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Researcher profile

Subhashini Venugopalan

Subhashini Venugopalan contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer VisionMachine Learningeess.IVComputation and LanguageNeural and Evolutionary ComputingQuantitative Methods

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Published work

8 published item(s)

preprint2026arXiv

MAgSeg: Segmentation of Agricultural Landscapes in High-Resolution Satellite Imagery using Multimodal Large Language Models

Agricultural landscape segmentation in the Global South is challenging as it is characterized by fragmented plots, high intra-class variance, and a scarcity of labeled training data. Recent advances in segmentation have been made by Multimodal Large Language Models (MLLMs). However, current approaches encounter critical context length bottlenecks and a domain alignment gap in understanding satellite features. We address these limitations through MAgSeg, a novel, decoder-free MLLM segmentation approach. MAgSeg is an architecturally efficient approach that enables standard MLLMs to perform segmentation of complex smallholder agricultural landscapes from high-resolution satellite imagery, without requiring auxiliary vision decoders. We introduce a novel instruction tuning data format designed to enable scalable fine-tuning and post-training on high resolution satellite imagery, which enables MAgSeg to learn from the global context of the image while generating text tokens for only a patch within the image. Extensive evaluations on datasets spanning three countries in the Global South demonstrate that MAgSeg significantly outperforms state-of-the-art MLLM baselines, offering a scalable solution to map smallholder agricultural environments.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Context-Aware Abbreviation Expansion Using Large Language Models

Motivated by the need for accelerating text entry in augmentative and alternative communication (AAC) for people with severe motor impairments, we propose a paradigm in which phrases are abbreviated aggressively as primarily word-initial letters. Our approach is to expand the abbreviations into full-phrase options by leveraging conversation context with the power of pretrained large language models (LLMs). Through zero-shot, few-shot, and fine-tuning experiments on four public conversation datasets, we show that for replies to the initial turn of a dialog, an LLM with 64B parameters is able to exactly expand over 70% of phrases with abbreviation length up to 10, leading to an effective keystroke saving rate of up to about 77% on these exact expansions. Including a small amount of context in the form of a single conversation turn more than doubles abbreviation expansion accuracies compared to having no context, an effect that is more pronounced for longer phrases. Additionally, the robustness of models against typo noise can be enhanced through fine-tuning on noisy data.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Attribution in Scale and Space

We study the attribution problem [28] for deep networks applied to perception tasks. For vision tasks, attribution techniques attribute the prediction of a network to the pixels of the input image. We propose a new technique called \emph{Blur Integrated Gradients}. This technique has several advantages over other methods. First, it can tell at what scale a network recognizes an object. It produces scores in the scale/frequency dimension, that we find captures interesting phenomena. Second, it satisfies the scale-space axioms [14], which imply that it employs perturbations that are free of artifact. We therefore produce explanations that are cleaner and consistent with the operation of deep networks. Third, it eliminates the need for a 'baseline' parameter for Integrated Gradients [31] for perception tasks. This is desirable because the choice of baseline has a significant effect on the explanations. We compare the proposed technique against previous techniques and demonstrate application on three tasks: ImageNet object recognition, Diabetic Retinopathy prediction, and AudioSet audio event identification.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

It's easy to fool yourself: Case studies on identifying bias and confounding in bio-medical datasets

Confounding variables are a well known source of nuisance in biomedical studies. They present an even greater challenge when we combine them with black-box machine learning techniques that operate on raw data. This work presents two case studies. In one, we discovered biases arising from systematic errors in the data generation process. In the other, we found a spurious source of signal unrelated to the prediction task at hand. In both cases, our prediction models performed well but under careful examination hidden confounders and biases were revealed. These are cautionary tales on the limits of using machine learning techniques on raw data from scientific experiments.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Predicting Risk of Developing Diabetic Retinopathy using Deep Learning

Diabetic retinopathy (DR) screening is instrumental in preventing blindness, but faces a scaling challenge as the number of diabetic patients rises. Risk stratification for the development of DR may help optimize screening intervals to reduce costs while improving vision-related outcomes. We created and validated two versions of a deep learning system (DLS) to predict the development of mild-or-worse (&#34;Mild+&#34;) DR in diabetic patients undergoing DR screening. The two versions used either three-fields or a single field of color fundus photographs (CFPs) as input. The training set was derived from 575,431 eyes, of which 28,899 had known 2-year outcome, and the remaining were used to augment the training process via multi-task learning. Validation was performed on both an internal validation set (set A; 7,976 eyes; 3,678 with known outcome) and an external validation set (set B; 4,762 eyes; 2,345 with known outcome). For predicting 2-year development of DR, the 3-field DLS had an area under the receiver operating characteristic curve (AUC) of 0.79 (95%CI, 0.78-0.81) on validation set A. On validation set B (which contained only a single field), the 1-field DLS&#39;s AUC was 0.70 (95%CI, 0.67-0.74). The DLS was prognostic even after adjusting for available risk factors (p<0.001). When added to the risk factors, the 3-field DLS improved the AUC from 0.72 (95%CI, 0.68-0.76) to 0.81 (95%CI, 0.77-0.84) in validation set A, and the 1-field DLS improved the AUC from 0.62 (95%CI, 0.58-0.66) to 0.71 (95%CI, 0.68-0.75) in validation set B. The DLSs in this study identified prognostic information for DR development from CFPs. This information is independent of and more informative than the available risk factors.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Scientific Discovery by Generating Counterfactuals using Image Translation

Model explanation techniques play a critical role in understanding the source of a model&#39;s performance and making its decisions transparent. Here we investigate if explanation techniques can also be used as a mechanism for scientific discovery. We make three contributions: first, we propose a framework to convert predictions from explanation techniques to a mechanism of discovery. Second, we show how generative models in combination with black-box predictors can be used to generate hypotheses (without human priors) that can be critically examined. Third, with these techniques we study classification models for retinal images predicting Diabetic Macular Edema (DME), where recent work showed that a CNN trained on these images is likely learning novel features in the image. We demonstrate that the proposed framework is able to explain the underlying scientific mechanism, thus bridging the gap between the model&#39;s performance and human understanding.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Predicting optical coherence tomography-derived diabetic macular edema grades from fundus photographs using deep learning

Diabetic eye disease is one of the fastest growing causes of preventable blindness. With the advent of anti-VEGF (vascular endothelial growth factor) therapies, it has become increasingly important to detect center-involved diabetic macular edema (ci-DME). However, center-involved diabetic macular edema is diagnosed using optical coherence tomography (OCT), which is not generally available at screening sites because of cost and workflow constraints. Instead, screening programs rely on the detection of hard exudates in color fundus photographs as a proxy for DME, often resulting in high false positive or false negative calls. To improve the accuracy of DME screening, we trained a deep learning model to use color fundus photographs to predict ci-DME. Our model had an ROC-AUC of 0.89 (95% CI: 0.87-0.91), which corresponds to a sensitivity of 85% at a specificity of 80%. In comparison, three retinal specialists had similar sensitivities (82-85%), but only half the specificity (45-50%, p<0.001 for each comparison with model). The positive predictive value (PPV) of the model was 61% (95% CI: 56-66%), approximately double the 36-38% by the retinal specialists. In addition to predicting ci-DME, our model was able to detect the presence of intraretinal fluid with an AUC of 0.81 (95% CI: 0.81-0.86) and subretinal fluid with an AUC of 0.88 (95% CI: 0.85-0.91). The ability of deep learning algorithms to make clinically relevant predictions that generally require sophisticated 3D-imaging equipment from simple 2D images has broad relevance to many other applications in medical imaging.

0 citations0 reviewsNo code linkedOpen access
preprint2017arXiv

Detecting Cancer Metastases on Gigapixel Pathology Images

Each year, the treatment decisions for more than 230,000 breast cancer patients in the U.S. hinge on whether the cancer has metastasized away from the breast. Metastasis detection is currently performed by pathologists reviewing large expanses of biological tissues. This process is labor intensive and error-prone. We present a framework to automatically detect and localize tumors as small as 100 x 100 pixels in gigapixel microscopy images sized 100,000 x 100,000 pixels. Our method leverages a convolutional neural network (CNN) architecture and obtains state-of-the-art results on the Camelyon16 dataset in the challenging lesion-level tumor detection task. At 8 false positives per image, we detect 92.4% of the tumors, relative to 82.7% by the previous best automated approach. For comparison, a human pathologist attempting exhaustive search achieved 73.2% sensitivity. We achieve image-level AUC scores above 97% on both the Camelyon16 test set and an independent set of 110 slides. In addition, we discover that two slides in the Camelyon16 training set were erroneously labeled normal. Our approach could considerably reduce false negative rates in metastasis detection.

0 citations0 reviewsNo code linkedOpen access