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Date
Paper
Diya Basrai, JeongYoon Lee, Amy Kristl, Peiyu Wang, Andrew Miri, and Joshua I. Glaser
Constraining inference of across-region interactions using neural activity perturbations
2025
Paper
Benjamin Kuznets-Speck, Jaekwon Jung, Pornchanan Pholraksa, Adrianne Zhong, Leon Schwartz, Ekta Prashnani, Suriyanarayanan Vaikuntanathan, Yogesh Goyal
Interpretable Thermodynamic Score-based Classification of Relaxation Excursions
2025
Paper
Benjamin Kuznets-Speck, Leon Schwartz, Hanxiao Sun, Madeline E. Melzer, Nitu Kumari, Benjamin Haley, Ekta Prashnani, Suriyanarayanan Vaikuntanathan, Yogesh Goyal
Fluctuation structure predicts genome-wide perturbation outcomes
2025
Paper
Jinming Wan; Qingyue Liu; Kathryn Zacks; Jia Zhao; Genki Ichinose; Michael Small; Changqing Cheng
Replicator dynamics and behavior-augmented multiscale epidemic modeling
2025
Paper
Elisheva Siegfried, Alvin Bayliss, Vladimir Volpert
Invasions in a Four-Species Fractured Cyclic Ecological System
2025
Paper
Maryn Carlson, Bryan Andrews, Yuval Simons
Distinguishing direct interactions from global epistasis using rank statistics
2025
Paper
Smayan Khanna, Doruk Efe Gökmen, Risi Kondor, Vincenzo Vitelli
Graph Contrastive Learning versus Untrained Baselines: The Role of Dataset Size
2025
Paper
Samuel Bird, Chiara Devescovi, Pascal Engeler, Agnes Valenti, Doruk Efe Gökmen, Robin Worreby, Valerio Peri, Sebastian D Huber
Design and characterization of all 2D fragile topological bands
2025
Paper
Patrick M Lenggenhager, M Michael Denner, Doruk Efe Gökmen, Maciej Koch-Janusz, Titus Neupert, Mark H Fischer
Computational access to lattice and long-wavelength physics in quantum mutual information
Paper
Sihan Chen, Doruk Efe Gökmen, Michel Fruchart, Miriam Krumbein, Pascal Silberzan, Victor Yashunsky, Vincenzo Vitelli
Chirality across scales in tissue dynamics
2025
Paper
Pablo Lechon-Alonso, Srilena Kundu, Paulinha Lemos-Costa, José A. Capitan, Stefano Allesina
Robust coexistence in competitive ecological communities
2025
Paper
Melissa Adrian, Jake A. Soloff, Rebecca Willett
Stabilizing black-box model selection with the inflated argmax
2025
Paper
Antonio Auffinger, Yuxin Zhou
The Spherical p+s Spin Glass at Zero Temperature
2025
Paper
Ming Han, John Devany, Michel Fruchart, Margaret L. Gardel, Vincenzo Vitelli
Learning noisy tissue dynamics across time scales
2025
Paper
Ryan A. Robinett, Sophia A. Madejski, Kyle Ruark, Samantha J. Riesenfeld, Lorenzo Orecchia
Atlas-based Manifold Representations for Interpretable Riemannian Machine Learning
Paper
Lunjun Zhang, Shuo Han, Hanrui Lyu, Bradly C Stadie
D2 Actor Critic: Diffusion Actor Meets Distributional Critic
2025
Paper
B Kuznets-Speck, BK Ogonor, TP Wytock, AE Motter
Generative prediction of causal gene sets responsible for complex traits
2025
Paper
A.N. Montanari, AED Barioni, C Duan, AE Motter
Optimal flock formation induced by agent heterogeneity
2025
Paper
Yu, Yang, Gozel, Oldenburg, Dipoppa, Rossi, Miller, Adesnik, Ji, Doiron.
Circuit-based understanding of fine spatial scale clustering of orientation tuning in mouse visual cortex
2025
Paper
Yang, Doiron
Causal Spike Timing Dependent Plasticity Prevents Assembly Fusion in Recurrent Networks
2025
Paper
Dunworth, Xu, Graupner, Ermentrout, Reyes, Doiron
Interleaving asynchronous and synchronous activity in balanced cortical networks with short term synaptic depression.
2025
Paper
Marie R Greaney, Ellie S Heckscher, Matthew T Kaufman
Multiple scales of coordination along the body axis during Drosophila larval locomotion
2025
Paper
Peter J. Malonis, Ankit Vishnubhotla, Nicholas G. Hatsopoulos, Jason N. MacLean, Matthew T. Kaufman
Combatting nonidentifiability to infer motor cortex inputs yields similar encoding of initial and corrective movements
2025
Paper
Sohrab Salimian, Harrison A Grier, Matthew T Kaufman
Neural activity profiles reveal overlapping, intermingled subpopulations spanning area borders in mouse sensorimotor cortex
2025
Paper
Harrison A Grier, Sohrab Salimian, Matthew T Kaufman
Mouse sensorimotor cortex reflects complex kinematic details during reaching and grasping
2025
Paper
Guy Amichay, Ruoming Gong, Daniel M. Abrams
Modeling the evolution of collective synchrony
Paper
Tom Röschinger , Heun Jin Lee , Rosalind Wenshan Pan , Grace Solini , Kian Faizi , Baiyi Quan , Tsui-Fen Chou, Madhav Mani, Stephen Quake, Rob Phillips
The Environment-Dependent Regulatory Landscape of the E. coliGenome
2025
Paper
Manuel Razo-Mejia, Madhav Mani, Dmitri A. Petrov
Learning the Shape of Evolutionary Landscapes: Geometric Deep Learning Reveals Hidden Structure in Phenotype-to-Fitness Maps
2025
Paper
Addison Howe, Madhav Mani
Learning Geometric Models for Developmental Dynamics
2025
Paper
Gengshuo John Tian, Ou Zhu, Vinay Shirhatti, Charles M Greenspon, John E Downey, David J Freedman, Brent Doiron
Firing rate diversity lowers the dimension of population covariability in neuronal networks
2024
Paper
Kyle Crocker, Abigail Skwara, Rathi Kannan, Arvind Murugan, Seppe Kuehn
Timescale of environmental change modulates metabolic guild cohesion in microbial communities
2025
Paper
Simon Fabiunke and Petia M. Vlahovska
Electrodeformation of DMPC vesicle membranes near the main phase transition
2025
Paper
Yihang Wang, Chris Chi, Aaron R. Dinner
Mitigating mode collapse in normalizing flows by annealing with an adaptive schedule: Application to parameter estimation
2025
Paper
Chris Chi, Jonathan Weare, and Aaron R. Dinner
Sampling parameters of ordinary differential equations with constrained Langevin dynamics
2025
Paper
Kiseok Lee, Siqi Liu, Kyle Crocker, Mikhail Tikhonov, Madhav Mani, Seppe Kuehn
Functional regimes define the response of the soil microbiome to environmental change
2025
Paper
Madeline Melzer, Yogesh Goyal
Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms
2024
Paper
Wioletta I. Nawrocka, Shouqiang Cheng, Bingjie Hao, Matthew C. Rosen, Elena Cortés, Elana E. Baltrusaitis, Zainab Aziz, István A. Kovács and Engin Özkan
Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways
2024
Paper
Madeline Melzer, Yogesh Goyal
Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells
2024
Paper
David Sabatini, Matthew Kaufman
Reach-dependent reorientation of rotational dynamics in motor cortex
2024
Paper
Benjamin Hoshal, Caroline Holmes, Kyle Bojanek, Jared Salisbury, Michael Berry, Olivier Marre, Stephanie Palmer
Stimulus invariant aspects of the retinal code drive discriminability of natural scenes
2024
Paper
Guy Amichay
Biological Coupled Oscillators in the Real World
2024
Paper
Stephen M Lander, Garth Fisher, Blake A Everett, Peter Tran, Arthur Prindle
Secreted nucleases reclaim extracellular DNA during biofilm development
2024
Paper
Jared Salisbury, Stephanie Palmer
A dynamic scale-mixture model of motion in natural scenes
2024
Paper
Matthew Capek, Oscar M Arenas, Michael H Alpert, Emanuela E Zaharieva, Iván D Méndez-González, José Miguel Simões, Hamin Gil, Aldair Acosta, Yuqing Su, Alessia Para, Marco Gallio
Evolution of temperature preference in flies of the genus Drosophila
2025
Paper
Haibei Zhang, Miles T. Wetherington, Hungtang Ko, Cody E. FitzGerald, Edwin M. Munro, Jasmine A Nirody
Bacterial motility patterns adapt smoothly in response to spatial confinement and disorder
2024
Paper
Xiaowen Chen, Kyle Crocker, Seppe Kuehn, Aleksandra M. Walczak, Thierry Mora
Inferring resource competition in microbial communities from time series
2025
Paper
Kyle Crocker, Abigail Skwara, Rathi Kannan, Arvind Murugan, Seppe Kuehn
Microbial functional guilds respond cohesively to rapidly fluctuating environments
2025
Paper
Guy Amichay, Vijay Balasubramanian, Daniel M. Abrams
A universal animal communication tempo resonates with the receiver's brain
2025
Paper
Adela DePavia, Vasileios Charisopoulos, Rebecca Willett
Faster Adaptive Optimization via Expected Gradient Outer Product Reparameterization
2025
Paper
Hannah Laus, Suzanna Parkinson, Vasileios Charisopoulos, Felix Krahmer, Rebecca Willett
Solving Inverse Problems with Deep Linear Networks: Global Convergence Guarantees for Gradient Descent with Weight Decay
2025
Paper
Vasileios Charisopoulos, Rebecca Willett
Nonlinear tomographic reconstruction via nonsmooth optimization
2025
Paper
Mahmoud Yousef, Kiseok Keith Lee, Jonathan Tang, Vasileios Charisopoulos, Rebecca Willett, Seppe Kuehn
Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design
2025
Paper
M. H. Alpert, N. Ding, W. L. Kath, M. Gallio
Cellular and molecular properties of a hot-sensing circuit in Drosophila
2024
Paper
Ziyu Zhao, Dae-Sung Hwangbo, Sumit Saurabh, Clark Rosensweig, Ravi Allada, William L. Kath, Rosemary Braun
Modeling Transient Changes in Circadian Rhythms
2024
Paper
Shuo Han, German Espinosa, Junda Huang, Malcolm A. MacIver, Daniel Dombeck, Bradly C. Stadie
Of Mice and Machines: A Comparison of Learning Between Real World Mice and RL Agents
2025
Paper
Hanna M. Hieromnimon, Anna Trzcinska, Frank T. Wen, Frederick M. Howard, James M. Dolezal, Emma Dyer, Sara Kochanny, Jefree J Schulte, Cindy Wang, Heather Chen, Jeffrey Chin, Elizabeth Blair, Nishant Agrawal, Ari Rosenberg, Everett Vokes, Rohan Katipally, Aditya Juloori, Evgeny Izumchenko, Mark W. Lingen, Nicole Cipriani, Jalal B. Jalaly, Devraj Basu, Samantha J. Riesenfeld, Alexander T. Pearson
Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas
2025
Paper
Carlos Floyd, Aaron Dinner, Arvind Murugan, Suriyanarayanan Vaikuntanathan
Limits on the computational experssivity of non-equilibrium biological processes
2024
Paper
HA Faizi, R Granek, PM Vlahovska
Curvature fluctuations of fluid vesicles reveal hydrodynamic dissipation within the bilayer
2024
Paper
Doran B.A., Chen R.Y., Giba H., Behera V., Barat B., Sundararajan A., Lin H., Sidebottom A., Pamer E.G., Raman A.S.
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom
2025
Paper
Behera V., Giba H., Pen U., Di Lello A., Doran B.A., Esposito A., Pezeshk A., Bestvina C.M., Kline J., Garassino M.C., Raman A.S.
Conserved principles of spatial biology define tumor heterogeneity and response to immunotherapy
2025
Software
Chris Chi and Aaron Dinner
Constrained Langevin and Hamiltonian Monte Carlo samplers
2024
Software
Bingjie Hao and István A. Kovács
Maximum-entropy based background correction
2024
Software
Madeline Melzer, Yogesh Goyal
Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells
2024
Research Products
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