arXiv subjects

Alexander W. Charney

Publications and source records attributed to Alexander W. Charney.

7 recordsLinked to original sources

arXiv2026

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures

Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature". While effective at capturing local syntax, these generative paradigms prioritize token-level reconstruction over high-level functional context. We introduce JEPA-DNA, a model-agnostic continual training framework that integrates a Joint-Embedding Predictive Architecture (JEPA) with traditional generative objectives. By supervising global sequence embeddings in a latent space, JEPA-DNA forces models to predict the functional representations of masked genomic segments, shifting the learning signal from token recovery to semantic alignment. We evaluate JEPA-DNA on 17 diverse genomic benchmark tasks, demonstrating consistent gains in linear probing and zero-shot performance regardless of the underlying GFM architecture or generative objective. Our framework establishes a new state-of-the-art for GFMs, surpassing the best existing models by bridging generative precision with latent semantic grounding. Through extensive ablation studies, we further characterize the synergistic interplay between generative and latent objectives. Our code is publicly available at https://github.com/NVIDIA-Digital-Bio/JEPA-DNA.

cs.AI↗

arXiv2026

Bias Detection in Emergency Psychiatry: Linking Negative Language to Diagnostic Disparities

The emergency department (ED) is a high stress environment with increased risk of clinician bias exposure. In the United States, Black patients are more likely than other racial/ethnic groups to obtain their first schizophrenia (SCZ) diagnosis in the ED, a highly stigmatizing disorder. Therefore, understanding the link between clinician bias exposure and psychiatric outcomes is critical for promoting nondiscriminatory decision-making in the ED. This study examines the association between clinician bias exposure and psychiatric diagnosis using a sample of patients with anxiety, bipolar, depression, trauma, and SCZ diagnoses (N=29,005) from a diverse, large medical center. Clinician bias exposure was quantified as the ratio of negative to total number of sentences in psychiatric notes, labeled using a large language model (Mistral). We utilized logistic regression to predict SCZ diagnosis when controlling for patient demographics, risk factors, and negative sentence ratio (NSR). A high NSR significantly increased one's odds of obtaining a SCZ diagnosis and attenuated the effects of patient race. Black male patients with high NSR had the highest odds of being diagnosed with SCZ. Our findings suggest sentiment-based metrics can operationalize clinician bias exposure with real world data and reveal disparities beyond race or ethnicity.

q-bio.OT↗

arXiv2026

Fine-Tune, Don't Prompt, Your Language Model to Identify Biased Language in Clinical Notes

Clinical documentation can contain emotionally charged language with stigmatizing or privileging valences. We present a framework for detecting and classifying such language as stigmatizing, privileging, or neutral. We constructed a curated lexicon of biased terms scored for emotional valence. We then used lexicon-based matching to extract text chunks from OB-GYN delivery notes (Mount Sinai Hospital, NY) and MIMIC-IV discharge summaries across multiple specialties. Three clinicians annotated all chunks, enabling characterization of valence patterns across specialties and healthcare systems. We benchmarked multiple classification strategies (zero-shot prompting, in-context learning, and supervised fine-tuning) across encoder-only models (GatorTron) and generative large language models (Llama). Fine-tuning with lexically primed inputs consistently outperformed prompting approaches. GatorTron achieved an F1 score of 0.96 on the OB-GYN test set, outperforming larger generative models while requiring minimal prompt engineering and fewer computational resources. External validation on MIMIC-IV revealed limited cross-domain generalizability (F1 < 0.70, 44% drop). Training on the broader MIMIC-IV dataset improved generalizability when testing on OB-GYN (F1 = 0.71, 11% drop), but at the cost of reduced precision. Our findings demonstrate that fine-tuning outperforms prompting for emotional valence classification and that models must be adapted to specific medical specialties to achieve clinically appropriate performance. The same terms can carry different emotional valences across specialties: words with clinical meaning in one context may be stigmatizing in another. For bias detection, where misclassification risks undermining clinician trust or perpetuating patient harm, specialty-specific fine-tuning is essential to capture these semantic shifts. * Equal contribution.

cs.CL↗

arXiv2025

The Point of View of a Sentiment: Towards Clinician Bias Detection in Psychiatric Notes

Negative patient descriptions and stigmatizing language can contribute to generating healthcare disparities in two ways: (1) read by patients, they can harm their trust and engagement with the medical center; (2) read by physicians, they may negatively influence their perspective of a future patient. In psychiatry, the patient-clinician therapeutic alliance is a major determinant of clinical outcomes. Therefore, language usage in psychiatric clinical notes may not only create healthcare disparities, but also perpetuate them. Recent advances in NLP systems have facilitated the efforts to detect discriminatory language in healthcare. However, such attempts have only focused on the perspectives of the medical center and its physicians. Considering both physicians and non-physicians' point of view is a more translatable approach to identifying potentially harmful language in clinical notes. By leveraging pre-trained and large language models (PLMs and LLMs), this work aims to characterize potentially harmful language usage in psychiatric notes by identifying the sentiment expressed in sentences describing patients based on the reader's point of view. Extracting 39 sentences from the Mount Sinai Health System containing psychiatric lexicon, we fine-tuned three PLMs (RoBERTa, GatorTron, and GatorTron + Task Adaptation) and implemented zero-shot and few-shot ICL approaches for three LLMs (GPT-3.5, Llama-3.1, and Mistral) to classify the sentiment of the sentences according to the physician or non-physician point of view. Results showed that GPT-3.5 aligned best to physician point of view and Mistral aligned best to non-physician point of view. These results underline the importance of recognizing the reader's point of view, not only for improving the note writing process, but also for the quantification, identification, and reduction of bias in computational systems for downstream analyses.

cs.CL↗

arXiv2024

Fair Machine Learning for Healthcare Requires Recognizing the Intersectionality of Sociodemographic Factors, a Case Study

As interest in implementing artificial intelligence (AI) in medical systems grows, discussion continues on how to evaluate the fairness of these systems, or the disparities they may perpetuate. Socioeconomic status (SES) is commonly included in machine learning models to control for health inequities, with the underlying assumption that increased SES is associated with better health. In this work, we considered a large cohort of patients from the Mount Sinai Health System in New York City to investigate the effect of patient SES, race, and sex on schizophrenia (SCZ) diagnosis rates via a logistic regression model. Within an intersectional framework, patient SES, race, and sex were found to have significant interactions. Our findings showed that increased SES is associated with a higher probability of obtaining a SCZ diagnosis in Black Americans ($β=4.1\times10^{-8}$, $SE=4.5\times10^{-9}$, $p < 0.001$). Whereas high SES acts as a protective factor for SCZ diagnosis in White Americans ($β=-4.1\times10^{-8}$, $SE=6.7\times10^{-9}$, $p < 0.001$). Further investigation is needed to reliably explain and quantify health disparities. Nevertheless, we advocate that building fair AI tools for the health care space requires recognizing the intersectionality of sociodemographic factors.

cs.CY↗

arXiv2024

Extracting Social Support and Social Isolation Information from Clinical Psychiatry Notes: Comparing a Rule-based NLP System and a Large Language Model

Background: Social support (SS) and social isolation (SI) are social determinants of health (SDOH) associated with psychiatric outcomes. In electronic health records (EHRs), individual-level SS/SI is typically documented as narrative clinical notes rather than structured coded data. Natural language processing (NLP) algorithms can automate the otherwise labor-intensive process of data extraction. Data and Methods: Psychiatric encounter notes from Mount Sinai Health System (MSHS, n=300) and Weill Cornell Medicine (WCM, n=225) were annotated and established a gold standard corpus. A rule-based system (RBS) involving lexicons and a large language model (LLM) using FLAN-T5-XL were developed to identify mentions of SS and SI and their subcategories (e.g., social network, instrumental support, and loneliness). Results: For extracting SS/SI, the RBS obtained higher macro-averaged f-scores than the LLM at both MSHS (0.89 vs. 0.65) and WCM (0.85 vs. 0.82). For extracting subcategories, the RBS also outperformed the LLM at both MSHS (0.90 vs. 0.62) and WCM (0.82 vs. 0.81). Discussion and Conclusion: Unexpectedly, the RBS outperformed the LLMs across all metrics. Intensive review demonstrates that this finding is due to the divergent approach taken by the RBS and LLM. The RBS were designed and refined to follow the same specific rules as the gold standard annotations. Conversely, the LLM were more inclusive with categorization and conformed to common English-language understanding. Both approaches offer advantages and are made available open-source for future testing.

cs.CL↗

arXiv2023

Clinical Text Deduplication Practices for Efficient Pretraining and Improved Clinical Tasks

Despite being a unique source of information on patients' status and disease progression, clinical notes are characterized by high levels of duplication and information redundancy. In general domain text, it has been shown that deduplication does not harm language model (LM) pretraining, thus helping reduce the training cost. Although large LMs have proven to learn medical knowledge, they still require specialized domain adaptation for improved downstream clinical tasks. By leveraging large real-world clinical corpora, we first provided a fine-grained characterization of duplicates stemming from common writing practices and clinical relevancy. Second, we demonstrated that deduplicating clinical text can help clinical LMs encode less redundant information in a more efficient manner and do not harm classification tasks via prompt-based learning.

cs.CL↗