Welcome to Abbasi Lab Webpage
The Abbasi Lab develops interpretable models and algorithms based on machine learning principles to understand functions of the brain and related disorders. To discover and model the functions of neurons, the lab studies applications of machine learning in the analysis of large-scale multi-modal datasets including electrophysiology, calcium imaging, electron microscopy, and spatial gene expression profiles. In the next step and to reconcile our understanding of the brain with related disorders, the Abbasi Lab builds computational tools for scientific discovery in large-scale neurological clinical datasets. This involves interpretable analysis and visualization of medical images, multi-omics datasets, and electronic health records.
We are hiring!
We have openings for one or multiple post-doctorate fellows to work with us at UCSF on exciting applied problems at the intersection of machine learning and computational/clinical neuroscience. The projects involve predictive modeling, biomedical image and signal processing, interpretation inference, neural networks, visualization, etc. Background in imaging and neuroscience is not required but is a plus!
Contact Reza directly via Reza.AbbasiAsl@ucsf.edu to learn more!
News and Events
August 2021: Congrats to Austin Jang and Shiladitya Dutta, two undergraduate students in the lab, for winning the UC Berkeley URAP fellowship for their research projects!
August 2021: New paper published in Frontiers in Big Data: Structural Compression of Convolutional Neural Networks with Applications in Interpretability.
June 2021: New paper on arXiv: Multi-Modal Prototype Learning for Interpretable Multivariable Time Series Classification.
June 2021: Congrats to Austin Jang and Shiladitya Dutta, for winning the URAP summer fellowship!
May 2021: We got awarded the New Frontiers Research Award from the Sandler Program for Breakthrough Biomedical Research.
May 2021: We are hiring a fully-funded postdoc fellow to lead efforts for our new Neuroscape-based project on computational models of multi-modal biosensor data! Reach out if you are interested!
May 2021: Gavin Cui joins the lab as a bioengineering PhD student. Welcome Gavin!
April 2021: Our NIH grant in collaboration with Neuroscape PIs (Ted Zanto and David Ziegler) on “Neural markers of impending task performance” just got funded!
Feb 2021: One abstract accepted at VSS 2021 on our large-scale standardized survey of neural receptive fields in an entire column in mouse V1.
Feb 2021: We are hiring two new postdoc fellows to join us at UCSF and lead our efforts on developing a computational pipeline to analyze spatial gene expression in mice.
Feb 2021: Reza will be giving a talk at the faculty seminar at the Kavli Institute.
Jan 2021: Reza becomes a Weill Neurohub Investigator.
Jan 2021: We got awarded the Weill Neurohub Next Great Ideas Fund! Our proposed project is focused on spatial gene expression analysis in mice.
Nov 2020: Reza will give an invited talk at the 2020 Basic and Clinical Neuroscience.
Oct 2020: One abstract accepted at CSHL NAISys meeting on interpretable models of neurons in visual cortex.
August 2020: One abstract accepted at JSM 2020 on Revealing Spatial Gene Patterns and Interactions in Mouse Brain via Stability-Driven NMF.
May 2020: One abstract accepted at CNS 2020 on compressed models of neurons in V4!
May 2020: Our paper featured on the cover of Neuron!
March 2020: Reza is now a joint faculty at the Department of Bioengineering and Therapeutic Sciences at UCSF.
March 2020: We are now officially affiliated with Neuroscape!
March 2020: The dataset from our recent eNeuro paper is now available on the CRCNS data repository.
March 2020: Here is a nice read from Allen Institute on our recent Neuron paper.
March 2020: Due to the recent Corona Virus outbreak, the lab has moved to fully remote mode! Hope everyone is staying safe and healthy!
March 2020: We are happy to welcome to the lab Oluwaseun Adegbite as rotation PhD student, Luke Chen as an RA, and five UC Berkeley undergraduates through the URAP program: Kevin Lin, Rohan Divate, Austin Jang, Anmol Parande, Felix Ching!
Feb 2020: Reza will give an invited talk at ITA 2020 on interpretation of neural networks with applications in comp neuroscience.
Jan 2020: We will be present at Cosyne 2020 with one invited talk and one accepted abstract on compressed interpretable models of neurons. Reza will give the invited talk at the workshop on “Scrutinizing models of brain function: from in-silico stimulus synthesis to direct brain perturbation”.
Jan 2020: Our paper titled “Systematic Integration of Structural and Functional Data into Multi-Scale Models of Mouse Primary Visual Cortex” has been accepted at Neuron.
Jan 2020: Our paper titled “Superficial bound of the depth limit of 2-photon imaging in mouse brain” appeared on eNeuro.
Jan 2020: We are now affiliated with Bakar Computational Health Sciences Institute at UCSF! Reza will be a faculty affiliate at the institute.
Dec 2019: Welcome to the lab Neel!
Nov 2019: Welcome to the lab Ahyeon and Franklin!
Nov 2019: Reza joined the UC Berkeley-UCSF graduate program in bioengineering. We have multiple openings for rotation students!
Oct 2019: Our paper titled “Definitions, methods, and applications in interpretable machine learning” appeared on PNAS.
Oct 2019: Reza is presenting at SfN on functional imaging of excitatory neurons in an entire column in mouse visual cortex. Here is the abstract.
Sep 2019: Abbasi Lab officially started!