arXiv subjects

William Yuan

Publications and source records attributed to William Yuan.

4 recordsLinked to original sources

arXiv2026

On the Error-Correcting Effects of Stochasticity in Discrete Diffusion

Discrete diffusion models achieve strong performance in text and image generation, but their inference remains slow and must inherently balance sampling efficiency and sample quality. In this work, we present a systematic study of how the \emph{degree of stochasticity} in Markov transitions governs the sampling tradeoff. We show that highly deterministic transitions converge rapidly but suffer from error accumulation, while more stochastic transitions converge more slowly yet can achieve higher final sample quality. Using an information-theoretic analysis, we identify the underlying mechanism as an error-correcting effect induced by \emph{redundant transitions} that symmetrically exchange mass between states, and show that these transitions can provably contract sampling errors. Motivated by this analysis, we propose \emph{Discrete Churn and Restart Sampling} (DCRS), a novel inference algorithm that injects controlled stochasticity by alternating between forward and reverse diffusion processes. Experiments on synthetic datasets and large-scale benchmarks show that DCRS improves the speed-quality tradeoff in the low number of function evaluations regime. On image datasets, DCRS achieves up to a $10\times$ reduction in sampling steps compared to standard samplers while maintaining competitive sample quality, whereas on language benchmarks, we observe more nuanced behavior depending on the corruption process and sampling procedure.

cs.LG↗

arXiv2024

Implications of mappings between ICD clinical diagnosis codes and Human Phenotype Ontology terms

Objective: Integrating EHR data with other resources is essential in rare disease research due to low disease prevalence. Such integration is dependent on the alignment of ontologies used for data annotation. The International Classification of Diseases (ICD) is used to annotate clinical diagnoses; the Human Phenotype Ontology (HPO) to annotate phenotypes. Although these ontologies overlap in biomedical entities described, the extent to which they are interoperable is unknown. We investigate how well aligned these ontologies are and whether such alignments facilitate EHR data integration. Materials and Methods: We conducted an empirical analysis of the coverage of mappings between ICD and HPO. We interpret this mapping coverage as a proxy for how easily clinical data can be integrated with research ontologies such as HPO. We quantify how exhaustively ICD codes are mapped to HPO by analyzing mappings in the UMLS Metathesaurus. We analyze the proportion of ICD codes mapped to HPO within a real-world EHR dataset. Results and Discussion: Our analysis revealed that only 2.2% of ICD codes have direct mappings to HPO in UMLS. Within our EHR dataset, less than 50% of ICD codes have mappings to HPO terms. ICD codes that are used frequently in EHR data tend to have mappings to HPO; ICD codes that represent rarer medical conditions are seldom mapped. Conclusion: We find that interoperability between ICD and HPO via UMLS is limited. While other mapping sources could be incorporated, there are no established conventions for what resources should be used to complement UMLS.

cs.DB↗

arXiv2023

Construction of extra-large scale screening tools for risks of severe mental illnesses using real world healthcare data

Importance: The prevalence of severe mental illnesses (SMIs) in the United States is approximately 3% of the whole population. The ability to conduct risk screening of SMIs at large scale could inform early prevention and treatment. Objective: A scalable machine learning based tool was developed to conduct population-level risk screening for SMIs, including schizophrenia, schizoaffective disorders, psychosis, and bipolar disorders,using 1) healthcare insurance claims and 2) electronic health records (EHRs). Design, setting and participants: Data from beneficiaries from a nationwide commercial healthcare insurer with 77.4 million members and data from patients from EHRs from eight academic hospitals based in the U.S. were used. First, the predictive models were constructed and tested using data in case-control cohorts from insurance claims or EHR data. Second, performance of the predictive models across data sources were analyzed. Third, as an illustrative application, the models were further trained to predict risks of SMIs among 18-year old young adults and individuals with substance associated conditions. Main outcomes and measures: Machine learning-based predictive models for SMIs in the general population were built based on insurance claims and EHR.

cs.AI↗

arXiv2018

Privacy-Preserving Distributed Deep Learning for Clinical Data

Deep learning with medical data often requires larger samples sizes than are available at single providers. While data sharing among institutions is desirable to train more accurate and sophisticated models, it can lead to severe privacy concerns due the sensitive nature of the data. This problem has motivated a number of studies on distributed training of neural networks that do not require direct sharing of the training data. However, simple distributed training does not offer provable privacy guarantees to satisfy technical safe standards and may reveal information about the underlying patients. We present a method to train neural networks for clinical data in a distributed fashion under differential privacy. We demonstrate these methods on two datasets that include information from multiple independent sites, the eICU collaborative Research Database and The Cancer Genome Atlas.

cs.LG↗