Small or Large? Zero-Shot or Finetuned? Guiding Language Model Choice for Specialized Applications in Healthcare

This study aims to guide language model selection by investigating: 1) the necessity of finetuning versus zero-shot usage, 2) the benefits of domain-adjacent versus generic pretrained models, 3) the value of further domain-specific pretraining, and 4) the continued relevance of Small Language Models (SLMs) compared to Large Language Models (LLMs) for specific tasks. Using electronic pathology reports from the British Columbia Cancer Registry (BCCR), three classification scenarios with varying difficulty and data size are evaluated. Models include various SLMs and an LLM. SLMs are evaluated both zero-shot and finetuned; the LLM is evaluated zero-shot only. Finetuning significantly improved SLM performance across all scenarios compared to their zero-shot results. The zero-shot LLM outperformed zero-shot SLMs but was consistently outperformed by finetuned SLMs. Domain-adjacent SLMs generally performed better than the generic SLM after finetuning, especially on harder tasks. Further domain-specific pretraining yielded modest gains on easier tasks but significant improvements on the complex, data-scarce task. The results highlight the critical role of finetuning for SLMs in specialized domains, enabling them to surpass zero-shot LLM performance on targeted classification tasks. Pretraining on domain-adjacent or domain-specific data provides further advantages, particularly for complex problems or limited finetuning data. While LLMs offer strong zero-shot capabilities, their performance on these specific tasks did not match that of appropriately finetuned SLMs. In the era of LLMs, SLMs remain relevant and effective, offering a potentially superior performance-resource trade-off compared to LLMs.

Leveraging Language Models for Automated Patient Record Linkage

Objective: Healthcare data fragmentation presents a major challenge for linking patient data, necessitating robust record linkage to integrate patient records from diverse sources. This study investigates the feasibility of leveraging language models for automated patient record linkage, focusing on two key tasks: blocking and matching. Materials and Methods: We utilized real-world healthcare data from the Missouri Cancer Registry and Research Center, linking patient records from two independent sources using probabilistic linkage as a baseline. A transformer-based model, RoBERTa, was fine-tuned for blocking using sentence embeddings. For matching, several language models were experimented under fine-tuned and zero-shot settings, assessing their performance against ground truth labels. Results: The fine-tuned blocking model achieved a 92% reduction in the number of candidate pairs while maintaining near-perfect recall. In the matching task, fine-tuned Mistral-7B achieved the best performance with only 6 incorrect predictions. Among zero-shot models, Mistral-Small-24B performed best, with a total of 55 incorrect predictions. Discussion: Fine-tuned language models achieved strong performance in patient record blocking and matching with minimal errors. However, they remain less accurate and efficient than a hybrid rule-based and probabilistic approach for blocking. Additionally, reasoning models like DeepSeek-R1 are impractical for large-scale record linkage due to high computational costs. Conclusion: This study highlights the potential of language models for automating patient record linkage, offering improved efficiency by eliminating the manual efforts required to perform patient record linkage. Overall, language models offer a scalable solution that can enhance data integration, reduce manual effort, and support disease surveillance and research.

A Clinical Trial Design Approach to Auditing Language Models in Healthcare Setting

We present an audit mechanism for language models, with a focus on models deployed in the healthcare setting. Our proposed mechanism takes inspiration from clinical trial design where we posit the language model audit as a single blind equivalence trial, with the comparison of interest being the subject matter experts. We show that using our proposed method, we can follow principled sample size and power calculations, leading to the requirement of sampling minimum number of records while maintaining the audit integrity and statistical soundness. Finally, we provide a real-world example of the audit used in a production environment in a large-scale public health network.

Differentially Private Ensemble Classifiers for Data Streams

Learning from continuous data streams via classification/regression is prevalent in many domains. Adapting to evolving data characteristics (concept drift) while protecting data owners' private information is an open challenge. We present a differentially private ensemble solution to this problem with two distinguishing features: it allows an \textit{unbounded} number of ensemble updates to deal with the potentially never-ending data streams under a fixed privacy budget, and it is \textit{model agnostic}, in that it treats any pre-trained differentially private classification/regression model as a black-box. Our method outperforms competitors on real-world and simulated datasets for varying settings of privacy, concept drift, and data distribution.

The Differentially Private Lottery Ticket Mechanism

We propose the differentially private lottery ticket mechanism (DPLTM). An end-to-end differentially private training paradigm based on the lottery ticket hypothesis. Using "high-quality winners", selected via our custom score function, DPLTM significantly improves the privacy-utility trade-off over the state-of-the-art. We show that DPLTM converges faster, allowing for early stopping with reduced privacy budget consumption. We further show that the tickets from DPLTM are transferable across datasets, domains, and architectures. Our extensive evaluation on several public datasets provides evidence to our claims.

Differentially Private Survival Function Estimation

Survival function estimation is used in many disciplines, but it is most common in medical analytics in the form of the Kaplan-Meier estimator. Sensitive data (patient records) is used in the estimation without any explicit control on the information leakage, which is a significant privacy concern. We propose a first differentially private estimator of the survival function and show that it can be easily extended to provide differentially private confidence intervals and test statistics without spending any extra privacy budget. We further provide extensions for differentially private estimation of the competing risk cumulative incidence function. Using nine real-life clinical datasets, we provide empirical evidence that our proposed method provides good utility while simultaneously providing strong privacy guarantees.

CrowdMI: Multiple Imputation via Crowdsourcing

Can humans impute missing data with similar proficiency as machines? This is the question we aim to answer in this paper. We present a novel idea of converting observations with missing data in to a survey questionnaire, which is presented to crowdworkers for completion. We replicate a multiple imputation framework by having multiple unique crowdworkers complete our questionnaire. Experimental results demonstrate that using our method, it is possible to generate valid imputations for qualitative and quantitative missing data, with results comparable to imputations generated by complex statistical models.

MIDA: Multiple Imputation using Denoising Autoencoders

Missing data is a significant problem impacting all domains. State-of-the-art framework for minimizing missing data bias is multiple imputation, for which the choice of an imputation model remains nontrivial. We propose a multiple imputation model based on overcomplete deep denoising autoencoders. Our proposed model is capable of handling different data types, missingness patterns, missingness proportions and distributions. Evaluation on several real life datasets show our proposed model significantly outperforms current state-of-the-art methods under varying conditions while simultaneously improving end of the line analytics.

Recovering Loss to Followup Information Using Denoising Autoencoders

Loss to followup is a significant issue in healthcare and has serious consequences for a study's validity and cost. Methods available at present for recovering loss to followup information are restricted by their expressive capabilities and struggle to model highly non-linear relations and complex interactions. In this paper we propose a model based on overcomplete denoising autoencoders to recover loss to followup information. Designed to work with high volume data, results on various simulated and real life datasets show our model is appropriate under varying dataset and loss to followup conditions and outperforms the state-of-the-art methods by a wide margin ($\ge 20\%$ in some scenarios) while preserving the dataset utility for final analysis.

Detecting Adversarial Samples Using Density Ratio Estimates

Machine learning models, especially based on deep architectures are used in everyday applications ranging from self driving cars to medical diagnostics. It has been shown that such models are dangerously susceptible to adversarial samples, indistinguishable from real samples to human eye, adversarial samples lead to incorrect classifications with high confidence. Impact of adversarial samples is far-reaching and their efficient detection remains an open problem. We propose to use direct density ratio estimation as an efficient model agnostic measure to detect adversarial samples. Our proposed method works equally well with single and multi-channel samples, and with different adversarial sample generation methods. We also propose a method to use density ratio estimates for generating adversarial samples with an added constraint of preserving density ratio.