Sukrit Gupta

Deepank Girish, Yi Hao Chan, Sukrit Gupta et al.

Several brain foundation models (FM) have recently been proposed to predict brain disorders by modelling dynamic functional connectivity (FC). While they demonstrate remarkable model performance and zero- or few-shot generalization, the salient features identified as potential biomarkers are yet to be thoroughly evaluated. We propose RE-CONFIRM, a framework for evaluating the robustness of potential biomarker candidates elucidated by deep learning (DL) models including FMs. From experiments on five large datasets of Autism Spectrum Disorder (ASD), Attention-deficit Hyperactivity Disorder (ADHD), and Alzheimer's Disease (AD), we found that although commonly used performance metrics provide an intuitive assessment of model predictions, they are insufficient for evaluating the robustness of biomarkers identified by these models. RE-CONFIRM metrics revealed that simply finetuning FMs leads to models that fail to capture regional hubs effectively, even in disorders where hubs are known to be implicated, such as ASD and ADHD. In view of this, we propose Hub-LoRA (Low-Rank Adaptation) as a fine-tuning technique that enables FMs to not only outperform customised DL models but also produce neurobiologically faithful biomarkers supported by meta-analyses. RE-CONFIRM is generalizable and can be easily applied to ascertain the robustness of DL models trained on functional MRI datasets. Code is available at: https://github.com/SCSE-Biomedical-Computing-Group/RE-CONFIRM.

Amit Kumar, Maninder Kaur, Raghvendra Mall et al.

Spatial Transcriptomics enables mapping of gene expression within its native tissue context, but current platforms measure only a limited set of genes due to experimental constraints and excessive costs. To overcome this, computational models integrate Single-Cell RNA Sequencing data with Spatial Transcriptomics to predict unmeasured genes. We propose CASPER, a cross-attention based framework that predicts unmeasured gene expression in Spatial Transcriptomics by leveraging centroid-level representations from Single-Cell RNA Sequencing. We performed rigorous testing over four state-of-the-art Spatial Transcriptomics/Single-Cell RNA Sequencing dataset pairs across four existing baseline models. CASPER shows significant improvement in nine out of the twelve metrics for our experiments. This work paves the way for further work in Spatial Transcriptomics to Single-Cell RNA Sequencing modality translation. The code for CASPER is available at https://github.com/AI4Med-Lab/CASPER.

Satya P. Singh, Aimé Lay-Ekuakille, Deepak Gangwar et al.

Decoding human activity accurately from wearable sensors can aid in applications related to healthcare and context awareness. The present approaches in this domain use recurrent and/or convolutional models to capture the spatio-temporal features from time-series data from multiple sensors. We propose a deep neural network architecture that not only captures the spatio-temporal features of multiple sensor time-series data but also selects, learns important time points by utilizing a self-attention mechanism. We show the validity of the proposed approach across different data sampling strategies on six public datasets and demonstrate that the self-attention mechanism gave a significant improvement in performance over deep networks using a combination of recurrent and convolution networks. We also show that the proposed approach gave a statistically significant performance enhancement over previous state-of-the-art methods for the tested datasets. The proposed methods open avenues for better decoding of human activity from multiple body sensors over extended periods of time. The code implementation for the proposed model is available at https://github.com/isukrit/encodingHumanActivity.

Yi Hao Chan, Deepank Girish, Sukrit Gupta et al.

Graph neural networks (GNN) have emerged as a popular tool for modelling functional magnetic resonance imaging (fMRI) datasets. Many recent studies have reported significant improvements in disorder classification performance via more sophisticated GNN designs and highlighted salient features that could be potential biomarkers of the disorder. However, existing methods of evaluating their robustness are often limited to cross-referencing with existing literature, which is a subjective and inconsistent process. In this review, we provide an overview of how GNN and model explainability techniques (specifically, feature attributors) have been applied to fMRI datasets for disorder prediction tasks, with an emphasis on evaluating the robustness of potential biomarkers produced for psychiatric disorders. Then, 65 studies using GNNs that reported potential fMRI biomarkers for psychiatric disorders (attention-deficit hyperactivity disorder, autism spectrum disorder, major depressive disorder, schizophrenia) published before 9 October 2024 were identified from 2 online databases (Scopus, PubMed). We found that while most studies have performant models, salient features highlighted in these studies (as determined by feature attribution scores) vary greatly across studies on the same disorder. Reproducibility of biomarkers is only limited to a small subset at the level of regions and few transdiagnostic biomarkers were identified. To address these issues, we suggest establishing new standards that are based on objective evaluation metrics to determine the robustness of these potential biomarkers. We further highlight gaps in the existing literature and put together a prediction-attribution-evaluation framework that could set the foundations for future research on discovering robust biomarkers of psychiatric disorders via GNNs.

Nishchala Thakur, Swati Kochhar, Deepti R. Bathula et al.

Active learning reduces annotation costs in medical imaging by strategically selecting the most informative samples for labeling. However, individual acquisition strategies often exhibit inconsistent behavior across different stages of the active learning cycle. We propose Cyclical and Performance-Adaptive Multi-Strategy Active Learning (WaveFuse-AL), a novel framework that adaptively fuses multiple established acquisition strategies-BALD, BADGE, Entropy, and CoreSet throughout the learning process. WaveFuse-AL integrates cyclical (sinusoidal) temporal priors with performance-driven adaptation to dynamically adjust strategy importance over time. We evaluate WaveFuse-AL on three medical imaging benchmarks: APTOS-2019 (multi-class classification), RSNA Pneumonia Detection (binary classification), and ISIC-2018 (skin lesion segmentation). Experimental results demonstrate that WaveFuse-AL consistently outperforms both single-strategy and alternating-strategy baselines, achieving statistically significant performance improvements (on ten out of twelve metric measurements) while maximizing the utility of limited annotation budgets.

Devansh Arora, Nitin Kumar, Sukrit Gupta

Image segmentation is an important and widely performed task in computer vision. Accomplishing effective image segmentation in diverse settings often requires custom model architectures and loss functions. A set of models that specialize in segmenting thin tubular structures are topology preservation-based loss functions. These models often utilize a pixel skeletonization process claimed to generate more precise segmentation masks of thin tubes and better capture the structures that other models often miss. One such model, Skeleton Recall Loss (SRL) proposed by Kirchhoff et al.~\cite {kirchhoff2024srl}, was stated to produce state-of-the-art results on benchmark tubular datasets. In this work, we performed a theoretical analysis of the gradients for the SRL loss. Upon comparing the performance of the proposed method on some of the tubular datasets (used in the original work, along with some additional datasets), we found that the performance of SRL-based segmentation models did not exceed traditional baseline models. By providing both a theoretical explanation and empirical evidence, this work critically evaluates the limitations of topology-based loss functions, offering valuable insights for researchers aiming to develop more effective segmentation models for complex tubular structures.

Satya P. Singh, Lipo Wang, Sukrit Gupta et al.

The rapid advancements in machine learning, graphics processing technologies and the availability of medical imaging data have led to a rapid increase in the use of deep learning models in the medical domain. This was exacerbated by the rapid advancements in convolutional neural network (CNN) based architectures, which were adopted by the medical imaging community to assist clinicians in disease diagnosis. Since the grand success of AlexNet in 2012, CNNs have been increasingly used in medical image analysis to improve the efficiency of human clinicians. In recent years, three-dimensional (3D) CNNs have been employed for the analysis of medical images. In this paper, we trace the history of how the 3D CNN was developed from its machine learning roots, we provide a brief mathematical description of 3D CNN and provide the preprocessing steps required for medical images before feeding them to 3D CNNs. We review the significant research in the field of 3D medical imaging analysis using 3D CNNs (and its variants) in different medical areas such as classification, segmentation, detection and localization. We conclude by discussing the challenges associated with the use of 3D CNNs in the medical imaging domain (and the use of deep learning models in general) and possible future trends in the field.