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...
Vivek gives keynote at CV4Animals
Vivek gave a remote keynote address for CV4Animals held in Nashville, TN. The talk can be found here.
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...
Vivek presents at the AGE meeting Shock Center Symposium
Vivek attended and presented at the 2025 AGE meeting in Anchorage, Alaska. Vivek was part of the Shock Center Director's Symposium. He presented on Gautam's frailty index work. ...
DO Frailty paper is now published in GeroScience
Free link here! Nice job, Gautam. https://rdcu.be/edXnG
Vivek Attends ODIN Conference at The Allen Institute for Neural Dynamics
Vivek attended the ODIN symposium, sponsored by The Allen Institute for Neural Dynamics and Massachusetts Institute of Technology (MIT). The 2025 Open Data in Neurophysiology (ODIN) Symposium group seeks to fill the pressing need to bridge scales and modalities in...
Vivek gives inaugural Maine INBRE Data Science Colloquium talk
The talk was at the University of Maine, Orono hosted by Drs. Ben King and Joel Graber. Several members of the lab attended the lecture.
The first Envision Discovery Rack is installed in the Kumar Lab
On April 2, 2025 Allentown and JAX installed the first Discovery Rack in the Kumar Lab. The lab has been working together with a large team on its development over the past 2+years. The system is based on the work that the Kumar Lab has done over the past 8 years....
Vivek Attends Simons Foundation SFARI meeting
Vivek attended the annual SFARI meeting hosted by the Simons Foundation in NYC. He presented a poster and had awesome pizza!...
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....
Vivek Presents at Northwestern University symposium
Vivek was invited to present at the Synaptic Dysfunction in Neurodevelopmental Disorders symposium. It was part of the NWU Conte Center and a satellite meeting to SfN 2024....
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...
The Kumar lab at TAGC24
The Kumar lab's doctoral students Jaycee and Yehya at TAGC 2024 presenting their ongoing work.
Jaycee and Vivek publish review in Neuroscience & Biobehavioral Reviews
Jaycee and Vivek published a commentary entitled, A new era in quantification of animal social behaviors, in the Journal of Neuroscience & Biobehavioral Reviews. Link to article: https://pubmed.ncbi.nlm.nih.gov/38160721/
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. ...
Vivek directs year 3 of the Short Course on the Impacts of Sleep and Circadian Biology on Alzheimer’s Disease and Aging
Year 3 of the R13 course was a success! Thank you to all who attended. https://www.jax.org/education-and-learning/education-calendar/2023/10-October/impacts-of-sleep-and-circadian-biology-on-alzheimers-disease-and-aging 2023_CC_Impacts of Sleep flyer v4...
Vivek organizes the 2nd ML based behavior quantification course
The second year of the course was a success. We had 20+ instructors and ~35 students attend the course from all over the world! Lots of good science and hiking. JC, Jake, and Anshul attended the course from the Kumar Lab. JC was also a TA with Brian....
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 and Jake attend NIDA Genetics and Epigenetics Cross-Cutting Research Team Meeting
The NIDA Genetics meeting was held on the main campus (Natcher Center). It was our first in person meeting in a couple of years. Jake presented a poster on the pain work. It was good to see many colleagues. ...
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...
Vivek organizes the 2nd course on IMPACTS OF SLEEP AND CIRCADIAN BIOLOGY ON ALZHEIMER’S DISEASE AND AGING
'The second year of the course was held at JAX on Oct 17-20 and brought together speakers and students ~40. [gallery columns="4"...
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.
Vivek presents poster at Gordon Research Conference on the Neurobiology of Addiction
Vivek attended the GRC on addiction at Newry, Maine. The conference consisted of ~200 neuroscientists.
Kumar Lab organizes a symposium on Machine Learning and Behavior Quantification at IBANGS
The International Brain and Neural Genetics Society organized its 23rd Annual Genes, Brain & Behavior Meeting on May 23rd-27th, 2022 in Memphis at the UTHSC. The meeting was hybrid with over 100 participants. Vivek organized a symposium titled Behavior...
Vivek attends the SFARI Investigator Meeting in New York
Vivek attended the SFARI Investigator's meeting on April 11-13 in NYC. The meeting booklet is here. The meeting had ~200 investigators with a wide array of topics from human genetics to systems...
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....
Gait and posture paper is now online at Cell Reports
A tour de force from Keith and Gautam. This is beautiful work. Full text is available here. https://www.cell.com/cell-reports/fulltext/S2211-1247(21)01740-X
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):...
Vivek Co-organizes Sleep/Circadian/AD Short Course at Highseas
Vivek was a co-organizer of the Impacts of Sleep and Circadian Biology on Alzheimer's Disease and Aging from Oct 16-22, 2021 at Highseas Conference Center. The short course had 25 residential students and over 100 virtual students. The instructors included leaders...
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...
Visual determination of frailty – preprint online now
Leinani's and Gautam's paper is online as a preprint. It is currently under review at Nature Aging.
Sleep Paper is accepted
Visual determination of sleep states is accepted in the journal Sleep. Congratulations to Brian and Mandy for leading this effort.
Press Release for two new grants for the lab
We received two new grants. The press release is here. We are looking for additional lab members. https://www.jax.org/news-and-insights/2021/september/untangling-the-biology-of-addiction
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...
Arojit’s paper demonstrating that TMOD2 is a regulator of cocaine responses is on Biorxiv.
The paper is currently under review and we hope it is published soon. Meanwhile, the preprint is available here. https://www.biorxiv.org/content/10.1101/648295v1
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...