BrainWideBench: Benchmarking large-scale pretraining and across-animal transfer in multi-region neural recordings
Mirrored from arXiv — Machine Learning for archival readability. Support the source by reading on the original site.
Computer Science > Machine Learning
arXiv:2609.22064 (cs)
[Submitted on 18 Sep 2026]
Title:BrainWideBench: Benchmarking large-scale pretraining and across-animal transfer in multi-region neural recordings
Authors:Alexandre Andre, Shivashriganesh P. Mahato, Vinam Arora, Keshav Balaji, Divyansha Lachi, Nanda H. Krishna, Jingyun Xiao, Yizi Zhang, Ximeng Mao, Wenrui Ma, Han Yu, International Brain Laboratory, Daniel Birman, Niccolò Bonacchi, Gaelle A. Chapuis, Joana A. Catarino, Felicia Davatolhagh, Mayo Faulkner, Laura Freitas-Silva, Fei Hu, Julia M. Huntenburg, Anup Khanal, Inês Laranjeira, Petrina Lau, Guido T. Meijer, Nathaniel J. Miska, Jean-Paul Noel, Alejandro Pan-Vazquez, Georg Raiser, Cyrille Rossant, Karolina Z. Socha, Anne E. Urai, Miles J. Wells, Steven J. West, Olivier Winter, Blake Richards, Guillaume Lajoie, Cole Hurwitz, Mehdi Azabou, Matthew R. Whiteway, Liam Paninski, Eva L. Dyer
View a PDF of the paper titled BrainWideBench: Benchmarking large-scale pretraining and across-animal transfer in multi-region neural recordings, by Alexandre Andre and 41 other authors
View PDF
HTML (experimental)
Abstract:Advances in large-scale neural recording have made it possible to collect data across many animals and distributed brain regions, raising the question of whether this scale can be exploited to learn general-purpose neural representations transferable across diverse downstream tasks. Yet, progress toward this goal has been limited by fragmented evaluation protocols and a narrow focus on individual task domains. Here, we present BrainWideBench, a benchmark for evaluating across-animal transfer on multi-region neural recordings, built on the International Brain Laboratory Brainwide Map dataset of neural and behavioral recordings spanning 276 brain regions from 139 mice performing a sensory-guided decision-making task. The benchmark is organized around three complementary task suites that evaluate whether learned representations support downstream decoding of behavior, can predict masked or future neural activity, and can recover biologically meaningful anatomical organization. With this benchmark, we systematically evaluate pretraining methods across transfer settings, including finetuning on downstream objectives and zero-shot generalization to unseen animals. Our results confirm pretraining improves performance over matched single-session baselines, but we show current methods exhibit heterogeneity in transfer capabilities: gains depend strongly on the alignment between pretraining objectives and downstream tasks. No single approach performs uniformly well across all three suites, and most methods are designed to only address a subset of them. Together, these findings suggest that learning representations that jointly generalize across behavior, dynamics, and anatomy remains an open challenge. By providing a unified and reproducible evaluation suite, BrainWideBench establishes a framework for measuring progress toward general-purpose models of the mouse brain.
| Subjects: | Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC) |
| Cite as: | arXiv:2609.22064 [cs.LG] |
| (or arXiv:2609.22064v1 [cs.LG] for this version) | |
| https://doi.org/10.48550/arXiv.2609.22064
arXiv-issued DOI via DataCite (pending registration)
|
Full-text links:
Access Paper:
- View PDF
- HTML (experimental)
- TeX Source
View a PDF of the paper titled BrainWideBench: Benchmarking large-scale pretraining and across-animal transfer in multi-region neural recordings, by Alexandre Andre and 41 other authors
Current browse context:
cs.LG
References & Citations
Loading...
Bookmark
Bibliographic Tools
Code, Data, Media
Demos
Related Papers
About arXivLabs
Bibliographic and Citation Tools
Bibliographic Explorer Toggle
Bibliographic Explorer (What is the Explorer?)
Connected Papers Toggle
Connected Papers (What is Connected Papers?)
Litmaps Toggle
Litmaps (What is Litmaps?)
scite.ai Toggle
scite Smart Citations (What are Smart Citations?)
Code, Data and Media Associated with this Article
alphaXiv Toggle
alphaXiv (What is alphaXiv?)
Links to Code Toggle
CatalyzeX Code Finder for Papers (What is CatalyzeX?)
DagsHub Toggle
DagsHub (What is DagsHub?)
GotitPub Toggle
Gotit.pub (What is GotitPub?)
Huggingface Toggle
Hugging Face (What is Huggingface?)
ScienceCast Toggle
ScienceCast (What is ScienceCast?)
Demos
Replicate Toggle
Replicate (What is Replicate?)
Spaces Toggle
Hugging Face Spaces (What is Spaces?)
Spaces Toggle
TXYZ.AI (What is TXYZ.AI?)
Recommenders and Search Tools
Link to Influence Flower
Influence Flower (What are Influence Flowers?)
Core recommender toggle
CORE Recommender (What is CORE?)
IArxiv recommender toggle
IArxiv Recommender
(What is IArxiv?)
arXivLabs: experimental projects with community collaborators
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.
Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.
Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
More from arXiv — Machine Learning
-
Stable and Faithful Explanations for Knowledge Tracing
Sep 25
-
SMILESGNN: Interpretable Clinical Toxicity Prediction via SMILES-Graph Cross-Attention Fusion
Sep 25
-
CFD Correction of Open Tip Clearance Flow in a Compressor Cascade Using VAE Latent Space Adaptation
Sep 25
-
CARE: Condition-Aware Representation Regularization for Diffusion Models
Sep 25
Discussion (0)
Sign in to join the discussion. Free account, 30 seconds — email code or GitHub.
Sign in →No comments yet. Sign in and be the first to say something.