arXiv subjects

Tanmay Shukla

Publications and source records attributed to Tanmay Shukla.

4 recordsLinked to original sources

arXiv2026

Cross-Modal Contrastive Learning from Histopathology and CT for Automated Renal Cell Carcinoma Grading

Background: Clear cell renal cell carcinoma (ccRCC) exhibits substantial clinical heterogeneity, and accurate grade assessment is essential for risk stratification and treatment planning. However, conventional grading requires invasive tissue sampling. We developed RCC-Align, a cross-modal contrastive learning framework that leverages paired histopathology and computed tomography (CT) data during training to improve noninvasive CT-based ccRCC grade prediction. Methods: RCC-Align aligns paired whole-slide histopathology images (WSIs) and CT scans through contrastive cross-modal objectives, transferring grade-discriminative information from microscopic tissue morphology to macroscopic radiologic representations. The framework was trained and evaluated on paired TCGA and CPTAC cohorts using patient-level five-fold cross-validation. Performance for low- versus high-grade ccRCC classification was compared against CT-only baselines (DINOv2-Base and DINOv2-Finetuned) and a WSI-based reference model (GigaPath-Finetuned). Cross-modal alignment was assessed using cosine similarity analysis. Results: RCC-Align achieved an AUC of 0.601 (95% CI, 0.524-0.673) and AUPRC of 0.599 (95% CI, 0.541-0.676), outperforming DINOv2-Finetuned (AUC 0.545; AUPRC 0.543) with significantly improved low-grade prediction (p = 0.004). RCC-Align also demonstrated stronger paired WSI-CT embedding alignment compared with baselines. The WSI-based GigaPath reference achieved an AUC of 0.719. Conclusion: Pathology-guided contrastive learning improves CT-based ccRCC grading while requiring only CT at inference. This approach may complement tissue diagnosis when biopsy is unsafe, infeasible, or limited by intratumoral heterogeneity. Validation in larger, multi-institutional cohorts with external testing is needed before clinical translation.

cs.CV↗

arXiv2026

HLSFactory-Agent: Large-Scale Agentic HLS Dataset Construction from Academic and Open-Source Projects

Building large, diverse datasets of high-level synthesis (HLS) designs beyond common community benchmarks remains an open challenge. This challenge is made urgent by the rise of deep learning and LLMs for hardware design, which demand such datasets to train QoR models and benchmark LLMs on HLS tasks. Despite ongoing efforts to broaden sources, dataset curation still depends on manual work: locating HLS designs across academic publications and open source, then extracting standalone designs from larger codebases. The process is error-prone and demands expert knowledge, iterative testing, and substantial per-repository engineering. To address this, we present HLSFactory-Agent, an LLM agent that automates large-scale HLS dataset curation by extracting standalone designs from larger codebases. HLSFactory-Agent runs the open-source Pi agent framework inside Docker containers to build and evaluate each extracted design. This turnkey automation allows users to pass a GitHub link or code directory to HLSFactory-Agent and receive a folder of extracted HLS designs ready to be integrated into the HLSFactory dataset framework. Additionally, we provide open-source scripts to scrape and index papers from computer architecture, EDA, and FPGA conferences that possibly implement or use HLS designs, allowing for faster human discovery and curation of HLS designs for HLSFactory-Agent. We report initial results from running HLSFactory-Agent across a small subset of our indexed repositories, demonstrating successful extraction of synthesizable designs from structured codebases. We open source HLSFactory-Agent and indexing scripts at https://github.com/sharc-lab/hlsfactory-agent.

cs.AR↗

arXiv2025

Conversation AI Dialog for Medicare powered by Finetuning and Retrieval Augmented Generation

Large language models (LLMs) have shown impressive capabilities in natural language processing tasks, including dialogue generation. This research aims to conduct a novel comparative analysis of two prominent techniques, fine-tuning with LoRA (Low-Rank Adaptation) and the Retrieval-Augmented Generation (RAG) framework, in the context of doctor-patient chat conversations with multiple datasets of mixed medical domains. The analysis involves three state-of-the-art models: Llama-2, GPT, and the LSTM model. Employing real-world doctor-patient dialogues, we comprehensively evaluate the performance of models, assessing key metrics such as language quality (perplexity, BLEU score), factual accuracy (fact-checking against medical knowledge bases), adherence to medical guidelines, and overall human judgments (coherence, empathy, safety). The findings provide insights into the strengths and limitations of each approach, shedding light on their suitability for healthcare applications. Furthermore, the research investigates the robustness of the models in handling diverse patient queries, ranging from general health inquiries to specific medical conditions. The impact of domain-specific knowledge integration is also explored, highlighting the potential for enhancing LLM performance through targeted data augmentation and retrieval strategies.

cs.CL↗

arXiv2024

Deep Learning for Classification of Inflammatory Bowel Disease Activity in Whole Slide Images of Colonic Histopathology

Grading inflammatory bowel disease (IBD) activity using standardized histopathological scoring systems remains challenging due to resource constraints and inter-observer variability. In this study, we developed a deep learning model to classify activity grades in hematoxylin and eosin-stained whole slide images (WSIs) from patients with IBD, offering a robust approach for general pathologists. We utilized 2,077 WSIs from 636 patients treated at Dartmouth-Hitchcock Medical Center in 2018 and 2019, scanned at 40x magnification (0.25 micron/pixel). Board-certified gastrointestinal pathologists categorized the WSIs into four activity classes: inactive, mildly active, moderately active, and severely active. A transformer-based model was developed and validated using five-fold cross-validation to classify IBD activity. Using HoVerNet, we examined neutrophil distribution across activity grades. Attention maps from our model highlighted areas contributing to its prediction. The model classified IBD activity with weighted averages of 0.871 [95% Confidence Interval (CI): 0.860-0.883] for the area under the curve, 0.695 [95% CI: 0.674-0.715] for precision, 0.697 [95% CI: 0.678-0.716] for recall, and 0.695 [95% CI: 0.674-0.714] for F1-score. Neutrophil distribution was significantly different across activity classes. Qualitative evaluation of attention maps by a gastrointestinal pathologist suggested their potential for improved interpretability. Our model demonstrates robust diagnostic performance and could enhance consistency and efficiency in IBD activity assessment.

cs.CV↗