arXiv subjects

Pratik Shah

Publications and source records attributed to Pratik Shah.

15 recordsLinked to original sources

arXiv2026

Deep Learning for Generating Computational PIN-4 Immunohistochemistry Staining from Prostate Biopsy H&E Images

Immunohistochemistry (IHC)is frequently used to resolve diagnostically ambiguous prostate cancer biopsy findings on hematoxylin and eosin (H&E)-stained tissue. However, PIN-4 IHC staining is typically performed on adjacent tissue sections, limiting direct spatial comparison between the H&E morphology and the corresponding immunophenotypic signal. A paired, registered H&E/PIN-4 dataset was constructed from routine clinical prostate biopsy whole-slide images (WSIs), and a conditional generative adversarial network (cGAN) was trained to synthesize PIN-4 staining patterns directly from native H&E image patches. The final dataset comprised 172 paired WSIs from 93 patients and 27,298 registered 1024x1024 patch pairs, spanning adenocarcinoma-positive and benign cases with representation across age, race, and ethnicity groups. The model was evaluated on a held-out test set of 1,814 patch pairs from 17 WSIs, achieving a mean peak signal-to-noise ratio (PSNR) of 21.88 dB, structural similarity index measure (SSIM) of 0.667, Pearson correlation coefficient (PCC) of 0.684, and learned perceptual image patch similarity (LPIPS) of 0.417. Qualitative review by a board-certified pathologist showed that generated images captured diagnostically relevant PIN-4 staining patterns, including AMACR/racemase expression and basal-cell-associated staining, while preserving spatial correspondence with the source H&E morphology. Accuracy of synthesis varied across morphologically complex regions, including high-grade carcinoma and intraductal carcinoma. These results support the feasibility of supervised PIN-4 synthesis from routinely acquired brightfield H&E prostate biopsy images. The approach enables direct interpretation of predicted PIN-4 marker patterns in the context of the source prostate H&E architecture, addressing a current spatial limitation of conventional adjacent-section IHC.

cs.CV↗

arXiv2026

Generative Deep Learning for Computational Destaining and Restaining of Unregistered Digital Pathology Images

Conditional generative adversarial networks (cGANs) have enabled high-fidelity computational staining and destaining of hematoxylin and eosin (H&E) in digital pathology whole-slide images (WSI). However, their ability to generalize to out-of-distribution WSI across institutions without retraining remains insufficiently characterized. Previously developed cGAN models trained on 102 registered prostate core biopsy WSIs from Brigham and Women's Hospital were evaluated on 82 spatially unregistered WSIs acquired at Stanford University. To mitigate domain shift without retraining, a preprocessing pipeline consisting of histogram-based stain normalization for H&E-stained WSIs and channel-wise intensity calibration for unstained WSIs was developed. Because image registration was intentionally omitted for real-world deployment conditions, the reported quantitative results are conservative lower bounds reflecting both model performance and limited spatial alignment. Under these conditions, virtual destaining achieved a Pearson correlation coefficient (PCC) of 0.854, structural similarity index measure (SSIM) of 0.699, and peak signal-to-noise ratio (PSNR) of 18.41 dB. H&E restaining from computationally destained outputs outperformed direct staining from ground-truth unstained inputs across all metrics (PCC: 0.798 vs. 0.715; SSIM: 0.756 vs. 0.718; PSNR: 20.08 vs. 18.51 dB), suggesting that preprocessing quality may be more limiting than model capacity. Qualitative pathological review indicated preservation of benign glandular structures while showing that malignant glands were often rendered with vessel-like morphologies. These findings support the feasibility of applying cGAN-based computational H&E staining and destaining generative models to external WSI datasets using preprocessing-based adaptation alone while defining specific morphological targets for future domain adaptation.

cs.CV↗

arXiv2025

RANGER -- Repository-Level Agent for Graph-Enhanced Retrieval

General-purpose automated software engineering (ASE) includes tasks such as code completion, retrieval, repair, QA, and summarization. These tasks require a code retrieval system that can handle specific queries about code entities, or code entity queries (for example, locating a specific class or retrieving the dependencies of a function), as well as general queries without explicit code entities, or natural language queries (for example, describing a task and retrieving the corresponding code). We present RANGER, a repository-level code retrieval agent designed to address both query types, filling a gap in recent works that have focused primarily on code-entity queries. We first present a tool that constructs a comprehensive knowledge graph of the entire repository, capturing hierarchical and cross-file dependencies down to the variable level, and augments graph nodes with textual descriptions and embeddings to bridge the gap between code and natural language. RANGER then operates on this graph through a dual-stage retrieval pipeline. Entity-based queries are answered through fast Cypher lookups, while natural language queries are handled by MCTS-guided graph exploration. We evaluate RANGER across four diverse benchmarks that represent core ASE tasks including code search, question answering, cross-file dependency retrieval, and repository-level code completion. On CodeSearchNet and RepoQA it outperforms retrieval baselines that use embeddings from strong models such as Qwen3-8B. On RepoBench, it achieves superior cross-file dependency retrieval over baselines, and on CrossCodeEval, pairing RANGER with BM25 delivers the highest exact match rate in code completion compared to other RAG methods.

cs.SE↗

arXiv2024

Uncertainty Quantified Deep Learning and Regression Analysis Framework for Image Segmentation of Skin Cancer Lesions

Deep learning models (DLMs) frequently achieve accurate segmentation and classification of tumors from medical images. However, DLMs lacking feedback on their image segmentation mechanisms, such as Dice coefficients and confidence in their performance, face challenges when processing previously unseen images in real-world clinical settings. Uncertainty estimates to identify DLM predictions at the cellular or single-pixel level that require clinician review can enhance trust. However, their deployment requires significant computational resources. This study reports two DLMs, one trained from scratch and another based on transfer learning, with Monte Carlo dropout or Bayes-by-backprop uncertainty estimations to segment lesions from the publicly available The International Skin Imaging Collaboration-19 dermoscopy image database with cancerous lesions. A novel approach to compute pixel-by-pixel uncertainty estimations of DLM segmentation performance in multiple clinical regions from a single dermoscopy image with corresponding Dice scores is reported for the first time. Image-level uncertainty maps demonstrated correspondence between imperfect DLM segmentation and high uncertainty levels in specific skin tissue regions, with or without lesions. Four new linear regression models that can predict the Dice performance of DLM segmentation using constants and uncertainty measures, either individually or in combination from lesions, tissue structures, and non-tissue pixel regions critical for clinical diagnosis and prognostication in skin images (Spearman's correlation, p < 0.05), are reported for the first time for low-compute uncertainty estimation workflows.

eess.IV↗

arXiv2024

Deep Learning with Uncertainty Quantification for Predicting the Segmentation Dice Coefficient of Prostate Cancer Biopsy Images

Deep learning models (DLMs) can achieve state-of-the-art performance in histopathology image segmentation and classification, but have limited deployment potential in real-world clinical settings. Uncertainty estimates of DLMs can increase trust by identifying predictions and images that need further review. Dice scores and coefficients (Dice) are benchmarks for evaluation of image segmentation performance, but are usually not evaluated with DLM uncertainty quantification. This study reports DLMs trained with uncertainty estimations, using randomly initialized weights and Monte Carlo dropout, to segment tumors from microscopic Hematoxylin and Eosin dye stained prostate core biopsy histology RGB images. Image-level maps showed significant correlation (Spearman's rank, p < 0.05) between overall and specific prostate tissue image sub-region uncertainties with model performance estimations by Dice. This study reports that linear models, which can predict Dice segmentation scores from multiple clinical sub-region-based uncertainties of prostate cancer, can serve as a more comprehensive performance evaluation metric without loss in predictive capability of DLMs, with a low root mean square error.

eess.IV↗

arXiv2024

Lagrangian Index Policy for Restless Bandits with Average Reward

We study the Lagrangian Index Policy (LIP) for restless multi-armed bandits with long-run average reward. In particular, we compare the performance of LIP with the performance of the Whittle Index Policy (WIP), both heuristic policies known to be asymptotically optimal under certain natural conditions. Even though in most cases their performances are very similar, in the cases when WIP shows bad performance, LIP continues to perform very well. We then propose reinforcement learning algorithms, both tabular and NN-based, to obtain online learning schemes for LIP in the model-free setting. The proposed reinforcement learning schemes for LIP require significantly less memory than the analogous schemes for WIP. We calculate analytically the Lagrangian index for the restart model, which applies to the optimal web crawling and the minimization of the weighted age of information. We also give a new proof of asymptotic optimality in case of homogeneous arms as the number of arms goes to infinity, based on exchangeability and de Finetti's theorem.

cs.LG↗

arXiv2024

Reinforcement Learning in Non-Markovian Environments

Motivated by the novel paradigm developed by Van Roy and coauthors for reinforcement learning in arbitrary non-Markovian environments, we propose a related formulation and explicitly pin down the error caused by non-Markovianity of observations when the Q-learning algorithm is applied on this formulation. Based on this observation, we propose that the criterion for agent design should be to seek good approximations for certain conditional laws. Inspired by classical stochastic control, we show that our problem reduces to that of recursive computation of approximate sufficient statistics. This leads to an autoencoder-based scheme for agent design which is then numerically tested on partially observed reinforcement learning environments.

eess.SY↗

arXiv2023

Responsible Deep Learning for Software as a Medical Device

Tools, models and statistical methods for signal processing and medical image analysis and training deep learning models to create research prototypes for eventual clinical applications are of special interest to the biomedical imaging community. But material and optical properties of biological tissues are complex and not easily captured by imaging devices. Added complexity can be introduced by datasets with underrepresentation of medical images from races and ethnicities for deep learning, and limited knowledge about the regulatory framework needed for commercialization and safety of emerging Artificial Intelligence (AI) and Machine Learning (ML) technologies for medical image analysis. This extended version of the workshop paper presented at the special session of the 2022 IEEE 19th International Symposium on Biomedical Imaging, describes strategy and opportunities by University of California professors engaged in machine learning (section I) and clinical research (section II), the Office of Science and Engineering Laboratories (OSEL) section III, and officials at the US FDA in Center for Devices & Radiological Health (CDRH) section IV. Performance evaluations of AI/ML models of skin (RGB), tissue biopsy (digital pathology), and lungs and kidneys (Magnetic Resonance, X-ray, Computed Tomography) medical images for regulatory evaluations and real-world deployment are discussed.

eess.IV↗

arXiv2020

Interpretable and synergistic deep learning for visual explanation and statistical estimations of segmentation of disease features from medical images

Deep learning (DL) models for disease classification or segmentation from medical images are increasingly trained using transfer learning (TL) from unrelated natural world images. However, shortcomings and utility of TL for specialized tasks in the medical imaging domain remain unknown and are based on assumptions that increasing training data will improve performance. We report detailed comparisons, rigorous statistical analysis and comparisons of widely used DL architecture for binary segmentation after TL with ImageNet initialization (TII-models) with supervised learning with only medical images(LMI-models) of macroscopic optical skin cancer, microscopic prostate core biopsy and Computed Tomography (CT) DICOM images. Through visual inspection of TII and LMI model outputs and their Grad-CAM counterparts, our results identify several counter intuitive scenarios where automated segmentation of one tumor by both models or the use of individual segmentation output masks in various combinations from individual models leads to 10% increase in performance. We also report sophisticated ensemble DL strategies for achieving clinical grade medical image segmentation and model explanations under low data regimes. For example; estimating performance, explanations and replicability of LMI and TII models described by us can be used for situations in which sparsity promotes better learning. A free GitHub repository of TII and LMI models, code and more than 10,000 medical images and their Grad-CAM output from this study can be used as starting points for advanced computational medicine and DL research for biomedical discovery and applications.

stat.ML↗

arXiv2019

High Accuracy Tumor Diagnoses and Benchmarking of Hematoxylin and Eosin Stained Prostate Core Biopsy Images Generated by Explainable Deep Neural Networks

Histopathological diagnoses of tumors in tissue biopsy after Hematoxylin and Eosin (H&E) staining is the gold standard for oncology care. H&E staining is slow and uses dyes, reagents and precious tissue samples that cannot be reused. Thousands of native nonstained RGB Whole Slide Image (RWSI) patches of prostate core tissue biopsies were registered with their H&E stained versions. Conditional Generative Adversarial Neural Networks (cGANs) that automate conversion of native nonstained RWSI to computational H&E stained images were then trained. High similarities between computational and H&E dye stained images with Structural Similarity Index (SSIM) 0.902, Pearsons Correlation Coefficient (CC) 0.962 and Peak Signal to Noise Ratio (PSNR) 22.821 dB were calculated. A second cGAN performed accurate computational destaining of H&E dye stained images back to their native nonstained form with SSIM 0.9, CC 0.963 and PSNR 25.646 dB. A single-blind study computed more than 95% pixel-by-pixel overlap between prostate tumor annotations on computationally stained images, provided by five-board certified MD pathologists, with those on H&E dye stained counterparts. We report the first visualization and explanation of neural network kernel activation maps during H&E staining and destaining of RGB images by cGANs. High similarities between kernel activation maps of computational and H&E stained images (Mean-Squared Errors <0.0005) provide additional mathematical and mechanistic validation of the staining system. Our neural network framework thus is automated, explainable and performs high precision H&E staining and destaining of low cost native RGB images, and is computer vision and physician authenticated for rapid and accurate tumor diagnoses.

q-bio.QM↗

arXiv2019

Machine Learning Algorithms for Classification of Microcirculation Images from Septic and Non-Septic Patients

Sepsis is a life-threatening disease and one of the major causes of death in hospitals. Imaging of microcirculatory dysfunction is a promising approach for automated diagnosis of sepsis. We report a machine learning classifier capable of distinguishing non-septic and septic images from dark field microcirculation videos of patients. The classifier achieves an accuracy of 89.45%. The area under the receiver operating characteristics of the classifier was 0.92, the precision was 0.92 and the recall was 0.84. Codes representing the learned feature space of trained classifier were visualized using t-SNE embedding and were separable and distinguished between images from critically ill and non-septic patients. Using an unsupervised convolutional autoencoder, independent of the clinical diagnosis, we also report clustering of learned features from a compressed representation associated with healthy images and those with microcirculatory dysfunction. The feature space used by our trained classifier to distinguish between images from septic and non-septic patients has potential diagnostic application.

cs.CV↗

arXiv2019

Computational Histological Staining and Destaining of Prostate Core Biopsy RGB Images with Generative Adversarial Neural Networks

Histopathology tissue samples are widely available in two states: paraffin-embedded unstained and non-paraffin-embedded stained whole slide RGB images (WSRI). Hematoxylin and eosin stain (H&E) is one of the principal stains in histology but suffers from several shortcomings related to tissue preparation, staining protocols, slowness and human error. We report two novel approaches for training machine learning models for the computational H&E staining and destaining of prostate core biopsy RGB images. The staining model uses a conditional generative adversarial network that learns hierarchical non-linear mappings between whole slide RGB image (WSRI) pairs of prostate core biopsy before and after H&E staining. The trained staining model can then generate computationally H&E-stained prostate core WSRIs using previously unseen non-stained biopsy images as input. The destaining model, by learning mappings between an H&E stained WSRI and a non-stained WSRI of the same biopsy, can computationally destain previously unseen H&E-stained images. Structural and anatomical details of prostate tissue and colors, shapes, geometries, locations of nuclei, stroma, vessels, glands and other cellular components were generated by both models with structural similarity indices of 0.68 (staining) and 0.84 (destaining). The proposed staining and destaining models can engender computational H&E staining and destaining of WSRI biopsies without additional equipment and devices.

cs.CV↗

arXiv2018

Automated Process Incorporating Machine Learning Segmentation and Correlation of Oral Diseases with Systemic Health

Imaging fluorescent disease biomarkers in tissues and skin is a non-invasive method to screen for health conditions. We report an automated process that combines intraoral fluorescent porphyrin biomarker imaging, clinical examinations and machine learning for correlation of systemic health conditions with periodontal disease. 1215 intraoral fluorescent images, from 284 consenting adults aged 18-90, were analyzed using a machine learning classifier that can segment periodontal inflammation. The classifier achieved an AUC of 0.677 with precision and recall of 0.271 and 0.429, respectively, indicating a learned association between disease signatures in collected images. Periodontal diseases were more prevalent among males (p=0.0012) and older subjects (p=0.0224) in the screened population. Physicians independently examined the collected images, assigning localized modified gingival indices (MGIs). MGIs and periodontal disease were then cross-correlated with responses to a medical history questionnaire, blood pressure and body mass index measurements, and optic nerve, tympanic membrane, neurological, and cardiac rhythm imaging examinations. Gingivitis and early periodontal disease were associated with subjects diagnosed with optic nerve abnormalities (p <0.0001) in their retinal scans. We also report significant co-occurrences of periodontal disease in subjects reporting swollen joints (p=0.0422) and a family history of eye disease (p=0.0337). These results indicate cross-correlation of poor periodontal health with systemic health outcomes and stress the importance of oral health screenings at the primary care level. Our screening process and analysis method, using images and machine learning, can be generalized for automated diagnoses and systemic health screenings for other diseases.

cs.LG↗

arXiv2013

Nyquist Filter Design using POCS Methods: Including Constraints in Design

The problem of constrained finite impulse response (FIR) filter design is central to signal processing and arises in a variety of disciplines. This paper surveys the design of such filters using Projection onto convex sets (POCS) and discusses certain commonly encountered time and frequency domain constraints. We study in particular the design of Nyquist filters and propose a simple extension to the work carried out by Haddad, Stark, and Galatsanos in [1]. The flexibility and the ease that this design method provides in terms of accommodating constraints is one of its outstanding features.

cs.IT↗

arXiv2010

Curve Reconstruction in Riemannian Manifolds: Ordering Motion Frames

In this article we extend the computational geometric curve reconstruction approach to curves in Riemannian manifolds. We prove that the minimal spanning tree, given a sufficiently dense sample, correctly reconstructs the smooth arcs and further closed and simple curves in Riemannian manifolds. The proof is based on the behaviour of the curve segment inside the tubular neighbourhood of the curve. To take care of the local topological changes of the manifold, the tubular neighbourhood is constructed in consideration with the injectivity radius of the underlying Riemannian manifold. We also present examples of successfully reconstructed curves and show an applications of curve reconstruction to ordering motion frames.

cs.CG↗