Electronic health records (EHRs) store an extensive array of patient information, encompassing medical histories, diagnoses, treatments, and test outcomes. These records are crucial for enabling healthcare providers to make well-informed decisions regarding patient care. Summarizing clinical notes further assists healthcare professionals in pinpointing potential health risks and making better-informed decisions. This process contributes to reducing errors and enhancing patient outcomes by ensuring providers have access to the most pertinent and current patient data. Recent research has shown that incorporating prompts with large language models (LLMs) substantially boosts the efficacy of summarization tasks. However, we show that this approach also leads to increased output variance, resulting in notably divergent outputs even when prompts share similar meanings. To tackle this challenge, we introduce a model-agnostic Soft Prompt-Based Calibration (SPeC) pipeline that employs soft prompts to diminish variance while preserving the advantages of prompt-based summarization. Experimental findings on multiple clinical note tasks and LLMs indicate that our method not only bolsters performance but also effectively curbs variance for various LLMs, providing a more uniform and dependable solution for summarizing vital medical information.
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In both natural and artificial studies, evolution is often seen as synonymous to natural selection. Individuals evolve under pressures set by environments that are either reset or do not carry over significant changes from previous generations. Thus, niche construction (NC), the reciprocal process to natural selection where individuals incur inheritable changes to their environment, is ignored. Arguably due to this lack of study, the dynamics of NC are today little understood, especially in real-world settings. In this work, we study NC in simulation environments that consist of multiple, diverse niches and populations that evolve their plasticity, evolvability and niche-constructing behaviors. Our empirical analysis reveals many interesting dynamics, with populations experiencing mass extinctions, arms races and oscillations. To understand these behaviors, we analyze the interaction between NC and adaptability and the effect of NC on the population's genomic diversity and dispersal, observing that NC diversifies niches. Our study suggests that complexifying the simulation environments studying NC, by considering multiple and diverse niches, is necessary for understanding its dynamics and can lend testable hypotheses to future studies of both natural and artificial systems.
Automated mental health analysis shows great potential for enhancing the efficiency and accessibility of mental health care, with recent methods using pre-trained language models (PLMs) and incorporated emotional information. The latest large language models (LLMs), such as ChatGPT, exhibit dramatic capabilities on diverse natural language processing tasks. However, existing studies on ChatGPT for mental health analysis bear limitations in inadequate evaluations, ignorance of emotional information, and lack of explainability. To bridge these gaps, we comprehensively evaluate the mental health analysis and emotional reasoning ability of ChatGPT on 11 datasets across 5 tasks, and analyze the effects of various emotion-based prompting strategies. Based on these prompts, we further explore LLMs for interpretable mental health analysis by instructing them to also generate explanations for each of their decisions. With an annotation protocol designed by domain experts, we convey human evaluations to assess the quality of explanations generated by ChatGPT and GPT-3. The annotated corpus will be released for future research. Experimental results show that ChatGPT outperforms traditional neural network-based methods but still has a significant gap with advanced task-specific methods. Prompt engineering with emotional cues can be effective in improving performance on mental health analysis but suffers from a lack of robustness and inaccurate reasoning. In addition, ChatGPT significantly outperforms GPT-3 on all criteria in human evaluations of the explanations and approaches to human performance, showing its great potential in explainable mental health analysis.
Injection drug use (IDU) is a dangerous health behavior that increases mortality and morbidity. Identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients' electronic health records (EHR) is difficult because there is no International Classification of Disease (ICD) code and the only place IDU information can be indicated are unstructured free-text clinical progress notes. Although natural language processing (NLP) can efficiently extract this information from unstructured data, there are no validated tools. To address this gap in clinical information, we design and demonstrate a question-answering (QA) framework to extract information on IDU from clinical progress notes. Unlike other methods discussed in the literature, the QA model is able to extract various types of information without being constrained by predefined entities, relations, or concepts. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. This paper also demonstrates the QA model's ability to extract IDU-related information on temporally out-of-distribution data. The results indicate that the majority (51%) of the extracted information by the QA model exactly matches the gold-standard answer and 73% of them contain the gold-standard answer with some additional surrounding words.
Being able to infer ground truth from the responses of multiple imperfect advisors is a problem of crucial importance in many decision-making applications, such as lending, trading, investment, and crowd-sourcing. In practice, however, gathering answers from a set of advisors has a cost. Therefore, finding an advisor selection strategy that retrieves a reliable answer and maximizes the overall utility is a challenging problem. To address this problem, we propose a novel strategy for optimally selecting a set of advisers in a sequential binary decision-making setting, where multiple decisions need to be made over time. Crucially, we assume no access to ground truth and no prior knowledge about the reliability of advisers. Specifically, our approach considers how to simultaneously (1) select advisors by balancing the advisors' costs and the value of making correct decisions, (2) learn the trustworthiness of advisers dynamically without prior information by asking multiple advisers, and (3) make optimal decisions without access to the ground truth, improving this over time. We evaluate our algorithm through several numerical experiments. The results show that our approach outperforms two other methods that combine state-of-the-art models.
Disorders of coronary arteries lead to severe health problems such as atherosclerosis, angina, heart attack and even death. Considering the clinical significance of coronary arteries, an efficient computational model is a vital step towards tissue engineering, enhancing the research of coronary diseases and developing medical treatment and interventional tools. In this work, we applied inverse uncertainty quantification to a microscale agent-based arterial tissue model, a component of a multiscale in-stent restenosis model. Inverse uncertainty quantification was performed to calibrate the arterial tissue model to achieve the mechanical response in line with tissue experimental data. Bayesian calibration with bias term correction was applied to reduce the uncertainty of unknown polynomial coefficients of the attractive force function and achieved agreement with the mechanical behaviour of arterial tissue based on the uniaxial strain tests. Due to the high computational costs of the model, a surrogate model based on Gaussian process was developed to ensure the feasibility of the computation.
Nonlinear model predictive control (NMPC) solves a multivariate optimization problem to estimate the system's optimal control inputs in each control cycle. Such optimization is made more difficult by several factors, such as nonlinearities inherited in the system, highly coupled inputs, and various constraints related to the system's physical limitations. These factors make the optimization to be non-convex and hard to solve traditionally. Genetic algorithm (GA) is typically used extensively to tackle such optimization in several application domains because it does not involve differential calculation or gradient evaluation in its solution estimation. However, the size of the search space in which the GA searches for the optimal control inputs is crucial for the applicability of the GA with systems that require fast response. This paper proposes an approach to accelerate the genetic optimization of NMPC by learning optimal search space size. The proposed approach trains a multivariate regression model to adaptively predict the best smallest search space in every control cycle. The estimated best smallest size of search space is fed to the GA to allow for searching the optimal control inputs within this search space. The proposed approach not only reduces the GA's computational time but also improves the chance of obtaining the optimal control inputs in each cycle. The proposed approach was evaluated on two nonlinear systems and compared with two other genetic-based NMPC approaches implemented on the GPU of a Nvidia Jetson TX2 embedded platform in a processor-in-the-loop (PIL) fashion. The results show that the proposed approach provides a 39-53\% reduction in computational time. Additionally, it increases the convergence percentage to the optimal control inputs within the cycle's time by 48-56\%, resulting in a significant performance enhancement. The source code is available on GitHub.
Real-world data, such as administrative claims and electronic health records, are increasingly used for safety monitoring and to help guide regulatory decision-making. In these settings, it is important to document analytic decisions transparently and objectively to ensure that analyses meet their intended goals. The Causal Roadmap is an established framework that can guide and document analytic decisions through each step of the analytic pipeline, which will help investigators generate high-quality real-world evidence. In this paper, we illustrate the utility of the Causal Roadmap using two case studies previously led by workgroups sponsored by the Sentinel Initiative -- a program for actively monitoring the safety of regulated medical products. Each case example focuses on different aspects of the analytic pipeline for drug safety monitoring. The first case study shows how the Causal Roadmap encourages transparency, reproducibility, and objective decision-making for causal analyses. The second case study highlights how this framework can guide analytic decisions beyond inference on causal parameters, improving outcome ascertainment in clinical phenotyping. These examples provide a structured framework for implementing the Causal Roadmap in safety surveillance and guide transparent, reproducible, and objective analysis.
This paper introduces and explores a new programming paradigm, Model-based Programming, designed to address the challenges inherent in applying deep learning models to real-world applications. Despite recent significant successes of deep learning models across a range of tasks, their deployment in real business scenarios remains fraught with difficulties, such as complex model training, large computational resource requirements, and integration issues with existing programming languages. To ameliorate these challenges, we propose the concept of 'Model-based Programming' and present a novel programming language - M Language, tailored to a prospective model-centered programming paradigm. M Language treats models as basic computational units, enabling developers to concentrate more on crucial tasks such as model loading, fine-tuning, evaluation, and deployment, thereby enhancing the efficiency of creating deep learning applications. We posit that this innovative programming paradigm will stimulate the extensive application and advancement of deep learning technology and provide a robust foundation for a model-driven future.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.
The new era of technology has brought us to the point where it is convenient for people to share their opinions over an abundance of platforms. These platforms have a provision for the users to express themselves in multiple forms of representations, including text, images, videos, and audio. This, however, makes it difficult for users to obtain all the key information about a topic, making the task of automatic multi-modal summarization (MMS) essential. In this paper, we present a comprehensive survey of the existing research in the area of MMS.
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