolina Wählby 🔗 |
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Learning relationships between histone modifications in single cells ( Poster ) > link | Jake Yeung · Maria Florescu · Peter Zeller · Buys de Barbanson · Max Wellenstein · Alexander van Oudenaarden 🔗 |
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Generative model for Pseudomonad genomes ( Poster ) > link | Manasa Kesapragada 🔗 |
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LANTERN-RD: Enabling Deep Learning for Mitigation of the Invasive Spotted Lanternfly ( Poster ) > link | Srivatsa Kundurthy 🔗 |
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Data-driven subgroup identification for linear regression ( Poster ) > link | Zachary Izzo · Ruishan Liu · James Zou 🔗 |
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Deep Fitness Inference for Drug Discovery with Directed Evolution ( Poster ) > link | Nathaniel Diamant · Ziqing Lu · Christina Helmling · Kangway Chuang · Christian Cunningham · Tommaso Biancalani · Gabriele Scalia · Max Shen 🔗 |
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Translating L-peptides into non-canonical linear and macrocyclic peptides ( Poster ) > link | Somesh Mohapatra 🔗 |
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Using hierarchical variational autoencoders to incorporate conditional independent priors for paired single-cell multi-omics data integration ( Poster ) > link | Ping-Han Hsieh · Ru-Xiu Hsiao · Tatiana Belova · Katalin Ferenc · Anthony Mathelier · Rebekka Burkholz · Chien-Yu Chen · Geir Kjetil Sandve · Marieke L Kuijjer 🔗 |
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3D single-cell shape analysis of cancer cells using geometric deep learning ( Poster ) > link | Matt De Vries · Lucas Dent · Nathan Curry · Leo Rowe-Brown · Adam Tyson · Chris Dunsby · Chris Bakal 🔗 |
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Kernelized Stein Discrepancies for Biological Sequences ( Poster ) > link | Alan Amin · Eli Weinstein · Debora Marks 🔗 |
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Representation Learning to Integrate and Interpret Omics Data ( Poster ) > link | Sara Masarone 🔗 |
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scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data ( Poster ) > link |
11 presentersTessa Green · Stefan Peidli · Ciyue Shen · Torsten Gross · Joseph Min · Samuele Garda · Jake Taylor-King · Debora Marks · Augustin Luna · Nils Blüthgen · Chris Sander |
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Utilizing Mutations to Evaluate Interpretability of Neural Networks on Genomic Data ( Poster ) > link | Utku Ozbulak · Solha Kang · Jasper Zuallaert · Stephen Depuydt · Joris Vankerschaver 🔗 |
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Box Prediction Rebalancing for Training Single-Stage Object Detectors with Partially Labeled Data ( Poster ) > link | Shafin Haque · R. Austin McEver 🔗 |
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Unsupervised language models for disease variant prediction ( Poster ) > link | Allan Zhou · Nicholas C. Landolfi · Daniel ONeill 🔗 |
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Benchmarking Graph Neural Network-based Imputation Methods on Single-Cell Transcriptomics Data ( Poster ) > link | Han-Bo Li · Ramon Viñas Torné · Pietro Lió 🔗 |
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Spatially-aware dimension reduction of transcriptomics data ( Poster ) > link | Lauren Okamoto · Andrew Jones · Archit Verma · Barbara E Engelhardt 🔗 |
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Multimodal deep transfer learning for the analysis of optical coherence tomography scans and retinal fundus photographs ( Poster ) > link | Zoi Tsangalidou · Edwin Fong · Josefine Vilsbøll Sundgaard · Trine J Abrahamsen · Kajsa Kvist 🔗 |
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Designing and Evolving Neuron-Specific Proteases ( Poster ) > link | Han Spinner · Colin Hemez · Julia McCreary · David Liu · Debora Marks 🔗 |
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Network-Based Clustering of Pan-Cancer Data Accounting for Clinical Covariates ( Poster ) > link | Fritz Bayer · Giusi Moffa · Niko Beerenwinkel · Jack Kuipers 🔗 |
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CoSpar identifies early cell fate biases from single cell transcriptomic and lineage information ( Poster ) > link | Shou-Wen Wang · Michael Herriges · Kilian Hurley · Darrell Kotton 🔗 |
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What cleaves? Is proteasomal cleavage prediction reaching a ceiling? ( Poster ) > link | Ingo Ziegler · Bolei Ma · Ercong Nie · Bernd Bischl · David Rügamer · Benjamin Schubert · Emilio Dorigatti 🔗 |
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Learning More Effective Cell Representations Efficiently ( Poster ) > link | Jason Xiaotian Dou · Minxue Jia · Nika Zaslavsky · Haiyi Mao · Runxue Bao · Ni Ke · Paul Pu Liang · Zhi-Hong Mao 🔗 |
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Biological Neurons vs Deep Reinforcement Learning: Sample efficiency in a simulated game-world ( Poster ) > link | Forough Habibollahi · Moein Khajehnejad · Amitesh Gaurav · Brett J. Kagan 🔗 |
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Self-Supervised Learning of Phenotypic Representations from Cell Images with Weak Labels ( Poster ) > link | Jan Cross-Zamirski · Guy Williams · Elizabeth Mouchet · Carola-Bibiane Schönlieb · Riku Turkki · Yinhai Wang 🔗 |