Jaycee at CVPR 2025

Jaycee Choi, PhD Candidate, recently attended the Computer Vision Pattern Recognition (CVPR) conference in Nashville, Tennessee. CVPR is one of the premier international conferences in computer science that brings together researchers in computer vision. Jaycee...

Kumar Lab hosts first SSPsyGene SING consortium meeting

In January 2025, the Kumar Lab was awarded a RM1 grant to analyze behavior in 100 mouse model of neurodevelopmental disorder. As part of the grant, we have annual meetings of the consortium members. The 2025 meeting was held in JAX, Bar Harbor and organized by...

Jake invited to share migraine ethology at IBANGS

This June Jake Beierle, post doctoral fellow in the lab, was invited to share his work at the International Behavioral and Neural Genetics Society meeting this year, and was recognized as an outstanding travel awardee. The work Jake shared leverages advances in...

Jake is awarded the Paigen Fellowship

Jake has been awarded the Paigen Fellowship. Paigen Endowed Fellowship recognizes promising postdoctoral talent at JAX. Congratulations, Jake! The award is well deserved....

Yehya Wins Out to Innovate Award

Congratulations to Yehya on getting this award. They proposed to continue to study the Crichton mouse model of age dependent changes in behavior. The Out to Innovate™ Scholarships, established in 2011, are intended for LGBTQ+ undergraduate and graduate students...

Malachy’s paper is published in Cell Patterns

Malachy worked for two years on how to use computer vision to determine mouse mass. We are really proud of his accomplishment! Gautam and Brian both were critical in his success. We look forward to all that Malachy will accomplish. Paper link...

Jake’s Trip to NAPS

Last week Dr. Jake Beierle, our post-doctoral fellow, traveled to Montebello Quebec to attend the prestigious North American Pain School (NAPS). At the weeklong event, Jake shared his work assessing migraine models using the Kumar Lab’s machine learning empowered...

Strain Survey Open Field Video Dataset made public!

We have released our Strain Survey Open Field video dataset to the public over on harvard dataverse here: https://doi.org/10.7910/DVN/SAPNJG What this release includes: 2509 55-minute open field assay experiments across 62 inbred and F1 hybrid strains 2509 pose...

Vivek gives a seminar at Scripps Florida

Vivek was invited to give a talk at The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology in February. Thank you for the invitation. I learned an incredible amount from my interactions with the faculty at Scripps Florida.  ...

Presentations at the Complex Trait Community 2023 Conference

Gautam, Brian, Jaycee, and Vivek gave oral presentations of their work at this year's CTC meeting in a session called "Machine learning for rodent behavior". https://complextrait.org/meetings/ctc-rg2023/program.html Talk Titles: A machine-vision-based frailty index...

Vivek gives a seminar at University of Texas-Houston

Vivek visited and gave a seminar in the Univeristy of Texas-Houston Department of Biochemistry and Molecular Biology. Dr. Seung Hee Yoo hosted Vivek. It was a fun visit to a great department. Houston was heavily affected by Hurricane Harvey. Here is a flood gate...

ML-Behavior Workshop

Vivek co-organized THE SHORT COURSE ON THE APPLICATION OF MACHINE LEARNING FOR AUTOMATED QUANTIFICATION OF BEHAVIOR at High Seas on Oct. 2022. Brian and Leinani ran a workshop and attended the course. [gallery columns="4"...

Vivek presents lab research at UTHSC

Vivek was invited by the graduate students of the UTHSC Neuroscience Program. He met with several colleagues and met new students. His talk focused on the use of computer vision for preclinical models of psychiatric disease.

Kumar Lab Receives a 2021 SFARI Director’s Award

Press announcement here - the work will fund monitoring of ASD models using our long-term methods. We appreciate the support from SFARI (Simons Foundation Autism Research Initiative) which is one of the most innovative funding agencies for biomedical research....

Sleep paper is now published online

Visual determination of sleep states is published in the journal Sleep. Congratulations to Brian and Mandy for leading this effort. The article can be found here. Standard link (you may share this link anywhere):...

Gait Paper is accepted to Cell Reports

The mouse gait paper has been accepted. A preprint is here - the final version will be shorter due to space limitations from the Journal. Congratulations to Keith and Gautam on leading this effort.  The work was started by Justin Gardin, a stellar postdoc in the...

Sleep Paper is accepted

Visual determination of sleep states is accepted in the journal Sleep. Congratulations to Brian and Mandy for leading this effort.

Updated paper: Gait analysis

An updated version of Gait analysis paper is on Biorxiv. https://www.biorxiv.org/content/10.1101/2020.12.29.424780v2 It has new analysis from Keith Sheppard and Gautam Sabnis including several new figures in the supplement. We look forward to getting reviews...

Grooming paper is published in eLife

Paper link is here https://elifesciences.org/articles/63207 Data associated with the paper is here with video data uploaded to Zenodo https://zenodo.org/record/4646088 We also share some videos of our network in action:...

Rotta Vocabulary

Cross Validation In cross validation, the classifier is trained on a set of labels (training set), then tested on a set of labels held-out of the training set (testing set). This is used to estimate the accuracy of the classifier. In Rotta, we use a 10-fold cross...

Left and Right Turn

Definition of Behavior Turn behavior is when a mouse changes directions. It can happen when the mouse is moving or when it starts from no movement. It can also occur after rearing on wall. The change in direction varies in amount. Sometimes a mouse can carry out a...

Kumar Lab receives a new grant from NIDA

The Kumar Lab received a grant from NIDA to build new models of addiction. The press release is here https://www.jax.org/news-and-insights/2020/july/building-better-mouse-models-for-addiction-research The project summary is available here: PROJECT SUMMARY Addiction...

PyTorch: keep the GPU busy

We all know it's important to use GPU resources efficiently, especially during inference. One easy and highly effective way to achieve this is to reorder some of your inference logic to exploit PyTorch's asynchronous GPU operations. This becomes especially...

HE Plots at a glance

Multivariate response data are routinely generated from experiments carried out in our lab. For example, several interrelated gait metrics such as stride length, step length, limb duty factor etc. are extracted from each stride of the mouse. The goal is to gain...

Singularity Container Efficiency Benchmark

Singularity is a relatively new tool that extends docker-style containerized compute into the hands of researchers on compute clusters. For security reasons, most compute clusters did not allow docker containers, and would require any software to be installed by...

Vivek attends the 2020 NIDA genetics consortium meeting

Vivek and Arojit attended the NIDA genetics meeting in Bethesda, MD. They presented two posters. Vivek presented our work on cloning of a mutation that regulates cocaine responses. This is a new gene that has not been linked to cocaine responses.  Abstract from the...

Vivek gives lecture at Dartmouth

Vivek was invited to give a seminar at Dartmouth University by Dr. Gio Bosco and his postdoctoral fellow Shiva Sathyanarayana. Vivek spoke about the lab's work on Cyfip2 (work of postdoctoral Arojit Mitra, Kyungin Kim, and others). He also spoke about the lab's...

2019 Gordon Research Conference – Neuroethology

The Kumar Lab attended the 2019 Gordon Research Conference on Neuroethology - Multimodal Strategies for Behavioral Control: Molecules, Neurons, Circuits, and Behavior in West Dover, Vermont from July 28 - August 2. Arojit presented the following poster - Enhanced...

Vivek presents at the 2019 Complex Trait Consortium Meeting

Vivek attended and presented at the CTC meeting in UCSD. The CTC meeting is an annual meeting of complex trait geneticists who use model organisms. Vivek spoke on the use of computer vision to extract heritable ethological endophenotypes from mice.  The meeting has...

Brian’s tracking paper published

Brian's paper on robust mouse tracking is published. This paper describes how to track mice in complicated environments. Sean and others contributed to this paper. https://doi.org/10.1038/s42003-019-0362-1 Data from the paper is here. [button...

Vivek speaks at the 2019 Maine State Science Fair

Vivek spoke about addiction genetics and neuroscience to high schools students from across the state of Maine. Over 200 students competed in over a dozen categories in this year's science fair.  More information about the event is here. Arojit Mitra was...

Vivek gives Maine Engineering Expo Keynote Address

Vivek presents the keynote address at the Maine Engineering Expo. Approximately 150 people attended the banquet. National Engineers Week was initiated to publicly promote the work and contributions of our nation's engineers. During this week, engineering...

Brian’s video compression tests

Visual examples of some of the compression tests. Original sub-panel of video and differences between original and compressed frames. Difference previews are amplified 2x to enhance visibility. Video Acquisition Imaging Hardware All data was acquired using the same...

JAXMice Mouse Models