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Research

What we work on

There are no biological markers for diagnosing mental illness or for indicating how best to treat it. Our group hopes to change that — building robust, predictive models of human health from neuroimaging, speech, and machine learning.

A fundamental problem in psychiatry is that there are no biological markers for diagnosing mental illness or for indicating how best to treat it. Treatment decisions are based entirely on symptoms, and doctors and their patients will typically try one treatment, then if it does not work, try another. Our research suggests that individual brain scans and speaking patterns can hold valuable information for guiding psychiatrists and patients. Current areas include depression, suicide, anxiety disorders, autism, Parkinson disease, and brain tumors.

To support this broader goal, our group develops novel analytic platforms that use such information to create robust, predictive models around human health. We believe that solving this problem will require complex integration of different types of sensors into an adaptive learning system together with patient, caregiver, and community feedback.

Many of the tools we develop can be used across domains. If you have a need we can address, we would like to hear from you. If you have solved problems associated with any of the projects below, we would love to hear from you too — for us, a solution typically implies available data, code, and/or replicated results.

Multi-sensory integration diagram

Filter by theme — click one or more; multiple selections combine with OR.

Active projects

What's happening in the group right now.

16
BBQS — Brain Behavior Quantification and Synchronization

NIDA U24 DA064429 (Lead PI; MPI Cabrera, Kennedy)

A BRAIN-Initiative consortium developing tools to capture and quantify behavior at high temporal resolution and across multiple dimensions, to synchronize behavior with simultaneously-recorded brain activity, and to build conceptual and computational models of behavior. The lab runs BARD.CC, the BBQS AI Resource and Data Coordinating Center.

People: Nader Nikbakht , Satrajit S Ghosh , Suliman Sharif , Tek Raj Chhetri

  • open-data-standards
  • ml-nlp-knowledge
4 links
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BICAN Knowledgebase (BrainKB)

NIMH U24 MH130918 (MPI with Mufti, Hawrylycz, Ng — Allen Institute)

An extensible, open-access Brain Cell Knowledge Base built for the BRAIN Initiative Cell Atlas Network. Ingests and standardizes cell-type information across multimodal, multi-species brain atlases and exposes it via the BrainKB platform, the bkbit toolkit, and LinkML-authored schemas. The lab maintains BrainKB, the StructSense extraction agent, and the schemas / data translators.

People: Dorota Jarecka , Nader Nikbakht , Nima Dehghani , Puja Trivedi , Satrajit S Ghosh , Suliman Sharif , Tek Raj Chhetri , Jai Amin*

  • open-data-standards
  • ml-nlp-knowledge
  • reproducibility-tooling
10 links 2 papers
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BICAN UM1 — Multi-Scale Multi-Omic Human Brain Atlas

NIMH UM1 MH134812 (Co-I)

A BRAIN Initiative UM1 center for multi-scale, multi-omic atlasing of the human brain, contributing analytics and platform integration for proteomic imaging and related modalities. The flagship consortium output to date is Park et al. (2024) in Science, an integrated multiscale molecular imaging and phenotyping platform for the human brain.

People: Kabilar Gunalan , Satrajit S Ghosh

  • connectomics-circuits
  • open-data-standards
2 links 1 paper
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LINC / CONNECTS — Large-scale Imaging of Neural Circuits

NINDS UM1 NS132358 (Site PI)

A multi-site center combining macaque and human dMRI (660 mT/m and 500 mT/m), light-sheet microscopy with tracers, polarization-sensitive OCT, HiP-CT, and micro-CT into integrated pipelines for clearing, imaging, storage, and dissemination of neural-circuit data. Use cases include DBS-circuit mapping and biophysical modeling.

People: Kabilar Gunalan , Satrajit S Ghosh

  • connectomics-circuits
  • neuroimaging-methods
  • open-data-standards
6 links 1 paper
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Bridge2AI Voice

NIH OD OT2 OD032720 (MPI)

Build an ethically-sourced, diverse, AI-ready database of 10 000 human voices linked to health information across five disease categories: cardio-respiratory, mood, pediatric speech, voice, and neurological disorders. The consortium develops standards for acoustic research data, technical infrastructure for collection / storage / sharing, ethical guidelines, and educational dissemination. The lab maintains b2aiprep (data packaging) and contributes to the protocol design, ethics, and pediatric arm.

People: Jordan Wilke , Kaley Jenney , Rahul Brito , Satrajit S Ghosh , Daniel M. Low* , Fabio Catania*

  • speech-voice-biomarkers
  • open-data-standards
  • mental-health-psychiatry
9 links 2 papers
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senselab

Research software toolkit for voice / speech / behavioral analysis and biomarker identification. "Streamlines, optimizes, and enforces best open-science practices for processing and analyzing behavioral data (primarily voice and speech, but also text and video) using robust, reproducible pipelines and utilities." Used by the Bridge2AI-Voice and Riverst / KIVA stacks.

People: Jordan Wilke , Satrajit S Ghosh , Bruke Wossenseged* , Fabio Catania* , Gasser Elbanna* , Isaac Bevers* , Miles Silva*

  • reproducibility-tooling
  • speech-voice-biomarkers
2 links
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Riverst / KIVA — Digital tutor for childhood literacy

MGAIC (MIT Generative AI Consortium), 2025–2026

Riverst is a digital-tutor platform for childhood literacy; KIVA is an instance focused on vocabulary learning. Built on Pipecat and senselab, integrating speech-feature extraction. Research questions: Can an avatar understand child speech? Can LLMs adapt to each child? Can an LLM effectively teach vocabulary?

People: Jordan Wilke , Satrajit S Ghosh , Fabio Catania*

  • child-development-education
  • ml-nlp-knowledge
  • speech-voice-biomarkers
5 links 1 paper
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ReproNim — Center for Reproducible Neuroimaging Computation

NIBIB P41 EB019936 (Site PI; PI Kennedy, UMass Med; Director TR&D Project 2)

A Center dedicated to improving reproducibility in neuroimaging via best practices, tools, and training. Current efforts include Simple 2 (re-executable neuroimaging publications with NIDM provenance), ReproSchema (standardized questionnaires / assessments for ABCD, HBCD, Bridge2AI), ReproBRAISE / ABCD-ReproNim (Reproducible BRAIn State Extraction), containerized BIDS apps (FreeSurfer / FSL / ANTs / MRIQC), and BABS (BIDS App Bootstrap).

People: Dorota Jarecka , Satrajit S Ghosh , Yibei Chen , Christopher J Markiewicz* , Daniel M. Low* , Isaac Bevers* , Jakub Kaczmarzyk* , Mathias Goncalves* , Sanu Ann Abraham* , Smruti Padhy*

  • reproducibility-tooling
  • neuroimaging-methods
  • open-data-standards
10 links 6 papers
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Nipype / Pydra

NIBIB R01 EB020740 (PI, 2016–2020; project ongoing as community software)

Nipype is a community-developed Python project providing a uniform interface to existing neuroimaging software (ANTS, SPM, FSL, FreeSurfer, Camino, MRtrix, MNE, AFNI, Slicer) and underpinning many popular pipelines including fmriprep. Pydra is a lightweight Python dataflow engine designed to succeed Nipype: reproducible, scalable workflows linking shell commands and Python functions.

People: Dorota Jarecka , Satrajit S Ghosh , Christopher J Markiewicz* , Jakub Kaczmarzyk* , Mathias Goncalves*

  • reproducibility-tooling
  • neuroimaging-methods
5 links 1 paper
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SAILS — Speech & Action In-home Learning System

Simons Foundation (Site PI, 2025–2026); Kennedy Krieger Institute partnership

Into the Wild — automated quantification of autism-relevant behaviors from naturalistic home videos. The study pipeline runs end-to-end: parents are reached through SPARK Research Match, submit questionnaires and home-video uploads, and complete a remote language assessment; videos pass automated metadata checks and human quality review; trained annotators produce ground-truth labels against a shared manual with ICC reliability checks; and VLM-based models score uniform frame samples for video-level behavior predictions. Brings together three theses: Manaal Mohammed's on target-child behavior detection (vocalizations via USC-SAIL / Whisper baseline; locomotion via S3D gated 3D CNN), Lucie Bierent's on socialization-behavior recognition (response to name, non-verbal communication, gesture prediction), and Bruke Wossenseged's thesis work.

People: Satrajit S Ghosh , Yibei Chen , Manaal Mohammed , Aparna BG , Bruke Wossenseged* , Lucie Bierent* , Fabio Catania*

  • child-development-education
  • mental-health-psychiatry
  • ml-nlp-knowledge
  • speech-voice-biomarkers
2 links
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Brain States

A brain state is a latent (hidden) variable representing a recurring whole-brain configuration of neural activity — characterized by emissions (spatial patterns), transition probabilities, and dwell time. Research questions: Is there systematic structure in how brain configurations relate to the world and behavior? How does this structure differ between the neurodivergent and neurotypical populations?

People: Satrajit S Ghosh , Yibei Chen

  • brain-dynamics-naturalistic
  • neuroimaging-methods
2 links 1 paper
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ReadNet — ML for verbal literacy screening

Harvard University gift (Schmidt Futures & Citadel; Site Co-I) + MIT GenAI Consortium

Manual scoring of verbal literacy screeners is time-consuming and unreliable; ReadNet is an ML approach to help teachers quickly and reliably identify children needing early-literacy intervention. The project ran the DrivenData "Goodnight Moon, Hello Early Literacy Screening" public competition in 2024–2025 (winning AUROC 0.97 vs Whisper baseline 0.59), with a voice-cloning anonymization scheme for data release.

People: Meral Hacikamiloglu , Satrajit S Ghosh , Fabio Catania*

  • child-development-education
  • ml-nlp-knowledge
  • speech-voice-biomarkers
6 links 2 papers
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StructSense — Agentic structured information extraction

A task-agnostic multi-agent system for structured information extraction. Used by BrainKB to extract causal mechanisms (not just entities) from neuroscience literature, with a prototype tool that converts flat NER data into valid, Marr-aligned JSON-LD. arXiv 2507.03674 (Chhetri, Chen, Trivedi, Jarecka et al., 2025).

People: Dorota Jarecka , Nader Nikbakht , Puja Trivedi , Satrajit S Ghosh , Suliman Sharif , Tek Raj Chhetri , Yibei Chen

  • ml-nlp-knowledge
2 links 1 paper
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Past projects

Completed or paused efforts. Asterisks (*) on contributor names indicate former members.

7
Nobrainer — Neural network tool suite for imagers

NIMH RF1 MH121885 (PI, 2020–2024)

Open Python library to simplify integrating deep learning into neuroimaging research, distributing user-friendly cloud-enabled end-user applications for the community. The Nobrainer / KWYK framework underlies several brain-segmentation and meningioma-detection studies.

People: Aakanksha Rana* , Jakub Kaczmarzyk* , Satrajit S Ghosh*

  • reproducibility-tooling
  • neuroimaging-methods
  • ml-nlp-knowledge
4 links 1 paper
Learn more
Mumble Melody — Musically-modulated auditory feedback for people who stutter

McGovern Institute NTP + MIT Deshpande Center (PI; co-PI Machover)

Mobile app and one-month clinical study using altered auditory feedback (AAF) — pitch shifts, delays, reverberation, whisper, harmony — to increase fluency for people who stutter. US Patent 11,727,949 B2 issued Aug 2023 for the underlying technique.

People: Akito van Troyer*, Alisha Kodibagkar* , George Stefanakis*, Megha Vemuri* , Mike Erkkinen*, Rebecca Kleinberger* , Satrajit S Ghosh* , Tod Machover*

  • speech-voice-biomarkers
  • mental-health-psychiatry
7 links
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Naturalistic Parcellation and audiovisual integration

NIMH R01 MH109682 (Site PI; PI Yarkoni)

A Neuroscout project generating cortical parcellations from naturalistic (movie-viewing) neuroimaging datasets, with goals including character-ID decoding, audiovisual-feature mapping, auditory-specific and whole-brain parcellations, and reproducibility across datasets.

People: Christopher J Markiewicz* , Jeff Mentch* , Satrajit S Ghosh*

  • brain-dynamics-naturalistic
  • neuroimaging-methods
2 links 1 paper
Learn more

Missing a project? Contributors not credited? Open a PR editing src/data/projects.yml — see PROJECTS.md for the schema.