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Workshop Sat, Dec 6, 2025 • 8:00 AM – 5:00 PM PST

Imageomics: Discovering Biological Knowledge from Images Using AI

Jianyang Gu ⋅ Sam Stevens ⋅ Zheda Mai ⋅ Kaiya Provost ⋅ Lily Weng ⋅ Sara Beery ⋅ Subhransu Maji ⋅ Anuj Karpatne ⋅ Ben Weinstein
Project Page [ OpenReview] 

Abstract

Video

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Schedule

Timezone: America/Los_Angeles
8:00 AM
Opening Remark
→ Scalable Rigid-Invariant Distance for Shape Matching and Alignment
Zakk Heile ⋅ Peilin He ⋅ Jayson Tran ⋅ Ruiling Wang ⋅ Shrikant Chand
→ Leveraging Model-Generated Annotations for Nuclei Segmentation in Computational Pathology
Christopher Hendra ⋅ Charlene Ong ⋅ Asad Abu Bakar Ali ⋅ Desiree Abdurrachim ⋅ Shubing Wang ⋅ Richard Baumgartner ⋅ Kelvin Chong ⋅ Chih-Liang Chin ⋅ Michelle Ngo
→ BarcodeMamba+: Advancing State-Space Models for Fungal Biodiversity Research
Tiancheng Gao ⋅ Scott C. Lowe ⋅ Brendan Furneaux ⋅ Angel Chang ⋅ Graham Taylor
→ SmartWilds: Multimodal Wildlife Monitoring Dataset
Jenna Kline ⋅ Anirudh Potlapally ⋅ Tanishka Wani ⋅ Vedant Patil ⋅ Penelope Covey ⋅ Rugved Katole ⋅ Sam Stevens ⋅ Hari Subramoni ⋅ Tanya Berger-Wolf ⋅ Christopher Stewart
→ A Machine Learning Framework for Automated Computational Ethology Using Markerless Pose Estimation
Prateek Verma ⋅ Minh-Hao Van ⋅ Christopher McEnaney ⋅ Amy Poe ⋅ Xintao Wu
→ Artificial Intelligence for Spatial Transcriptomics: A Scoping Review of Architectures and Models
Agampreet Saini ⋅ Supragya Gandotra ⋅ Abhijit Kumar ⋅ Pratik Dutta ⋅ Tirthankar Ghosal
→ Toward Generalizable Whole Brain Representations with High-Resolution Light-Sheet Data
Minyoung Kim ⋅ Dae Hee Yun ⋅ Aditi Patel ⋅ Madeline Hon ⋅ Taegeon Lee ⋅ Webster Guan ⋅ Brian Nguyen
→ FaceTTD: Time-to-Death from Imageomic Facial Time Series for Rapid Mortality Risk Profiling and Longevity Interventions
Saleem Al Dajani ⋅ Dmitrii Glubokov ⋅ Alexander Tyshkovskiy ⋅ John Williams ⋅ Jesse Poganik ⋅ Omar Abudayyeh ⋅ Jonathan Gootenberg ⋅ Vadim Gladyshev
→ Structural MRI–Informed Multimodal Fusion for Robust Alzheimer’s Disease Prediction
Juhyun Lee ⋅ Sungjoon Park ⋅ Kyungwook Lee ⋅ Soorin Yim ⋅ Doyeong Hwang ⋅ Dongyun Kim ⋅ Kiwoong Yoo ⋅ Soonyoung Lee ⋅ Kiyoung Kim
→ ProteinPNet: Prototypical Part Networks for Concept Learning in Spatial Proteomics
Louis McConnell ⋅ Jieran Sun ⋅ Theo Maffei ⋅ Raphael Gottardo ⋅ Marianna Rapsomaniki
→ DentalNet: Geometric Aware Multi-View Transformer for Occlusion Grade Prediction in Dental 3D Scans
Arnesh Batra ⋅ Arush Gumber ⋅ Vaibhav Sharma ⋅ Peemit ⋅ Rinkle Sardana ⋅ Tulika Tripathi ⋅ Anubha Gupta
→ Hyperbolic Multimodal Representation Learning for Biological Taxonomies
ZeMing Gong ⋅ Chuanqi Tang ⋅ Xiaoliang Huo ⋅ Nicholas Pellegrino ⋅ Austin T. Wang ⋅ Graham Taylor ⋅ Angel Chang ⋅ Scott C. Lowe ⋅ Joakim Bruslund Haurum
→ Bi-Encoder Contrastive Learning for Fingerprint and Iris Biometrics
Matthew So ⋅ Judah Goldfeder ⋅ Mark Lis ⋅ Hod Lipson
→ Exploring simulators for particle picking in cryo-electron tomography
Serena M Arghittu ⋅ Lars Dingeldein ⋅ Geoffrey Woollard ⋅ Lingli Kong ⋅ Magnus Petersen ⋅ Sonya Hanson ⋅ Roberto Covino ⋅ Pilar Cossio
→ Photorealistic Inpainting for Perturbation-based Explanations in Ecological Monitoring
Gunel Aghakishiyeva ⋅ Jiayi Zhou ⋅ Saagar Arya ⋅ Julian Dale ⋅ James Poling ⋅ Holly Houliston ⋅ Jamie Womble ⋅ Gregory Larsen ⋅ David W. Johnston ⋅ Brinnae Bent
→ Simulation-based inference of yeast centromeres
Eloïse Touron ⋅ Pedro Rodrigues ⋅ Julyan Arbel ⋅ Nelle Varoquaux ⋅ Michael Arbel
→ A Survey on Computational Pathology Foundation Models
Dong Li ⋅ Guihong Wan ⋅ Xintao Wu ⋅ Xinyu Wu ⋅ Yi He ⋅ Zhong Chen ⋅ Ninghui Hao ⋅ Chen Zhao
→ Evaluating the Utility of Sparse Autoencoders for Interpreting a Pathology Foundation Model
Nhat Le ⋅ Ciyue Shen ⋅ Neel Patel ⋅ Chintan Shah ⋅ Darpan Sanghavi ⋅ Blake Martin ⋅ Alfred Eng ⋅ Harshith Padigela ⋅ Raymond Biju ⋅ Sean Grullon ⋅ Dinkar Juyal ⋅ Syed Ashar Javed
→ Advancing Fluorescence Detection and Ranging in Scattering Media with Mixture-of-Experts and Evidential Critics
Ismail Erbas ⋅ Ferhat Demirkiran ⋅ Karthik Swaminathan ⋅ Naigang Wang ⋅ Navid Nizam ⋅ Nanxue Yuan ⋅ Saif Ragab ⋅ Luis Chavez ⋅ Kaoutar El Maghraoui ⋅ Xavier Intes ⋅ Vikas Pandey
9:30 AM
Welcome Keynote
12:00 PM
Lunch Break
→ BeetleFlow: An Integrative Deep Learning Pipeline for Beetle Image Processing
Fangxun Liu ⋅ S M Rayeed ⋅ Sam Stevens ⋅ Alyson East ⋅ Cheng Chiang ⋅ Colin Lee ⋅ Daniel Yi ⋅ Junke Yang ⋅ Tejas Naik ⋅ Ziyi Wang ⋅ Connor Kilrain ⋅ Elijah Buckwalter ⋅ Jiacheng Hou ⋅ Saul Bueno ⋅ Shuheng Wang ⋅ Xinyue Ma ⋅ Yifan Liu ⋅ Zhiyuan Tao ⋅ Ziheng Zhang ⋅ Eric Sokol ⋅ Michael Belitz ⋅ Sydne Record ⋅ Charles Stewart ⋅ Wei-Lun (Harry) Chao
→ Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution
Mridul Khurana ⋅ Arka Daw ⋅ M. Maruf ⋅ Josef Uyeda ⋅ Wasila Dahdul ⋅ Caleb Charpentier ⋅ Yasin Bakis ⋅ Henry Bart ⋅ Paula Mabee ⋅ Hilmar Lapp ⋅ James Balhoff ⋅ Wei-Lun (Harry) Chao ⋅ Charles Stewart ⋅ Tanya Berger-Wolf ⋅ Anuj Karpatne
→ Hybrid Diffusion Model for Breast Ultrasound Image Augmentation
Farhan Fuad Abir ⋅ Sanjeda Jennifer ⋅ Niloofar Yousefi ⋅ Laura Brattain
→ Continually Adapt or Not (CAN)? A Continual Learning Benchmark of Camera Trap Species Classification over Time
Sooyoung Jeon ⋅ Zheda Mai ⋅ Hongjie Tian ⋅ Vidhi Bakshi ⋅ Lemeng Wang ⋅ Jiacheng Hou ⋅ Ping Zhang ⋅ Arpita Chowdhury ⋅ Wei-Lun (Harry) Chao
→ Coarse-to-Fine 3D MRI Reconstruction via 3D Neural Operators
Armeet Jatyani ⋅ Jiayun (Peter) Wang ⋅ Ryan Lin ⋅ Valentin Duruisseaux ⋅ Animashree Anandkumar
→ Detection in Progress - A Multimodal Segmentation-based Approach for Predicting Glioblastoma Recurrence
Harshita Kukreja ⋅ Nate Tran ⋅ Bo Liu ⋅ Tracy Luks ⋅ Angela Jakary ⋅ Oluwaseun Adegbite ⋅ Yan Li ⋅ Annette Molinaro ⋅ Javier Villanueva-Meyer ⋅ Steve Braunstein ⋅ Hui Lin ⋅ Janine Lupo
→ Distortion-Free Registration of Whole-Slide Images via Tile-Based Refinement
Sungyun Kim ⋅ Sehoon Kim ⋅ Dong Kang ⋅ Jae Song ⋅ Kwangsoo Kim ⋅ Eun Kim
→ Novel Finetuning Strategies for Adapting Biomedical Vision Language Models to Organ-Centered Pathology Microscopy Tasks
Siddharth Venkatesh ⋅ Benjamin Liu ⋅ Ayman Sheikh ⋅ Anne Essien ⋅ Pratibh - ⋅ Rayhan Roswendi ⋅ Jeremiah Zhang ⋅ Kevin Zhu ⋅ Sunishchal Dev
→ MATCH: Multi-faceted Adaptive Topo-Consistency for Semi-Supervised Histopathology Segmentation
Meilong Xu ⋅ Xiaoling Hu ⋅ Shahira Abousamra ⋅ Chen Li ⋅ Chao Chen
→ From Pixels to Pregnancies: AI-Driven Oocyte Grading for Scalable Livestock Breeding
Parkash Singh ⋅ Grace Koppelman ⋅ Tanya Berger-Wolf ⋅ John Fulton
→ BugSR: Improving Tiny Instance Segmentation on the MassID45 Dataset
John Quinto ⋅ Scott C. Lowe ⋅ Akshita Gupta ⋅ Johanna Orsholm ⋅ Prajakta Darade ⋅ Iuliia Eyriay ⋅ Brendan Furneaux ⋅ Tommi Mononen ⋅ Tomas Roslin ⋅ Graham Taylor
→ Benchmarking Parameter Efficient Adaptation of Vision Language Models on Pathology
Shivam Rai Sharma ⋅ Xiaoguang Zhu ⋅ Luca Cerny Oliveira ⋅ Kartik Patwari ⋅ La Vasquez ⋅ David Garcia ⋅ Louise Sevilla ⋅ Brittany Dugger ⋅ Chen-Nee Chuah
→ A multi-modal dataset for insect biodiversity with imagery and DNA at the trap and individual level
John Quinto ⋅ Johanna Orsholm ⋅ Brendan Furneaux ⋅ Tommi Mononen ⋅ Ellen Nein ⋅ Tomas Roslin ⋅ Iuliia Eyriay ⋅ Akshita Gupta ⋅ Prajakta Darade ⋅ Scott C. Lowe ⋅ Graham Taylor
→ Trait2Vec: Ontology-aware embeddings for organismal trait descriptions
Juan J Garcia ⋅ James Balhoff ⋅ Hilmar Lapp
→ Embedding cell state dynamics via contrastive learning of representations of 3D dynamic imaging datasets
Eduardo Hirata Miyasaki ⋅ Soorya Pradeep ⋅ Ziwen Liu ⋅ Alishba Imran ⋅ Taylla Theodoro ⋅ Ivan Ivanov ⋅ Sudip Khadka ⋅ See-Chi Lee ⋅ Michelle Grunberg ⋅ Hunter Woosley ⋅ Madhura Bhave ⋅ Carolina Arias ⋅ Shalin Mehta
→ BenthicNet: A global compilation of seafloor images for deep learning applications
Scott C. Lowe ⋅ Benjamin Misiuk ⋅ Isaac Xu ⋅ Shakhboz Abdulazizov ⋅ Amit Baroi ⋅ Vicki Ferrini ⋅ Ariell Friedman ⋅ Deborah Hart ⋅ Daniel Ierodiaconou ⋅ Jacquomo Monk ⋅ John O'Brien ⋅ Elizabeth Oh ⋅ Luba Reshitnyk ⋅ Chris Roelfsema ⋅ Jessica Sameoto ⋅ Alexandre Schimel ⋅ Craig Brown ⋅ Thomas Trappenberg
→ On Thin Ice: Towards Explainable Conservation Monitoring via Attribution and Perturbations
Jiayi Zhou ⋅ Gunel Aghakishiyeva ⋅ Saagar Arya ⋅ Julian Dale ⋅ James Poling ⋅ Holly Houliston ⋅ Jamie Womble ⋅ Gregory Larsen ⋅ David W. Johnston ⋅ Brinnae Bent
→ Geometric Shape Matching for Explainable and Accurate Medical Image Segmentation: A Post-Processing Refinement Framework
Ruhaib Muhammad ⋅ Shivaram Velayutham ⋅ Jey Sivaraj ⋅ Dhiraj Gambhire ⋅ Lakshminarayanan Subramanian
3:45 PM
Panel
4:45 PM
Closing Remark