Check out new work by Elisabeth Rennert, with Agnish & Yuqing: can a generative AI model predict the drivers of cortical flow from just images — trained only on minimal, extremal data? We show how it can 👉 doi.org/10.64898/202...
Suri Vaikuntanathan
@vaikuntsuri.bsky.social
https://vaikuntanathan-group.uchicago.edu
Excited to share a (long overdue revised version of) work arxiv.org/pdf/2411.07233 : Non-equilibrium active noise enhances generative memory in diffusion models -- TLDR. the ⟨x·η⟩ correlations that drive pressure like effects in active matter help with generative properties and speciation.
Super excited to share new work by Cal and Hector arxiv.org/abs/2601.06712 Can In-Context Learning (i.e. a mode of computation typically associated with transformer architectures) emerge in simple chemical reactions ?
Excited to share new work by Daiki and Hector in collaboration with Monika: arxiv.org/abs/2512.13859 We introduce a gating mechanism in classic associative memory models and find capacity is increased far above the Hopfield limit without the usual catastrophic breakdown.
Neuromodulation-inspired gated associative memory networks:extended memory retrieval and emergent multistability
Classical autoassociative memory models have been central to understanding emergent computations in recurrent neural circuits across diverse biological contexts. However, they typically neglect neurom...
arxiv.org
Super happy to be associated with this work !!
Ben Kuznets-Speck@biophysben.bsky.social · 8mo agoToday we’re excited to share Keeping SCORE, a framework that turns any diffusion model into a thermodynamic inference machine. Using only a model’s score function, we compute exact class likelihoods and uncertainty—and even decompose which features drove the decision. www.biorxiv.org/content/10.1...
Check out new work by Agnish, Matt and co-workers. Active, persistent dynamics can mimic Hebbian “unlearning,” hinting that nonequilibrium physics offers a new route to sharpen associative recall in neural nets. go.aps.org/49O1yHO @uchichemistry.bsky.social
Connection between Hebbian Unlearning and Steady States Generated by Nonequilibrium Dynamics
Active persistent dynamics are shown to mimic some aspects of Hebbian unlearning --- suggesting that nonequilibrium dynamics can provide an alternative way to improve associative recall in neural netw...
go.aps.org
Preprint 🚨! B cells form localized patterns in the immune synapse when mature, allowing improved affinity discrimination. How? We suggest a new mechanism using dynamic active forces and feedback! Read more @ arxiv.org/abs/2510.18771. Great colab with Shenshen Wang, Tom Chou and Tony Wong (UCLA).
This paper was a truly @uchichemistry.bsky.social team effort, jointly led by Shannon Lu, Matt Styles, and Frank Gao with me, Aaron Dinner, and @vaikuntsuri.bsky.social – along with a critical support cast. 12/12
Check out arxiv.org/abs/2507.07295 by Cal Floyd where we derived the new non-equilibrium thermodynamic constraint: Intuitively, it says that if we know a system's response at low drive, it will have the same sign at arbitrarily high drive— no matter how close or far from equilibrium !!
Local imperfect feedback control in non-equilibrium biophysical systems enabled by thermodynamic constraints
Understanding how biological systems achieve robust control despite relying on imperfect local information remains a challenging problem. Here, we consider non-equilibrium models which are generically...
arxiv.org
Very happy to share work by Cal Floyd now out in Nature Communications nature.com/articles/s41... . We show that the "expressivity" of biophysical decision making circuits is constrained in unexpected ways by non-equilibrium thermodynamics.
Limits on the computational expressivity of non-equilibrium biophysical processes - Nature Communications
How cells use biophysical processes to interpret complex input signals is not well understood. This study reveals limits to the computational power of generic non-equilibrium systems and shows how the...
nature.com
This is was a wonderful collaboration ! Hopefully many more ! :)
Yogesh Goyal@goyallab.bsky.social · last yr.Super collaboration with @labohaley.bsky.social @vaikuntsuri.bsky.social Ekta Prashnani (NVIDIA) and lab members Hanxiao Sun @nitukumari24.bsky.social @madelinemelzer.bsky.social Leon Schwartz
check out new work by Deb in collaboration with Martin, @squishycell.bsky.social , Aleks Walczak and Thierry Mora : arxiv.org/abs/2504.15107 o on how simple mechanosensitive agents can enable learning mechanisms
Learning via mechanosensitivity and activity in cytoskeletal networks
In this work we show how a network inspired by a coarse-grained description of actomyosin cytoskeleton can learn - in a contrastive learning framework - from environmental perturbations if it is endow...
arxiv.org
Check out new work by Jordan in collaboration with Aaron Dinner and Petia Vlahovska ! arxiv.org/abs/2503.24120 We consider minimal protocels under non-equilibrium growth conditions and extract low (2) dimensional rules to describe their shapes.
Very happy to share new work in collaboration with Sergey Semenov and coworkers. Lissa and Yuqing analyzed the waves in latent space and found a low dimensional representation of the waves. pubs.rsc.org/en/content/a...
Chemical waves in reaction-diffusion networks of small organic molecules
Chemical waves represent one of the fundamental behaviors that emerge in nonlinear, out-of-equilibrium chemical systems. They also play a central role in regulating behaviors and development of biolog...
pubs.rsc.org
Very excited to share a thread about our new preprint! It's a highly collaborative project, w key contributions from @josephlannan.bsky.social (in my lab) @bhamlalab.bsky.social (+ GS Luke Xu), Dinner Lab (+ PD Cal Floyd), Jerry Honts, Marshall lab (+ GS Connie Yan), and Suri Vaikuntanathan 1/13
bioRxivpreprint@biorxivpreprint.bsky.social · 2y agoFishnet mesh of centrin-Sfi1 drives ultrafast calcium-activated contraction of the giant cell Spirostomum ambiguum https://www.biorxiv.org/content/10.1101/2024.11.07.622534v1
We need to have a ‘code of conduct’ for reviewing manuscripts, like (1) if you say that something is not novel then provide the reference. (2) If you propose an experiment, state precisely to which claim it is crucial. (3) If you want to say something nasty then sign your name.
Check out new work by Cal on using Reinforcement Learning to control the dynamics of defects in an active nematic arxiv.org/abs/2411.09588
Tailoring interactions between active nematic defects with reinforcement learning
Active nematics, formed from a liquid crystalline suspension of active force dipoles, are a paradigmatic active matter system whose study provides insights into how chemical driving produces the cellu...
arxiv.org
(Older post from the other side) Very happy to share work by Cal (w Aaron and Arvind Murugan ) arxiv.org/abs/2409.05827 ! We show how the expressivity/computational ability of non-equilibrium biological processes may expected to be fundamentally limited.
Check out new work arxiv.org/abs/2411.07233 by Alexandra, Agnish, Aditya and Cal on generative diffusion but with correlated or ``active" noise.
Score-based generative diffusion with "active" correlated noise sources
Diffusion models exhibit robust generative properties by approximating the underlying distribution of a dataset and synthesizing data by sampling from the approximated distribution. In this work, we e...
arxiv.org