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