arXiv subjects

Satrajit Ghosh

Publications and source records attributed to Satrajit Ghosh.

6 recordsLinked to original sources

arXiv2025

Standards in the Preparation of Biomedical Research Metadata: A Bridge2AI Perspective

AI-readiness describes the degree to which data may be optimally and ethically used for subsequent AI and Machine Learning (AI/ML) methods, where those methods may involve some combination of model training, data classification, and ethical, explainable prediction. The Bridge2AI consortium has defined the particular criteria a biomedical dataset may possess to render it AI-ready: in brief, a dataset's readiness is related to its FAIRness, provenance, degree of characterization, explainability, sustainability, and computability, in addition to its accompaniment with documentation about ethical data practices. To ensure AI-readiness and to clarify data structure and relationships within Bridge2AI's Grand Challenges (GCs), particular types of metadata are necessary. The GCs within the Bridge2AI initiative include four data-generating projects focusing on generating AI/ML-ready datasets to tackle complex biomedical and behavioral research problems. These projects develop standardized, multimodal data, tools, and training resources to support AI integration, while addressing ethical data practices. Examples include using voice as a biomarker, building interpretable genomic tools, modeling disease trajectories with diverse multimodal data, and mapping cellular and molecular health indicators across the human body. This report assesses the state of metadata creation and standardization in the Bridge2AI GCs, provides guidelines where required, and identifies gaps and areas for improvement across the program. New projects, including those outside the Bridge2AI consortium, would benefit from what we have learned about creating metadata as part of efforts to promote AI readiness.

q-bio.OT↗

arXiv2025

Evaluating Contrast Localizer for Identifying Causal Units in Social & Mathematical Tasks in Language Models

This work adapts a neuroscientific contrast localizer to pinpoint causally relevant units for Theory of Mind (ToM) and mathematical reasoning tasks in large language models (LLMs) and vision-language models (VLMs). Across 11 LLMs and 5 VLMs ranging in size from 3B to 90B parameters, we localize top-activated units using contrastive stimulus sets and assess their causal role via targeted ablations. We compare the effect of lesioning functionally selected units against low-activation and randomly selected units on downstream accuracy across established ToM and mathematical benchmarks. Contrary to expectations, low-activation units sometimes produced larger performance drops than the highly activated ones, and units derived from the mathematical localizer often impaired ToM performance more than those from the ToM localizer. These findings call into question the causal relevance of contrast-based localizers and highlight the need for broader stimulus sets and more accurately capture task-specific units.

cs.CL↗

arXiv2024

ODIN: Open Data In Neurophysiology: Advancements, Solutions & Challenges

Across the life sciences, an ongoing effort over the last 50 years has made data and methods more reproducible and transparent. This openness has led to transformative insights and vastly accelerated scientific progress. For example, structural biology and genomics have undertaken systematic collection and publication of protein sequences and structures over the past half-century, and these data have led to scientific breakthroughs that were unthinkable when data collection first began. We believe that neuroscience is poised to follow the same path, and that principles of open data and open science will transform our understanding of the nervous system in ways that are impossible to predict at the moment. To this end, new social structures along with active and open scientific communities are essential to facilitate and expand the still limited adoption of open science practices in our field. Unified by shared values of openness, we set out to organize a symposium for Open Data in Neuroscience (ODIN) to strengthen our community and facilitate transformative neuroscience research at large. In this report, we share what we learned during this first ODIN event. We also lay out plans for how to grow this movement, document emerging conversations, and propose a path toward a better and more transparent science of tomorrow.

q-bio.NC↗

arXiv2023

SciOps: Achieving Productivity and Reliability in Data-Intensive Research

Scientists are increasingly leveraging advances in instruments, automation, and collaborative tools to scale up their experiments and research goals, leading to new bursts of discovery. Various scientific disciplines, including neuroscience, have adopted key technologies to enhance collaboration, reproducibility, and automation. Drawing inspiration from advancements in the software industry, we present a roadmap to enhance the reliability and scalability of scientific operations for diverse research teams tackling large and complex projects. We introduce a five-level Capability Maturity Model describing the principles of rigorous scientific operations in projects ranging from small-scale exploratory studies to large-scale, multi-disciplinary research endeavors. Achieving higher levels of operational maturity necessitates the adoption of new, technology-enabled methodologies, which we refer to as SciOps. This concept is derived from the DevOps methodologies that have revolutionized the software industry. SciOps involves digital research environments that seamlessly integrate computational, automation, and AI-driven efforts throughout the research cycle-from experimental design and data collection to analysis and dissemination, ultimately leading to closed-loop discovery. This maturity model offers a framework for assessing and improving operational practices in multidisciplinary research teams, guiding them towards greater efficiency and effectiveness in scientific inquiry.

q-bio.NC↗

arXiv2023

A Comparison of Neuroelectrophysiology Databases

As data sharing has become more prevalent, three pillars - archives, standards, and analysis tools - have emerged as critical components in facilitating effective data sharing and collaboration. This paper compares four freely available intracranial neuroelectrophysiology data repositories: Data Archive for the BRAIN Initiative (DABI), Distributed Archives for Neurophysiology Data Integration (DANDI), OpenNeuro, and Brain-CODE. The aim of this review is to describe archives that provide researchers with tools to store, share, and reanalyze both human and non-human neurophysiology data based on criteria that are of interest to the neuroscientific community. The Brain Imaging Data Structure (BIDS) and Neurodata Without Borders (NWB) are utilized by these archives to make data more accessible to researchers by implementing a common standard. As the necessity for integrating large-scale analysis into data repository platforms continues to grow within the neuroscientific community, this article will highlight the various analytical and customizable tools developed within the chosen archives that may advance the field of neuroinformatics.

q-bio.QM↗

arXiv2021

Uncertainty-Aware Boosted Ensembling in Multi-Modal Settings

Reliability of machine learning (ML) systems is crucial in safety-critical applications such as healthcare, and uncertainty estimation is a widely researched method to highlight the confidence of ML systems in deployment. Sequential and parallel ensemble techniques have shown improved performance of ML systems in multi-modal settings by leveraging the feature sets together. We propose an uncertainty-aware boosting technique for multi-modal ensembling in order to focus on the data points with higher associated uncertainty estimates, rather than the ones with higher loss values. We evaluate this method on healthcare tasks related to Dementia and Parkinson's disease which involve real-world multi-modal speech and text data, wherein our method shows an improved performance. Additional analysis suggests that introducing uncertainty-awareness into the boosted ensembles decreases the overall entropy of the system, making it more robust to heteroscedasticity in the data, as well as better calibrating each of the modalities along with high quality prediction intervals. We open-source our entire codebase at https://github.com/usarawgi911/Uncertainty-aware-boosting

cs.LG↗