arXiv subjects

Rajna Fani

Publications and source records attributed to Rajna Fani.

5 recordsLinked to original sources

arXiv2026

Croissant Baker: Metadata Generation for Discoverable, Governable, and Reusable ML Datasets

Croissant has emerged as the metadata standard for machine learning datasets, providing a structured, JSON-LD-based format that makes dataset discovery, automated ingestion, and reproducible analysis machine-checkable across ML platforms. Adoption has accelerated, and NeurIPS now requires Croissant metadata in every submission to its dataset tracks. Yet in practice Croissant generation usually starts with uploading data to a public platform, a path infeasible for governed and large local repositories that hold much of the high-value data ML increasingly relies on. We release Croissant Baker, a local-first, open-source command-line tool that generates validated Croissant metadata directly from a dataset directory through a modular handler registry. We evaluate Croissant Baker on over 140 datasets, scaling to MIMIC-IV at 886 million rows and 374 Parquet files. On held-out comparisons against producer-authored or standards-derived ground truth, Croissant Baker reaches 97-100% agreement across multiple domains.

cs.LG↗

arXiv2025

Coefficient of Variation Masking: A Volatility-Aware Strategy for EHR Foundation Models

Masked autoencoders (MAEs) are increasingly applied to electronic health records (EHR) for learning general-purpose representations that support diverse clinical tasks. However, existing approaches typically rely on uniform random masking, implicitly assuming all features are equally predictable. In reality, laboratory tests exhibit substantial heterogeneity in volatility: some biomarkers (e.g., sodium) remain stable, while others (e.g., lactate) fluctuate considerably and are more difficult to model. Clinically, volatile biomarkers often signal acute pathophysiology and require more sophisticated modeling to capture their complex temporal patterns. We propose a volatility-aware pretraining strategy, Coefficient of Variation Masking (CV-Masking), that adaptively adjusts masking probabilities according to the intrinsic variability of each feature. Combined with a value-only masking objective aligned with clinical workflows, CV-Masking yields systematic improvements over random and variance-based strategies. Experiments on a large panel of laboratory tests show that CV-Masking enhances reconstruction, improves downstream predictive performance, and accelerates convergence, producing more robust and clinically meaningful EHR representations.

cs.LG↗

arXiv2025

Rethinking Tokenization for Clinical Time Series: When Less is More

Tokenization strategies shape how models process electronic health records, yet fair comparisons of their effectiveness remain limited. We present a systematic evaluation of tokenization approaches for clinical time series modeling using transformer-based architectures, revealing task-dependent and sometimes counterintuitive findings about temporal and value feature importance. Through controlled ablations across four clinical prediction tasks on MIMIC-IV, we demonstrate that explicit time encodings provide no consistent statistically significant benefit for the evaluated downstream tasks. Value features show task-dependent importance, affecting mortality prediction but not readmission, suggesting code sequences alone can carry sufficient predictive signal. We further show that frozen pretrained code encoders dramatically outperform their trainable counterparts while requiring dramatically fewer parameters. Larger clinical encoders provide consistent improvements across tasks, benefiting from frozen embeddings that eliminate computational overhead. Our controlled evaluation enables fairer tokenization comparisons and demonstrates that simpler, parameter-efficient approaches can, in many cases, achieve strong performance, though the optimal tokenization strategy remains task-dependent.

cs.LG↗

arXiv2025

M3: Conversational LLMs Simplify Secure Clinical Data Access, Understanding, and Analysis

Large-scale clinical databases offer opportunities for medical research, but their complexity creates barriers to effective use. The Medical Information Mart for Intensive Care (MIMIC-IV), one of the world's largest open-source electronic health record databases, traditionally requires both SQL proficiency and clinical domain expertise. We introduce M3, a system that enables natural language querying of MIMIC-IV data through the Model Context Protocol. With a single command, M3 retrieves MIMIC-IV from PhysioNet, launches a local SQLite instance or connects to hosted BigQuery, and allows researchers to pose clinical questions in plain English. We evaluated M3 using samples from the EHRSQL 2024 benchmark with two language models. On one hundred answerable questions, the proprietary Claude Sonnet 4 achieved 94% accuracy and the open-weights gpt-oss-20B (deployable locally on consumer hardware) achieved 93%; on a matched sample of one hundred unanswerable questions, where correct behavior is to abstain rather than produce SQL, gpt-oss-20B correctly abstained on 69%. Both models translate natural language into SQL, execute queries against MIMIC-IV, and return structured results alongside the underlying query for verification. Error analysis revealed that most failures stemmed from complex temporal reasoning or ambiguous question phrasing rather than fundamental architectural limitations. The comparable performance of a smaller open-weights model demonstrates that privacy-preserving local deployment is viable for sensitive clinical data analysis. M3 lowers technical barriers to critical care data analysis and is designed with security measures including OAuth2 authentication, query validation, and audit logging.

cs.IR↗

arXiv2024

Towards Optimizing and Evaluating a Retrieval Augmented QA Chatbot using LLMs with Human in the Loop

Large Language Models have found application in various mundane and repetitive tasks including Human Resource (HR) support. We worked with the domain experts of SAP SE to develop an HR support chatbot as an efficient and effective tool for addressing employee inquiries. We inserted a human-in-the-loop in various parts of the development cycles such as dataset collection, prompt optimization, and evaluation of generated output. By enhancing the LLM-driven chatbot's response quality and exploring alternative retrieval methods, we have created an efficient, scalable, and flexible tool for HR professionals to address employee inquiries effectively. Our experiments and evaluation conclude that GPT-4 outperforms other models and can overcome inconsistencies in data through internal reasoning capabilities. Additionally, through expert analysis, we infer that reference-free evaluation metrics such as G-Eval and Prometheus demonstrate reliability closely aligned with that of human evaluation.

cs.CL↗