Daily Papers

Differential diagnosis is crucial for medicine as it helps healthcare providers systematically distinguish between conditions that share similar symptoms. This study assesses the impact of lab test results on differential diagnoses (DDx) made by large language models (LLMs). Clinical vignettes from 50 case reports from PubMed Central were created incorporating patient demographics, symptoms, and lab results. Five LLMs GPT-4, GPT-3.5, Llama-2-70b, Claude-2, and Mixtral-8x7B were tested to generate Top 10, Top 5, and Top 1 DDx with and without lab data. A comprehensive evaluation involving GPT-4, a knowledge graph, and clinicians was conducted. GPT-4 performed best, achieving 55% accuracy for Top 1 diagnoses and 60% for Top 10 with lab data, with lenient accuracy up to 80%. Lab results significantly improved accuracy, with GPT-4 and Mixtral excelling, though exact match rates were low. Lab tests, including liver function, metabolic/toxicology panels, and serology/immune tests, were generally interpreted correctly by LLMs for differential diagnosis.

Electronic health records (EHRs) are multimodal by nature, consisting of structured tabular features like lab tests and unstructured clinical notes. In real-life clinical practice, doctors use complementary multimodal EHR data sources to get a clearer picture of patients' health and support clinical decision-making. However, most EHR predictive models do not reflect these procedures, as they either focus on a single modality or overlook the inter-modality interactions/redundancy. In this work, we propose MEDFuse, a Multimodal EHR Data Fusion framework that incorporates masked lab-test modeling and large language models (LLMs) to effectively integrate structured and unstructured medical data. MEDFuse leverages multimodal embeddings extracted from two sources: LLMs fine-tuned on free clinical text and masked tabular transformers trained on structured lab test results. We design a disentangled transformer module, optimized by a mutual information loss to 1) decouple modality-specific and modality-shared information and 2) extract useful joint representation from the noise and redundancy present in clinical notes. Through comprehensive validation on the public MIMIC-III dataset and the in-house FEMH dataset, MEDFuse demonstrates great potential in advancing clinical predictions, achieving over 90% F1 score in the 10-disease multi-label classification task.

In this work we introduce Labrador, a pre-trained Transformer model for laboratory data. Labrador and BERT were pre-trained on a corpus of 100 million lab test results from electronic health records (EHRs) and evaluated on various downstream outcome prediction tasks. Both models demonstrate mastery of the pre-training task but neither consistently outperform XGBoost on downstream supervised tasks. Our ablation studies reveal that transfer learning shows limited effectiveness for BERT and achieves marginal success with Labrador. We explore the reasons for the failure of transfer learning and suggest that the data generating process underlying each patient cannot be characterized sufficiently using labs alone, among other factors. We encourage future work to focus on joint modeling of multiple EHR data categories and to include tree-based baselines in their evaluations.

Accurate interpretation of lab results is crucial in clinical medicine, yet most patient portals use universal normal ranges, ignoring conditional factors like age and gender. This study introduces Lab-AI, an interactive system that offers personalized normal ranges using retrieval-augmented generation (RAG) from credible health sources. Lab-AI has two modules: factor retrieval and normal range retrieval. We tested these on 122 lab tests: 40 with conditional factors and 82 without. For tests with factors, normal ranges depend on patient-specific information. Our results show GPT-4-turbo with RAG achieved a 0.948 F1 score for factor retrieval and 0.995 accuracy for normal range retrieval. GPT-4-turbo with RAG outperformed the best non-RAG system by 33.5% in factor retrieval and showed 132% and 100% improvements in question-level and lab-level performance, respectively, for normal range retrieval. These findings highlight Lab-AI's potential to enhance patient understanding of lab results.

The INTERSPEECH 2020 Deep Noise Suppression (DNS) Challenge is intended to promote collaborative research in real-time single-channel Speech Enhancement aimed to maximize the subjective (perceptual) quality of the enhanced speech. A typical approach to evaluate the noise suppression methods is to use objective metrics on the test set obtained by splitting the original dataset. While the performance is good on the synthetic test set, often the model performance degrades significantly on real recordings. Also, most of the conventional objective metrics do not correlate well with subjective tests and lab subjective tests are not scalable for a large test set. In this challenge, we open-sourced a large clean speech and noise corpus for training the noise suppression models and a representative test set to real-world scenarios consisting of both synthetic and real recordings. We also open-sourced an online subjective test framework based on ITU-T P.808 for researchers to reliably test their developments. We evaluated the results using P.808 on a blind test set. The results and the key learnings from the challenge are discussed. The datasets and scripts can be found here for quick access https://github.com/microsoft/DNS-Challenge.

Large language models (LLMs) are increasingly used in healthcare, but their reliability is heavily influenced by user-driven factors such as question phrasing and the completeness of clinical information. In this study, we examined how misinformation framing, source authority, model persona, and omission of key clinical details affect the diagnostic accuracy and reliability of LLM outputs. We conducted two experiments: one introducing misleading external opinions with varying assertiveness (perturbation test), and another removing specific categories of patient information (ablation test). Using public datasets (MedQA and Medbullets), we evaluated proprietary models (GPT-4o, Claude 3.5 Sonnet, Claude 3.5 Haiku, Gemini 1.5 Pro, Gemini 1.5 Flash) and open-source models (LLaMA 3 8B, LLaMA 3 Med42 8B, DeepSeek R1 8B). All models were vulnerable to user-driven misinformation, with proprietary models especially affected by definitive and authoritative language. Assertive tone had the greatest negative impact on accuracy. In the ablation test, omitting physical exam findings and lab results caused the most significant performance drop. Although proprietary models had higher baseline accuracy, their performance declined sharply under misinformation. These results highlight the need for well-structured prompts and complete clinical context. Users should avoid authoritative framing of misinformation and provide full clinical details, especially for complex cases.

Laboratory test results are an important and generally high dimensional component of a patient's Electronic Health Record (EHR). We train embedding representations (via Word2Vec and GloVe) for LOINC codes of laboratory tests from the EHRs of about 80,000 patients at a cancer center. To include information about lab test outcomes, we also train embeddings on the concatenation of a LOINC code with a symbol indicating normality or abnormality of the result. We observe several clinically meaningful similarities among LOINC embeddings trained over our data. For the embeddings of the concatenation of LOINCs with abnormality codes, we evaluate the performance for mortality prediction tasks and the ability to preserve ordinality properties: i.e. a lab test with normal outcome should be more similar to an abnormal one than to the a very abnormal one.

Acid mine drainage (AMD) is one of the common environmental problems in the coal mining industry that was formed by the oxidation of sulfide minerals in the overburden or waste rock. The prediction of acid generation through AMD is important to do in overburden management and planning the post-mining land use. One of the methods used to predict AMD is a lab-scale kinetic test to determine the rate of acid formation over time using representative samples in the field. However, this test requires a long-time procedure and large amount of chemical reagents lead to inefficient cost. On the other hand, there is potential for machine learning to learn the pattern behind the lab-scale kinetic test data. This study describes an approach to use artificial neural network (ANN) modeling to predict the result from lab-scale kinetic tests. Various ANN model is used based on 83 weeks experiments of lab-scale kinetic tests with 100\% potential acid-forming rock. The model approaches the monitoring of pH, ORP, conductivity, TDS, sulfate, and heavy metals (Fe and Mn). The overall Nash-Sutcliffe Efficiency (NSE) obtained in this study was 0.99 on training and validation data, indicating a strong correlation and accurate prediction compared to the actual lab-scale kinetic tests data. This show the ANN ability to learn patterns, trends, and seasonality from past data for accurate forecasting, thereby highlighting its significant contribution to solving AMD problems. This research is also expected to establish the foundation for a new approach to predict AMD, with time efficient, accurate, and cost-effectiveness in future applications.

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and reasoning on textbook-style science questions, but few if any benchmarks are designed to evaluate language model performance on practical tasks required for scientific research, such as literature search, protocol planning, and data analysis. As a step toward building such benchmarks, we introduce the Language Agent Biology Benchmark (LAB-Bench), a broad dataset of over 2,400 multiple choice questions for evaluating AI systems on a range of practical biology research capabilities, including recall and reasoning over literature, interpretation of figures, access and navigation of databases, and comprehension and manipulation of DNA and protein sequences. Importantly, in contrast to previous scientific benchmarks, we expect that an AI system that can achieve consistently high scores on the more difficult LAB-Bench tasks would serve as a useful assistant for researchers in areas such as literature search and molecular cloning. As an initial assessment of the emergent scientific task capabilities of frontier language models, we measure performance of several against our benchmark and report results compared to human expert biology researchers. We will continue to update and expand LAB-Bench over time, and expect it to serve as a useful tool in the development of automated research systems going forward. A public subset of LAB-Bench is available for use at the following URL: https://huggingface.co/datasets/futurehouse/lab-bench

This study investigates GPT-4's assessment of its performance in healthcare applications. A simple prompting technique was used to prompt the LLM with questions taken from the United States Medical Licensing Examination (USMLE) questionnaire and it was tasked to evaluate its confidence score before posing the question and after asking the question. The questionnaire was categorized into two groups-questions with feedback (WF) and questions with no feedback(NF) post-question. The model was asked to provide absolute and relative confidence scores before and after each question. The experimental findings were analyzed using statistical tools to study the variability of confidence in WF and NF groups. Additionally, a sequential analysis was conducted to observe the performance variation for the WF and NF groups. Results indicate that feedback influences relative confidence but doesn't consistently increase or decrease it. Understanding the performance of LLM is paramount in exploring its utility in sensitive areas like healthcare. This study contributes to the ongoing discourse on the reliability of AI, particularly of LLMs like GPT-4, within healthcare, offering insights into how feedback mechanisms might be optimized to enhance AI-assisted medical education and decision support.

Laboratory accidents pose significant risks to human life and property, underscoring the importance of robust safety protocols. Despite advancements in safety training, laboratory personnel may still unknowingly engage in unsafe practices. With the increasing reliance on large language models (LLMs) for guidance in various fields, including laboratory settings, there is a growing concern about their reliability in critical safety-related decision-making. Unlike trained human researchers, LLMs lack formal lab safety education, raising questions about their ability to provide safe and accurate guidance. Existing research on LLM trustworthiness primarily focuses on issues such as ethical compliance, truthfulness, and fairness but fails to fully cover safety-critical real-world applications, like lab safety. To address this gap, we propose the Laboratory Safety Benchmark (LabSafety Bench), a comprehensive evaluation framework based on a new taxonomy aligned with Occupational Safety and Health Administration (OSHA) protocols. This benchmark includes 765 multiple-choice questions verified by human experts, assessing LLMs and vision language models (VLMs) performance in lab safety contexts. Our evaluations demonstrate that while GPT-4o outperforms human participants, it is still prone to critical errors, highlighting the risks of relying on LLMs in safety-critical environments. Our findings emphasize the need for specialized benchmarks to accurately assess the trustworthiness of LLMs in real-world safety applications.

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

In Brazil, all legal professionals must demonstrate their knowledge of the law and its application by passing the OAB exams, the national bar exams. The OAB exams therefore provide an excellent benchmark for the performance of legal information systems since passing the exam would arguably signal that the system has acquired capacity of legal reasoning comparable to that of a human lawyer. This article describes the construction of a new data set and some preliminary experiments on it, treating the problem of finding the justification for the answers to questions. The results provide a baseline performance measure against which to evaluate future improvements. We discuss the reasons to the poor performance and propose next steps.

The complexity of laboratory environments requires solutions that simplify instrument interaction and enhance measurement automation. Traditional tools often require configuration, software, and programming skills, creating barriers to productivity. Previous approaches, including dedicated software suites and custom scripts, frequently fall short in providing user-friendly solutions that align with programming practices. We present LABIIUM, an AI-enhanced, zero-configuration measurement automation system designed to streamline experimental workflows and improve user productivity. LABIIUM integrates an AI assistant powered by Large Language Models (LLMs) to generate code. LABIIUM's Lab-Automation-Measurement Bridges (LAMBs) enable seamless instrument connectivity using standard tools such as VSCode and Python, eliminating setup overhead. To demonstrate its capabilities, we conducted experiments involving the measurement of the parametric transfer curve of a simple two-transistor inverting amplifier with a current source load. The AI assistant was evaluated using different prompt scenarios and compared with multiple models, including Claude Sonnet 3.5, Gemini Pro 1.5, and GPT-4o. An expert solution implementing the Gradient-Weighted Adaptive Stochastic Sampling (GWASS) method was used as a baseline. The solutions generated by the AI assistant were compared with the expert solution and a uniform linear sweep baseline with 10,000 points. The graph results show that the LLMs were able to successfully complete the most basic uniform sweep, but LLMs were unable to develop adaptive sweeping algorithms to compete with GWASS. The evaluation underscores LABIIUM's ability to enhance laboratory productivity and support digital transformation in research and industry, and emphasizes the future work required to improve LLM performance in Electronic Measurement Science Tasks.

Introduction: Recently, the effectiveness of Large Language Models (LLMs) has increased rapidly, allowing them to be used in a great number of applications. However, the risks posed by the generation of false information through LLMs significantly limit their applications in sensitive areas such as healthcare, highlighting the necessity for rigorous validations to determine their utility and reliability. To date, no study has extensively compared the performance of LLMs on Polish medical examinations across a broad spectrum of specialties on a very large dataset. Objectives: This study evaluated the performance of three Generative Pretrained Transformer (GPT) models on the Polish Board Certification Exam (Pa\'nstwowy Egzamin Specjalizacyjny, PES) dataset, which consists of 297 tests. Methods: We developed a software program to download and process PES exams and tested the performance of GPT models using OpenAI Application Programming Interface. Results: Our findings reveal that GPT-3.5 did not pass any of the analyzed exams. In contrast, the GPT-4 models demonstrated the capability to pass the majority of the exams evaluated, with the most recent model, gpt-4-0125, successfully passing 222 (75%) of them. The performance of the GPT models varied significantly, displaying excellence in exams related to certain specialties while completely failing others. Conclusions: The significant progress and impressive performance of LLM models hold great promise for the increased application of AI in the field of medicine in Poland. For instance, this advancement could lead to the development of AI-based medical assistants for healthcare professionals, enhancing the efficiency and accuracy of medical services.

Global healthcare providers are exploring use of large language models (LLMs) to provide medical advice to the public. LLMs now achieve nearly perfect scores on medical licensing exams, but this does not necessarily translate to accurate performance in real-world settings. We tested if LLMs can assist members of the public in identifying underlying conditions and choosing a course of action (disposition) in ten medical scenarios in a controlled study with 1,298 participants. Participants were randomly assigned to receive assistance from an LLM (GPT-4o, Llama 3, Command R+) or a source of their choice (control). Tested alone, LLMs complete the scenarios accurately, correctly identifying conditions in 94.9% of cases and disposition in 56.3% on average. However, participants using the same LLMs identified relevant conditions in less than 34.5% of cases and disposition in less than 44.2%, both no better than the control group. We identify user interactions as a challenge to the deployment of LLMs for medical advice. Standard benchmarks for medical knowledge and simulated patient interactions do not predict the failures we find with human participants. Moving forward, we recommend systematic human user testing to evaluate interactive capabilities prior to public deployments in healthcare.

Null Hypothesis Significance Testing is the de facto tool for assessing effectiveness differences between Information Retrieval systems. Researchers use statistical tests to check whether those differences will generalise to online settings or are just due to the samples observed in the laboratory. Much work has been devoted to studying which test is the most reliable when comparing a pair of systems, but most of the IR real-world experiments involve more than two. In the multiple comparisons scenario, testing several systems simultaneously may inflate the errors committed by the tests. In this paper, we use a new approach to assess the reliability of multiple comparison procedures using simulated and real TREC data. Experiments show that Wilcoxon plus the Benjamini-Hochberg correction yields Type I error rates according to the significance level for typical sample sizes while being the best test in terms of statistical power.

This paper describes Meta's TestGen-LLM tool, which uses LLMs to automatically improve existing human-written tests. TestGen-LLM verifies that its generated test classes successfully clear a set of filters that assure measurable improvement over the original test suite, thereby eliminating problems due to LLM hallucination. We describe the deployment of TestGen-LLM at Meta test-a-thons for the Instagram and Facebook platforms. In an evaluation on Reels and Stories products for Instagram, 75% of TestGen-LLM's test cases built correctly, 57% passed reliably, and 25% increased coverage. During Meta's Instagram and Facebook test-a-thons, it improved 11.5% of all classes to which it was applied, with 73% of its recommendations being accepted for production deployment by Meta software engineers. We believe this is the first report on industrial scale deployment of LLM-generated code backed by such assurances of code improvement.

This paper presents CG-Eval, the first comprehensive evaluation of the generation capabilities of large Chinese language models across a wide range of academic disciplines. The models' performance was assessed based on their ability to generate accurate and relevant responses to different types of questions in six disciplines, namely, Science and Engineering, Humanities and Social Sciences, Mathematical Calculations, Medical Practitioner Qualification Examination, Judicial Examination, and Certified Public Accountant Examination. This paper also presents Gscore, a composite index derived from the weighted sum of multiple metrics to measure the quality of model's generation against a reference. The test data and test results can be found at http://cgeval.besteasy.com/.

This is the 1st part of the dissertation for my master degree and compares the power consumption using the default floating point (32bit) and Nvidia mixed precision (16bit and 32bit) while training a classification ML model. A custom PC with specific hardware was built to perform the experiments, and different ML hyper-parameters, such as batch size, neurons, and epochs, were chosen to build Deep Neural Networks (DNN). Additionally, various software was used during the experiments to collect the power consumption data in Watts from the Graphics Processing Unit (GPU), Central Processing Unit (CPU), Random Access Memory (RAM) and manually from a wattmeter connected to the wall. A benchmarking test with default hyper parameter values for the DNN was used as a reference, while the experiments used a combination of different settings. The results were recorded in Excel, and descriptive statistics were chosen to calculate the mean between the groups and compare them using graphs and tables. The outcome was positive when using mixed precision combined with specific hyper-parameters. Compared to the benchmarking, the optimisation for the classification reduced the power consumption between 7 and 11 Watts. Similarly, the carbon footprint is reduced because the calculation uses the same power consumption data. Still, a consideration is required when configuring hyper-parameters because it can negatively affect hardware performance. However, this research required inferential statistics, specifically ANOVA and T-test, to compare the relationship between the means. Furthermore, tests indicated no statistical significance of the relationship between the benchmarking and experiments. However, a more extensive implementation with a cluster of GPUs can increase the sample size significantly, as it is an essential factor and can change the outcome of the statistical analysis.

Safe and trustworthy use of Large Language Models (LLM) in the processing of healthcare documents and scientific papers could substantially help clinicians, scientists and policymakers in overcoming information overload and focusing on the most relevant information at a given moment. Retrieval Augmented Generation (RAG) is a promising method to leverage the potential of LLMs while enhancing the accuracy of their outcomes. This report assesses the potentials and shortcomings of such approaches in the automatic knowledge synthesis of different types of documents in the health domain. To this end, it describes: (1) an internally developed proof of concept pipeline that employs state-of-the-art practices to deliver safe and trustable analysis for healthcare documents and scientific papers called RAGEv (Retrieval Augmented Generation Evaluation); (2) a set of evaluation tools for LLM-based document retrieval and generation; (3) a benchmark dataset to verify the accuracy and veracity of the results called RAGEv-Bench. It concludes that careful implementations of RAG techniques could minimize most of the common problems in the use of LLMs for document processing in the health domain, obtaining very high scores both on short yes/no answers and long answers. There is a high potential for incorporating it into the day-to-day work of policy support tasks, but additional efforts are required to obtain a consistent and trustworthy tool.

We present the Virology Capabilities Test (VCT), a large language model (LLM) benchmark that measures the capability to troubleshoot complex virology laboratory protocols. Constructed from the inputs of dozens of PhD-level expert virologists, VCT consists of 322 multimodal questions covering fundamental, tacit, and visual knowledge that is essential for practical work in virology laboratories. VCT is difficult: expert virologists with access to the internet score an average of 22.1% on questions specifically in their sub-areas of expertise. However, the most performant LLM, OpenAI's o3, reaches 43.8% accuracy, outperforming 94% of expert virologists even within their sub-areas of specialization. The ability to provide expert-level virology troubleshooting is inherently dual-use: it is useful for beneficial research, but it can also be misused. Therefore, the fact that publicly available models outperform virologists on VCT raises pressing governance considerations. We propose that the capability of LLMs to provide expert-level troubleshooting of dual-use virology work should be integrated into existing frameworks for handling dual-use technologies in the life sciences.

In recent years, advancements in Natural Language Processing (NLP) techniques have revolutionized the field of accessibility and exclusivity of testing, particularly for visually impaired students (VIS). CBT has shown in years back its relevance in terms of administering exams electronically, making the test process easier, providing quicker and more accurate results, and offering greater flexibility and accessibility for candidates. Yet, its relevance was not felt by the visually impaired students as they cannot access printed documents. Hence, in this paper, we present an NLP-driven Computer-Based Test guide for visually impaired students. It employs a speech technology pre-trained methods to provide real-time assistance and support to visually impaired students. The system utilizes NLP technologies to convert the text-based questions and the associated options in a machine-readable format. Subsequently, the speech technology pre-trained model processes the converted text enabling the VIS to comprehend and analyze the content. Furthermore, we validated that this pre-trained model is not perverse by testing for accuracy using sample audio datasets labels (A, B, C, D, E, F, G) to compare with the voice recordings obtained from 20 VIS which is been predicted by the system to attain values for precision, recall, and F1-scores. These metrics are used to assess the performance of the pre-trained model and have indicated that it is proficient enough to give its better performance to the evaluated system. The methodology adopted for this system is Object Oriented Analysis and Design Methodology (OOADM) where Objects are discussed and built by modeling real-world instances.

This paper introduces a new testbed CLIFT (Clinical Shift) for the clinical domain Question-answering task. The testbed includes 7.5k high-quality question answering samples to provide a diverse and reliable benchmark. We performed a comprehensive experimental study and evaluated several QA deep-learning models under the proposed testbed. Despite impressive results on the original test set, the performance degrades when applied to new test sets, which shows the distribution shift. Our findings emphasize the need for and the potential for increasing the robustness of clinical domain models under distributional shifts. The testbed offers one way to track progress in that direction. It also highlights the necessity of adopting evaluation metrics that consider robustness to natural distribution shifts. We plan to expand the corpus by adding more samples and model results. The full paper and the updated benchmark are available at github.com/openlifescience-ai/clift

Hypertension, defined as blood pressure (BP) that is above normal, holds paramount significance in the realm of public health, as it serves as a critical precursor to various cardiovascular diseases (CVDs) and significantly contributes to elevated mortality rates worldwide. However, many existing BP measurement technologies and standards might be biased because they do not consider clinical outcomes, comorbidities, or demographic factors, making them inconclusive for diagnostic purposes. There is limited data-driven research focused on studying the variance in BP measurements across these variables. In this work, we employed GPT-35-turbo, a large language model (LLM), to automatically extract the mean and standard deviation values of BP for both males and females from a dataset comprising 25 million abstracts sourced from PubMed. 993 article abstracts met our predefined inclusion criteria (i.e., presence of references to blood pressure, units of blood pressure such as mmHg, and mention of biological sex). Based on the automatically-extracted information from these articles, we conducted an analysis of the variations of BP values across biological sex. Our results showed the viability of utilizing LLMs to study the BP variations across different demographic factors.

As the field of artificial intelligence progresses, assistive technologies are becoming more widely used across all industries. The healthcare industry is no different, with numerous studies being done to develop assistive tools for healthcare professionals. Automatic diagnostic systems are one such beneficial tool that can assist with a variety of tasks, including collecting patient information, analyzing test results, and diagnosing patients. However, the idea of developing systems that can provide a differential diagnosis has been largely overlooked in most of these research studies. In this study, we propose a transformer-based approach for providing differential diagnoses based on a patient's age, sex, medical history, and symptoms. We use the DDXPlus dataset, which provides differential diagnosis information for patients based on 49 disease types. Firstly, we propose a method to process the tabular patient data from the dataset and engineer them into patient reports to make them suitable for our research. In addition, we introduce two data modification modules to diversify the training data and consequently improve the robustness of the models. We approach the task as a multi-label classification problem and conduct extensive experiments using four transformer models. All the models displayed promising results by achieving over 97% F1 score on the held-out test set. Moreover, we design additional behavioral tests to get a broader understanding of the models. In particular, for one of our test cases, we prepared a custom test set of 100 samples with the assistance of a doctor. The results on the custom set showed that our proposed data modification modules improved the model's generalization capabilities. We hope our findings will provide future researchers with valuable insights and inspire them to develop reliable systems for automatic differential diagnosis.

Large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding and generation across various domains, including medicine. We present a comprehensive evaluation of GPT-4, a state-of-the-art LLM, on medical competency examinations and benchmark datasets. GPT-4 is a general-purpose model that is not specialized for medical problems through training or engineered to solve clinical tasks. Our analysis covers two sets of official practice materials for the USMLE, a three-step examination program used to assess clinical competency and grant licensure in the United States. We also evaluate performance on the MultiMedQA suite of benchmark datasets. Beyond measuring model performance, experiments were conducted to investigate the influence of test questions containing both text and images on model performance, probe for memorization of content during training, and study probability calibration, which is of critical importance in high-stakes applications like medicine. Our results show that GPT-4, without any specialized prompt crafting, exceeds the passing score on USMLE by over 20 points and outperforms earlier general-purpose models (GPT-3.5) as well as models specifically fine-tuned on medical knowledge (Med-PaLM, a prompt-tuned version of Flan-PaLM 540B). In addition, GPT-4 is significantly better calibrated than GPT-3.5, demonstrating a much-improved ability to predict the likelihood that its answers are correct. We also explore the behavior of the model qualitatively through a case study that shows the ability of GPT-4 to explain medical reasoning, personalize explanations to students, and interactively craft new counterfactual scenarios around a medical case. Implications of the findings are discussed for potential uses of GPT-4 in medical education, assessment, and clinical practice, with appropriate attention to challenges of accuracy and safety.

AI has achieved remarkable mastery over games such as Chess, Go, and Poker, and even Jeopardy, but the rich variety of standardized exams has remained a landmark challenge. Even in 2016, the best AI system achieved merely 59.3% on an 8th Grade science exam challenge. This paper reports unprecedented success on the Grade 8 New York Regents Science Exam, where for the first time a system scores more than 90% on the exam's non-diagram, multiple choice (NDMC) questions. In addition, our Aristo system, building upon the success of recent language models, exceeded 83% on the corresponding Grade 12 Science Exam NDMC questions. The results, on unseen test questions, are robust across different test years and different variations of this kind of test. They demonstrate that modern NLP methods can result in mastery on this task. While not a full solution to general question-answering (the questions are multiple choice, and the domain is restricted to 8th Grade science), it represents a significant milestone for the field.

Purpose: To evaluate the performance of an automated deep learning method in detecting ascites and subsequently quantifying its volume in patients with liver cirrhosis and ovarian cancer. Materials and Methods: This retrospective study included contrast-enhanced and non-contrast abdominal-pelvic CT scans of patients with cirrhotic ascites and patients with ovarian cancer from two institutions, National Institutes of Health (NIH) and University of Wisconsin (UofW). The model, trained on The Cancer Genome Atlas Ovarian Cancer dataset (mean age, 60 years +/- 11 [s.d.]; 143 female), was tested on two internal (NIH-LC and NIH-OV) and one external dataset (UofW-LC). Its performance was measured by the Dice coefficient, standard deviations, and 95% confidence intervals, focusing on ascites volume in the peritoneal cavity. Results: On NIH-LC (25 patients; mean age, 59 years +/- 14 [s.d.]; 14 male) and NIH-OV (166 patients; mean age, 65 years +/- 9 [s.d.]; all female), the model achieved Dice scores of 0.855 +/- 0.061 (CI: 0.831-0.878) and 0.826 +/- 0.153 (CI: 0.764-0.887), with median volume estimation errors of 19.6% (IQR: 13.2-29.0) and 5.3% (IQR: 2.4-9.7) respectively. On UofW-LC (124 patients; mean age, 46 years +/- 12 [s.d.]; 73 female), the model had a Dice score of 0.830 +/- 0.107 (CI: 0.798-0.863) and median volume estimation error of 9.7% (IQR: 4.5-15.1). The model showed strong agreement with expert assessments, with r^2 values of 0.79, 0.98, and 0.97 across the test sets. Conclusion: The proposed deep learning method performed well in segmenting and quantifying the volume of ascites in concordance with expert radiologist assessments.

The global cost of drug discovery and development exceeds $200 billion annually. The main results of drug discovery and development are the outcomes of clinical trials, which directly influence the regulatory approval of new drug candidates and ultimately affect patient outcomes. Despite their significance, large-scale, high-quality clinical trial outcome data are not readily available to the public. Suppose a large clinical trial outcome dataset is provided; machine learning researchers can potentially develop accurate prediction models using past trials and outcome labels, which could help prioritize and optimize therapeutic programs, ultimately benefiting patients. This paper introduces Clinical Trial Outcome (CTO) dataset, the largest trial outcome dataset with around 479K clinical trials, aggregating outcomes from multiple sources of weakly supervised labels, minimizing the noise from individual sources, and eliminating the need for human annotation. These sources include large language model (LLM) decisions on trial-related documents, news headline sentiments, stock prices of trial sponsors, trial linkages across phases, and other signals such as patient dropout rates and adverse events. CTO's labels show unprecedented agreement with supervised clinical trial outcome labels from test split of the supervised TOP dataset, with a 91 F1.

Hampering the interpretation of benchmark scores, evaluation data contamination has become a growing concern in the evaluation of LLMs, and an active area of research studies its effects. While evaluation data contamination is easily understood intuitively, it is surprisingly difficult to define precisely which samples should be considered contaminated and, consequently, how it impacts benchmark scores. We propose that these questions should be addressed together and that contamination metrics can be assessed based on whether models benefit from the examples they mark contaminated. We propose a novel analysis method called ConTAM, and show with a large scale survey of existing and novel n-gram based contamination metrics across 13 benchmarks and 7 models from 2 different families that ConTAM can be used to better understand evaluation data contamination and its effects. We find that contamination may have a much larger effect than reported in recent LLM releases and benefits models differently at different scales. We also find that considering only the longest contaminated substring provides a better signal than considering a union of all contaminated substrings, and that doing model and benchmark specific threshold analysis greatly increases the specificity of the results. Lastly, we investigate the impact of hyperparameter choices, finding that, among other things, both using larger values of n and disregarding matches that are infrequent in the pre-training data lead to many false negatives. With ConTAM, we provide a method to empirically ground evaluation data contamination metrics in downstream effects. With our exploration, we shed light on how evaluation data contamination can impact LLMs and provide insight into the considerations important when doing contamination analysis. We end our paper by discussing these in more detail and providing concrete suggestions for future work.

We test whether Large Language Models (LLMs) can be used to simulate human participants in social-science studies. To do this, we run replications of 14 studies from the Many Labs 2 replication project with OpenAI's text-davinci-003 model, colloquially known as GPT3.5. Based on our pre-registered analyses, we find that among the eight studies we could analyse, our GPT sample replicated 37.5% of the original results and 37.5% of the Many Labs 2 results. However, we were unable to analyse the remaining six studies due to an unexpected phenomenon we call the "correct answer" effect. Different runs of GPT3.5 answered nuanced questions probing political orientation, economic preference, judgement, and moral philosophy with zero or near-zero variation in responses: with the supposedly "correct answer." In one exploratory follow-up study, we found that a "correct answer" was robust to changing the demographic details that precede the prompt. In another, we found that most but not all "correct answers" were robust to changing the order of answer choices. One of our most striking findings occurred in our replication of the Moral Foundations Theory survey results, where we found GPT3.5 identifying as a political conservative in 99.6% of the cases, and as a liberal in 99.3% of the cases in the reverse-order condition. However, both self-reported 'GPT conservatives' and 'GPT liberals' showed right-leaning moral foundations. Our results cast doubts on the validity of using LLMs as a general replacement for human participants in the social sciences. Our results also raise concerns that a hypothetical AI-led future may be subject to a diminished diversity-of-thought.

Online medical consultation (OMC) restricts doctors to gathering patient information solely through inquiries, making the already complex sequential decision-making process of diagnosis even more challenging. Recently, the rapid advancement of large language models has demonstrated a significant potential to transform OMC. However, most studies have primarily focused on improving diagnostic accuracy under conditions of relatively sufficient information, while paying limited attention to the "inquiry" phase of the consultation process. This lack of focus has left the relationship between "inquiry" and "diagnosis" insufficiently explored. In this paper, we first extract real patient interaction strategies from authentic doctor-patient conversations and use these strategies to guide the training of a patient simulator that closely mirrors real-world behavior. By inputting medical records into our patient simulator to simulate patient responses, we conduct extensive experiments to explore the relationship between "inquiry" and "diagnosis" in the consultation process. Experimental results demonstrate that inquiry and diagnosis adhere to the Liebig's law: poor inquiry quality limits the effectiveness of diagnosis, regardless of diagnostic capability, and vice versa. Furthermore, the experiments reveal significant differences in the inquiry performance of various models. To investigate this phenomenon, we categorize the inquiry process into four types: (1) chief complaint inquiry; (2) specification of known symptoms; (3) inquiry about accompanying symptoms; and (4) gathering family or medical history. We analyze the distribution of inquiries across the four types for different models to explore the reasons behind their significant performance differences. We plan to open-source the weights and related code of our patient simulator at https://github.com/LIO-H-ZEN/PatientSimulator.

Urine sediment examination (USE) is one of the main tests used in the evaluation of diseases such as kidney, urinary, metabolic, and diabetes and to determine the density and number of various cells in the urine. USE's manual microscopy is a labor-intensive and time-consuming, imprecise, subjective process. Recently, automatic analysis of urine sediment has become inevitable in the medical field. In this study, we propose a dataset that can be used by artificial intelligence techniques to automatically identify particles in urine sediment images. The data set consists of 8509 particle images obtained by examining the particles in the urine sediment obtained from 409 patients from the Biochemistry Clinics of Elazig Fethi Sekin Central Hospital. Particle images are collected in 8 classes in total and these are Erythrocyte, Leukocyte, Epithelial, Bacteria, Yeast, Cylinders, Crystals, and others (sperm, etc.).

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

Context: Test-driven development (TDD) is a widely employed software development practice that involves developing test cases based on requirements prior to writing the code. Although various methods for automated test case generation have been proposed, they are not specifically tailored for TDD, where requirements instead of code serve as input. Objective: In this paper, we introduce a text-to-testcase generation approach based on a large language model (GPT-3.5) that is fine-tuned on our curated dataset with an effective prompt design. Method: Our approach involves enhancing the capabilities of basic GPT-3.5 for text-to-testcase generation task that is fine-tuned on our curated dataset with an effective prompting design. We evaluated the effectiveness of our approach using a span of five large-scale open-source software projects. Results: Our approach generated 7k test cases for open source projects, achieving 78.5% syntactic correctness, 67.09% requirement alignment, and 61.7% code coverage, which substantially outperforms all other LLMs (basic GPT-3.5, Bloom, and CodeT5). In addition, our ablation study demonstrates the substantial performance improvement of the fine-tuning and prompting components of the GPT-3.5 model. Conclusions: These findings lead us to conclude that fine-tuning and prompting should be considered in the future when building a language model for the text-to-testcase generation task

Large language models (LLMs) have been widely applied to assist test generation with the source code under test provided as the context. This paper aims to answer the question: If the source code under test is incorrect, will LLMs be misguided when generating tests? The effectiveness of test cases is measured by their accuracy, coverage, and bug detection effectiveness. Our evaluation results with five open- and six closed-source LLMs on four datasets demonstrate that incorrect code can significantly mislead LLMs in generating correct, high-coverage, and bug-revealing tests. For instance, in the HumanEval dataset, LLMs achieve 80.45% test accuracy when provided with task descriptions and correct code, but only 57.12% when given task descriptions and incorrect code. For the APPS dataset, prompts with correct code yield tests that detect 39.85% of the bugs, while prompts with incorrect code detect only 19.61%. These findings have important implications for the deployment of LLM-based testing: using it on mature code may help protect against future regression, but on early-stage immature code, it may simply bake in errors. Our findings also underscore the need for further research to improve LLMs resilience against incorrect code in generating reliable and bug-revealing tests.

Despite growing interest in using large language models (LLMs) in healthcare, current explorations do not assess the real-world utility and safety of LLMs in clinical settings. Our objective was to determine whether two LLMs can serve information needs submitted by physicians as questions to an informatics consultation service in a safe and concordant manner. Sixty six questions from an informatics consult service were submitted to GPT-3.5 and GPT-4 via simple prompts. 12 physicians assessed the LLM responses' possibility of patient harm and concordance with existing reports from an informatics consultation service. Physician assessments were summarized based on majority vote. For no questions did a majority of physicians deem either LLM response as harmful. For GPT-3.5, responses to 8 questions were concordant with the informatics consult report, 20 discordant, and 9 were unable to be assessed. There were 29 responses with no majority on "Agree", "Disagree", and "Unable to assess". For GPT-4, responses to 13 questions were concordant, 15 discordant, and 3 were unable to be assessed. There were 35 responses with no majority. Responses from both LLMs were largely devoid of overt harm, but less than 20% of the responses agreed with an answer from an informatics consultation service, responses contained hallucinated references, and physicians were divided on what constitutes harm. These results suggest that while general purpose LLMs are able to provide safe and credible responses, they often do not meet the specific information need of a given question. A definitive evaluation of the usefulness of LLMs in healthcare settings will likely require additional research on prompt engineering, calibration, and custom-tailoring of general purpose models.