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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

Project Page [ Contact: lmrl@lmrl.org ]

Abstract

All events will be in a non-NeurIPS Zoom and on Gather.Town, without embedded streaming. Links below.

Video

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Schedule

Timezone: America/Los_Angeles

4:30 AM

Poster Preview on Gather.Town Poster Session

5:00 AM

Keynote - Rich Bonneau Talks

Richard Bonneau

6:00 AM

Contributed & Lightning talks Talks

7:00 AM

Poster Session Poster Session

8:00 AM

Keynote - Shantanu Singh Keynote

Shantanu Singh

9:00 AM

Contributed & Lightning talks Talks

10:00 AM

Keynote - Pulin Li Talks

11:00 AM

Contributed & Lightning talks Talks

12:00 PM

Itai Yanai - "Night Science:" The creative side of the scientific process Talk

1:00 PM

Poster Session Poster Session

Personalised drug recommendation from augmented gene expression data - the right drug(s) for the right patient Poster

Manuela Salvucci · Francesca Mulas · Marika Catapano

Simultaneous alignment of cells and features of unpaired single-cell multi-omics datasets with co-optimal transport Poster

Pinar Demetci · Quang Huy TRAN · Ievgen Redko · Ritambhara Singh

How can we use natural evolution and genetic experiments to design protein functions? Poster

Ada Shaw · June Shin · Debora Marks

Using co-localization priors and microenvironment statistics to reconstruct tissue organization from single-cell data Poster

Yitzchak Vaknin · Noa Moriel · Mor Nitzan

A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction Poster

Krzysztof Koras · Marcin Możejko · Paulina Szymczak · Adam Izdebski · Eike Staub · Ewa Szczurek

Energy-based Modelling for Single-cell Data Annotation Poster

Tianyi Liu · Philip Fradkin · Lazar Atanackovic · Leo J Lee

Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps Poster

Luca Eyring · Dominik Klein · Giovanni Palla · Sören Becker · Philipp Weiler · Niki Kilbertus · Fabian Theis

Biological Cartography: Building and Benchmarking Representations of Life Poster

Safiye Celik · Jan-Christian Huetter · Sandra Melo · Nathan Lazar · Rahul Mohan · Conor Tillinghast · Tommaso Biancalani · Marta Fay · Berton Earnshaw · Imran Haque

Protein language model rescue mutations highlight variant effects and structure in clinically relevant genes Poster

Onuralp Soylemez · Pablo Cordero

Regression-Based Elastic Metric Learning on Shape Spaces of Cell Curves Poster

Adele Myers · Nina Miolane

Learning Canonical Cellular Environments from Spatial Transcriptomic Data via Optimal Transport Poster

Shouvik Mani · Doron Haviv · Dana Peer

Designing active and thermostable enzymes with sequence-only predictive models Poster

Clara Fannjiang · Micah Olivas · Eric Greene · Craig Markin · Bram Wallace · Ben Krause · Margaux Pinney · James Fraser · Polly Fordyce · Ali Madani · Nikhil Naik

Joint Protein Sequence-Structure Co-Design via Equivariant Diffusion Poster

Ria Vinod

Interpretable visualization of single cell data using Janus autoencoders Poster

Gokul Gowri · Phillipa Richter · Xiaokang Lun · Peng Yin

Machine Learning enabled Pooled Optical Screening in Human Lung Cancer Cells Poster

Srinivasan Sivanandan · Max Salick · Bobby Leitmann · Kara Liu · Navpreet Ranu · Cynthia Hao · Owen Chen · John Bisognano · Eric Lubeck · Ajamete Kaykas · Eilon Sharon · Ci Chu

An Empirical Study of ML-based Phenotyping and Denoising for Improved Genomic Discovery Poster

Bo Yuan · Cory McLean · Farhad Hormozdiari · Justin Cosentino

EpiAttend: A transformer model of gene regulation combining single cell epigenomes with DNA sequence Poster

Eran A Mukamel · Russell Li

Multimodal Cell-Free DNA Embeddings are Informative for Early Cancer Detection Poster

Felix Jackson

Continuous cell-state density inference and applications for single-cell data Poster

Dominik Otto · Manu Setty · Brennan Dury

Find your microenvironments faster with Neural Spatial LDA Poster

Sivaramakrishnan Sankarapandian · Zhenghao Chen · Jun Xu

TranceptEVE: Combining Family-specific and Family-agnostic Models of Protein Sequences for Improved Fitness Prediction Poster

Pascal Notin · Lodevicus van Niekerk · Aaron Kollasch · Daniel Ritter · Yarin Gal · Debora Marks

Tuned Quadratic Landscapes for Benchmarking Model-Guided Protein Design Poster

Neil Thomas · Atish Agarwala · David Belanger · Yun Song · Lucy Colwell

Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings Poster

Frederike Lübeck · Charlotte Bunne · Gabriele Gut · Jacobo Sarabia del Castillo · Lucas Pelkmans · David Alvarez-Melis

ChromFormer: A transformer-based model for 3D genome structure prediction Poster

Henry Valeyre · Pushpak Pati · Federico Gossi · Vignesh Ram Somnath · Adriano Martinelli · Maria Anna Rapsomaniki

Improving Protein Subcellular Localization Prediction with Structural Prediction & Graph Neural Networks Poster

Geoffroy Dubourg-Felonneau · Arash Abbasi · Eyal Akiva · Lawrence Lee

A single-cell gene expression language model Poster

William Connell · Umair Khan · Michael Keiser

Standards, tooling and benchmarks to probe representation learning on proteins Poster

Joaquin Gomez Sanchez · Sebastian Franz · Michael Heinzinger · Burkhard Rost · Christian Dallago

A Modelling Framework for Catalysing Progress in the Rod-Shaped Bacterial Cell Growth Discourse Poster

Shashi Nagarajan · Fredrik Lindsten

CP2Image: generating high-quality single-cell images using CellProfiler representations Poster

Yanni Ji · Marie Cutiongco · Bjørn S Jensen · Ke Yuan

Knowledge distillation for fast and accurate DNA sequence correction Poster

Anastasiya 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

meTCRs - Learning a metric for T-cell receptors Poster

Felix Drost · Lennard Schiefelbein · Benjamin Schubert

Is brightfield all you need for MoA prediction? Poster

Ankit Gupta · Philip Harrison · Håkan Wieslander · Jonne Rietdijk · Jordi Puigvert · Polina Georgiev · Carolina Wählby · Ola Spjuth · Ida-Maria Sintorn

MolE: a molecular foundation model for drug discovery Poster

Oscar Méndez-Lucio · Christos Nicolaou · Berton Earnshaw

Learning representations of cell populations for image-based profiling using contrastive learning Poster

Robert van Dijk · John Arevalo · Shantanu Singh · Anne Carpenter

Forecasting labels under distribution-shift for machine-guided sequence design Poster

Lauren B Wheelock · Stephen Malina · Jeffrey Gerold · Sam Sinai

Double trouble: Predicting new variant counts across two heterogeneous populations Poster

Yunyi Shen · Tamara Broderick

decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods Poster

Camila Duitama González · Riccardo Vicedomini · Teo Lemane · Nicolas Rascovan · Hugues Richard · Rayan Chikhi

Transformer Model for Genome Sequence Analysis Poster

Noah Hurmer · Xiao-Yin To · Martin Binder · Hüseyin Anil Gündüz · Philipp Münch · René Mreches · Alice McHardy · Bernd Bischl · Mina Rezaei

SCOOTR: Single-Cell Multimodal Data Integration with Contrastive Learning and Optimal Transport Poster

Federico Gossi · Pushpak Pati · Adriano Martinelli · Maria Anna Rapsomaniki

Conditional Neural Processes for Molecules Poster

Miguel Garcia-Ortegon · Andreas Bender · Sergio Bacallado

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

Seeded iterative clustering for histology region identification Poster

Eduard Artur Chelebian Kocharyan · Francesco Ciompi · Carolina Wählby

Learning relationships between histone modifications in single cells Poster

Jake Yeung · Maria Florescu · Peter Zeller · Buys de Barbanson · Max Wellenstein · Alexander van Oudenaarden

Generative model for Pseudomonad genomes Poster

Manasa Kesapragada

LANTERN-RD: Enabling Deep Learning for Mitigation of the Invasive Spotted Lanternfly Poster

Srivatsa Kundurthy

Data-driven subgroup identification for linear regression Poster

Zachary Izzo · Ruishan Liu · James Zou

Deep Fitness Inference for Drug Discovery with Directed Evolution Poster

Nathaniel Diamant · Ziqing Lu · Christina Helmling · Kangway Chuang · Christian Cunningham · Tommaso Biancalani · Gabriele Scalia · Max Shen

Translating L-peptides into non-canonical linear and macrocyclic peptides Poster

Somesh Mohapatra

Using hierarchical variational autoencoders to incorporate conditional independent priors for paired single-cell multi-omics data integration Poster

Ping-Han Hsieh · Ru-Xiu Hsiao · Tatiana Belova · Katalin Ferenc · Anthony Mathelier · Rebekka Burkholz · Chien-Yu Chen · Geir Kjetil Sandve · Marieke L Kuijjer

3D single-cell shape analysis of cancer cells using geometric deep learning Poster

Matt De Vries · Lucas Dent · Nathan Curry · Leo Rowe-Brown · Adam Tyson · Chris Dunsby · Chris Bakal

Kernelized Stein Discrepancies for Biological Sequences Poster

Alan Amin · Eli Weinstein · Debora Marks

Representation Learning to Integrate and Interpret Omics Data Poster

Sara Masarone

scPerturb: Information Resource for Harmonized Single-Cell Perturbation Data Poster

Tessa Green · Stefan Peidli · Ciyue Shen · Torsten Gross · Joseph Min · Samuele Garda · Jake Taylor-King · Debora Marks · Augustin Luna · Nils Blüthgen · Chris Sander

Utilizing Mutations to Evaluate Interpretability of Neural Networks on Genomic Data Poster

Utku Ozbulak · Solha Kang · Jasper Zuallaert · Stephen Depuydt · Joris Vankerschaver

Box Prediction Rebalancing for Training Single-Stage Object Detectors with Partially Labeled Data Poster

Shafin Haque · R. Austin McEver

Unsupervised language models for disease variant prediction Poster

Allan Zhou · Nicholas C. Landolfi · Daniel ONeill

Benchmarking Graph Neural Network-based Imputation Methods on Single-Cell Transcriptomics Data Poster

Han-Bo Li · Ramon Viñas Torné · Pietro Lió

Spatially-aware dimension reduction of transcriptomics data Poster

Lauren Okamoto · Andrew Jones · Archit Verma · Barbara E Engelhardt

Multimodal deep transfer learning for the analysis of optical coherence tomography scans and retinal fundus photographs Poster

Zoi Tsangalidou · Edwin Fong · Josefine Vilsbøll Sundgaard · Trine J Abrahamsen · Kajsa Kvist

Designing and Evolving Neuron-Specific Proteases Poster

Han Spinner · Colin Hemez · Julia McCreary · David Liu · Debora Marks

Network-Based Clustering of Pan-Cancer Data Accounting for Clinical Covariates Poster

Fritz Bayer · Giusi Moffa · Niko Beerenwinkel · Jack Kuipers

CoSpar identifies early cell fate biases from single cell transcriptomic and lineage information Poster

Shou-Wen Wang · Michael Herriges · Kilian Hurley · Darrell Kotton

What cleaves? Is proteasomal cleavage prediction reaching a ceiling? Poster

Ingo Ziegler · Bolei Ma · Ercong Nie · Bernd Bischl · David Rügamer · Benjamin Schubert · Emilio Dorigatti

Learning More Effective Cell Representations Efficiently Poster

Jason Xiaotian Dou · Minxue Jia · Nika Zaslavsky · Haiyi Mao · Runxue Bao · Ni Ke · Paul Pu Liang · Zhi-Hong Mao

Biological Neurons vs Deep Reinforcement Learning: Sample efficiency in a simulated game-world Poster

Forough Habibollahi · Moein Khajehnejad · Amitesh Gaurav · Brett J. Kagan

Self-Supervised Learning of Phenotypic Representations from Cell Images with Weak Labels Poster

Jan Cross-Zamirski · Guy Williams · Elizabeth Mouchet · Carola-Bibiane Schönlieb · Riku Turkki · Yinhai Wang