new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Nov 25

Citrus: Leveraging Expert Cognitive Pathways in a Medical Language Model for Advanced Medical Decision Support

Large language models (LLMs), particularly those with reasoning capabilities, have rapidly advanced in recent years, demonstrating significant potential across a wide range of applications. However, their deployment in healthcare, especially in disease reasoning tasks, is hindered by the challenge of acquiring expert-level cognitive data. In this paper, we introduce Citrus, a medical language model that bridges the gap between clinical expertise and AI reasoning by emulating the cognitive processes of medical experts. The model is trained on a large corpus of simulated expert disease reasoning data, synthesized using a novel approach that accurately captures the decision-making pathways of clinicians. This approach enables Citrus to better simulate the complex reasoning processes involved in diagnosing and treating medical conditions.To further address the lack of publicly available datasets for medical reasoning tasks, we release the last-stage training data, including a custom-built medical diagnostic dialogue dataset. This open-source contribution aims to support further research and development in the field. Evaluations using authoritative benchmarks such as MedQA, covering tasks in medical reasoning and language understanding, show that Citrus achieves superior performance compared to other models of similar size. These results highlight Citrus potential to significantly enhance medical decision support systems, providing a more accurate and efficient tool for clinical decision-making.

  • 12 authors
·
Feb 25

Understanding the Role of Human Intuition on Reliance in Human-AI Decision-Making with Explanations

AI explanations are often mentioned as a way to improve human-AI decision-making, but empirical studies have not found consistent evidence of explanations' effectiveness and, on the contrary, suggest that they can increase overreliance when the AI system is wrong. While many factors may affect reliance on AI support, one important factor is how decision-makers reconcile their own intuition -- beliefs or heuristics, based on prior knowledge, experience, or pattern recognition, used to make judgments -- with the information provided by the AI system to determine when to override AI predictions. We conduct a think-aloud, mixed-methods study with two explanation types (feature- and example-based) for two prediction tasks to explore how decision-makers' intuition affects their use of AI predictions and explanations, and ultimately their choice of when to rely on AI. Our results identify three types of intuition involved in reasoning about AI predictions and explanations: intuition about the task outcome, features, and AI limitations. Building on these, we summarize three observed pathways for decision-makers to apply their own intuition and override AI predictions. We use these pathways to explain why (1) the feature-based explanations we used did not improve participants' decision outcomes and increased their overreliance on AI, and (2) the example-based explanations we used improved decision-makers' performance over feature-based explanations and helped achieve complementary human-AI performance. Overall, our work identifies directions for further development of AI decision-support systems and explanation methods that help decision-makers effectively apply their intuition to achieve appropriate reliance on AI.

  • 4 authors
·
Jan 17, 2023

Text2MDT: Extracting Medical Decision Trees from Medical Texts

Knowledge of the medical decision process, which can be modeled as medical decision trees (MDTs), is critical to build clinical decision support systems. However, the current MDT construction methods rely heavily on time-consuming and laborious manual annotation. In this work, we propose a novel task, Text2MDT, to explore the automatic extraction of MDTs from medical texts such as medical guidelines and textbooks. We normalize the form of the MDT and create an annotated Text-to-MDT dataset in Chinese with the participation of medical experts. We investigate two different methods for the Text2MDT tasks: (a) an end-to-end framework which only relies on a GPT style large language models (LLM) instruction tuning to generate all the node information and tree structures. (b) The pipeline framework which decomposes the Text2MDT task to three subtasks. Experiments on our Text2MDT dataset demonstrate that: (a) the end-to-end method basd on LLMs (7B parameters or larger) show promising results, and successfully outperform the pipeline methods. (b) The chain-of-thought (COT) prompting method Wei2022ChainOT can improve the performance of the fine-tuned LLMs on the Text2MDT test set. (c) the lightweight pipelined method based on encoder-based pretrained models can perform comparably with LLMs with model complexity two magnititudes smaller. Our Text2MDT dataset is open-sourced at https://tianchi.aliyun.com/dataset/95414, and the source codes are open-sourced at https://github.com/michael-wzhu/text2dt.

  • 9 authors
·
Jan 3, 2024

Clinical Evaluation of Medical Image Synthesis: A Case Study in Wireless Capsule Endoscopy

Synthetic Data Generation (SDG) based on Artificial Intelligence (AI) can transform the way clinical medicine is delivered by overcoming privacy barriers that currently render clinical data sharing difficult. This is the key to accelerating the development of digital tools contributing to enhanced patient safety. Such tools include robust data-driven clinical decision support systems, and example-based digital training tools that will enable healthcare professionals to improve their diagnostic performance for enhanced patient safety. This study focuses on the clinical evaluation of medical SDG, with a proof-of-concept investigation on diagnosing Inflammatory Bowel Disease (IBD) using Wireless Capsule Endoscopy (WCE) images. Its scientific contributions include a) a novel protocol for the systematic Clinical Evaluation of Medical Image Synthesis (CEMIS); b) a novel variational autoencoder-based model for the generation of high-resolution synthetic WCE images; and c) a comprehensive evaluation of the synthetic images using the CEMIS protocol by 10 international WCE specialists, in terms of image quality, diversity, and realism, as well as their utility for clinical decision-making. The results show that TIDE-II generates clinically plausible, very realistic WCE images, of improved quality compared to relevant state-of-the-art generative models. Concludingly, CEMIS can serve as a reference for future research on medical image-generation techniques, while the adaptation/extension of the architecture of TIDE-II to other imaging domains can be promising.

  • 13 authors
·
Oct 31, 2024

COVID-BLUeS -- A Prospective Study on the Value of AI in Lung Ultrasound Analysis

As a lightweight and non-invasive imaging technique, lung ultrasound (LUS) has gained importance for assessing lung pathologies. The use of Artificial intelligence (AI) in medical decision support systems is promising due to the time- and expertise-intensive interpretation, however, due to the poor quality of existing data used for training AI models, their usability for real-world applications remains unclear. In a prospective study, we analyze data from 63 COVID-19 suspects (33 positive) collected at Maastricht University Medical Centre. Ultrasound recordings at six body locations were acquired following the BLUE protocol and manually labeled for severity of lung involvement. Several AI models were applied and trained for detection and severity of pulmonary infection. The severity of the lung infection, as assigned by human annotators based on the LUS videos, is not significantly different between COVID-19 positive and negative patients (p = 0.89). Nevertheless, the predictions of image-based AI models identify a COVID-19 infection with 65% accuracy when applied zero-shot (i.e., trained on other datasets), and up to 79% with targeted training, whereas the accuracy based on human annotations is at most 65%. Multi-modal models combining images and CBC improve significantly over image-only models. Although our analysis generally supports the value of AI in LUS assessment, the evaluated models fall short of the performance expected from previous work. We find this is due to 1) the heterogeneity of LUS datasets, limiting the generalization ability to new data, 2) the frame-based processing of AI models ignoring video-level information, and 3) lack of work on multi-modal models that can extract the most relevant information from video-, image- and variable-based inputs. To aid future research, we publish the dataset at: https://github.com/NinaWie/COVID-BLUES.

  • 13 authors
·
Sep 9

Rare Disease Differential Diagnosis with Large Language Models at Scale: From Abdominal Actinomycosis to Wilson's Disease

Large language models (LLMs) have demonstrated impressive capabilities in disease diagnosis. However, their effectiveness in identifying rarer diseases, which are inherently more challenging to diagnose, remains an open question. Rare disease performance is critical with the increasing use of LLMs in healthcare settings. This is especially true if a primary care physician needs to make a rarer prognosis from only a patient conversation so that they can take the appropriate next step. To that end, several clinical decision support systems are designed to support providers in rare disease identification. Yet their utility is limited due to their lack of knowledge of common disorders and difficulty of use. In this paper, we propose RareScale to combine the knowledge LLMs with expert systems. We use jointly use an expert system and LLM to simulate rare disease chats. This data is used to train a rare disease candidate predictor model. Candidates from this smaller model are then used as additional inputs to black-box LLM to make the final differential diagnosis. Thus, RareScale allows for a balance between rare and common diagnoses. We present results on over 575 rare diseases, beginning with Abdominal Actinomycosis and ending with Wilson's Disease. Our approach significantly improves the baseline performance of black-box LLMs by over 17% in Top-5 accuracy. We also find that our candidate generation performance is high (e.g. 88.8% on gpt-4o generated chats).

  • 3 authors
·
Feb 20 2

Kvasir-VQA-x1: A Multimodal Dataset for Medical Reasoning and Robust MedVQA in Gastrointestinal Endoscopy

Medical Visual Question Answering (MedVQA) is a promising field for developing clinical decision support systems, yet progress is often limited by the available datasets, which can lack clinical complexity and visual diversity. To address these gaps, we introduce Kvasir-VQA-x1, a new, large-scale dataset for gastrointestinal (GI) endoscopy. Our work significantly expands upon the original Kvasir-VQA by incorporating 159,549 new question-answer pairs that are designed to test deeper clinical reasoning. We developed a systematic method using large language models to generate these questions, which are stratified by complexity to better assess a model's inference capabilities. To ensure our dataset prepares models for real-world clinical scenarios, we have also introduced a variety of visual augmentations that mimic common imaging artifacts. The dataset is structured to support two main evaluation tracks: one for standard VQA performance and another to test model robustness against these visual perturbations. By providing a more challenging and clinically relevant benchmark, Kvasir-VQA-x1 aims to accelerate the development of more reliable and effective multimodal AI systems for use in clinical settings. The dataset is fully accessible and adheres to FAIR data principles, making it a valuable resource for the wider research community. Code and data: https://github.com/Simula/Kvasir-VQA-x1 and https://huggingface.co/datasets/SimulaMet/Kvasir-VQA-x1

  • 3 authors
·
Jun 11 2

PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology

Foundation models in computational pathology promise to unlock the development of new clinical decision support systems and models for precision medicine. However, there is a mismatch between most clinical analysis, which is defined at the level of one or more whole slide images, and foundation models to date, which process the thousands of image tiles contained in a whole slide image separately. The requirement to train a network to aggregate information across a large number of tiles in multiple whole slide images limits these models' impact. In this work, we present a slide-level foundation model for H&E-stained histopathology, PRISM, that builds on Virchow tile embeddings and leverages clinical report text for pre-training. Using the tile embeddings, PRISM produces slide-level embeddings with the ability to generate clinical reports, resulting in several modes of use. Using text prompts, PRISM achieves zero-shot cancer detection and sub-typing performance approaching and surpassing that of a supervised aggregator model. Using the slide embeddings with linear classifiers, PRISM surpasses supervised aggregator models. Furthermore, we demonstrate that fine-tuning of the PRISM slide encoder yields label-efficient training for biomarker prediction, a task that typically suffers from low availability of training data; an aggregator initialized with PRISM and trained on as little as 10% of the training data can outperform a supervised baseline that uses all of the data.

  • 22 authors
·
May 16, 2024

VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images

Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerSe) was organised in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) in 2019 and 2020, with a call for algorithms towards labelling and segmentation of vertebrae. Two datasets containing a total of 374 multi-detector CT scans from 355 patients were prepared and 4505 vertebrae have individually been annotated at voxel-level by a human-machine hybrid algorithm (https://osf.io/nqjyw/, https://osf.io/t98fz/). A total of 25 algorithms were benchmarked on these datasets. In this work, we present the the results of this evaluation and further investigate the performance-variation at vertebra-level, scan-level, and at different fields-of-view. We also evaluate the generalisability of the approaches to an implicit domain shift in data by evaluating the top performing algorithms of one challenge iteration on data from the other iteration. The principal takeaway from VerSe: the performance of an algorithm in labelling and segmenting a spine scan hinges on its ability to correctly identify vertebrae in cases of rare anatomical variations. The content and code concerning VerSe can be accessed at: https://github.com/anjany/verse.

  • 69 authors
·
Jan 24, 2020

PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

  • 4 authors
·
Feb 28, 2022

DR.BENCH: Diagnostic Reasoning Benchmark for Clinical Natural Language Processing

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

  • 7 authors
·
Sep 29, 2022

Automating Safety Enhancement for LLM-based Agents with Synthetic Risk Scenarios

Large Language Model (LLM)-based agents are increasingly deployed in real-world applications such as "digital assistants, autonomous customer service, and decision-support systems", where their ability to "interact in multi-turn, tool-augmented environments" makes them indispensable. However, ensuring the safety of these agents remains a significant challenge due to the diverse and complex risks arising from dynamic user interactions, external tool usage, and the potential for unintended harmful behaviors. To address this critical issue, we propose AutoSafe, the first framework that systematically enhances agent safety through fully automated synthetic data generation. Concretely, 1) we introduce an open and extensible threat model, OTS, which formalizes how unsafe behaviors emerge from the interplay of user instructions, interaction contexts, and agent actions. This enables precise modeling of safety risks across diverse scenarios. 2) we develop a fully automated data generation pipeline that simulates unsafe user behaviors, applies self-reflective reasoning to generate safe responses, and constructs a large-scale, diverse, and high-quality safety training dataset-eliminating the need for hazardous real-world data collection. To evaluate the effectiveness of our framework, we design comprehensive experiments on both synthetic and real-world safety benchmarks. Results demonstrate that AutoSafe boosts safety scores by 45% on average and achieves a 28.91% improvement on real-world tasks, validating the generalization ability of our learned safety strategies. These results highlight the practical advancement and scalability of AutoSafe in building safer LLM-based agents for real-world deployment. We have released the project page at https://auto-safe.github.io/.

  • 10 authors
·
May 23 1

Benchmarking emergency department triage prediction models with machine learning and large public electronic health records

The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care.

  • 13 authors
·
Nov 22, 2021

FairLay-ML: Intuitive Remedies for Unfairness in Data-Driven Social-Critical Algorithms

This thesis explores open-sourced machine learning (ML) model explanation tools to understand whether these tools can allow a layman to visualize, understand, and suggest intuitive remedies to unfairness in ML-based decision-support systems. Machine learning models trained on datasets biased against minority groups are increasingly used to guide life-altering social decisions, prompting the urgent need to study their logic for unfairness. Due to this problem's impact on vast populations of the general public, it is critical for the layperson -- not just subject matter experts in social justice or machine learning experts -- to understand the nature of unfairness within these algorithms and the potential trade-offs. Existing research on fairness in machine learning focuses mostly on the mathematical definitions and tools to understand and remedy unfair models, with some directly citing user-interactive tools as necessary for future work. This thesis presents FairLay-ML, a proof-of-concept GUI integrating some of the most promising tools to provide intuitive explanations for unfair logic in ML models by integrating existing research tools (e.g. Local Interpretable Model-Agnostic Explanations) with existing ML-focused GUI (e.g. Python Streamlit). We test FairLay-ML using models of various accuracy and fairness generated by an unfairness detector tool, Parfait-ML, and validate our results using Themis. Our study finds that the technology stack used for FairLay-ML makes it easy to install and provides real-time black-box explanations of pre-trained models to users. Furthermore, the explanations provided translate to actionable remedies.

  • 3 authors
·
Jul 11, 2023

FastPathology: An open-source platform for deep learning-based research and decision support in digital pathology

Deep convolutional neural networks (CNNs) are the current state-of-the-art for digital analysis of histopathological images. The large size of whole-slide microscopy images (WSIs) requires advanced memory handling to read, display and process these images. There are several open-source platforms for working with WSIs, but few support deployment of CNN models. These applications use third-party solutions for inference, making them less user-friendly and unsuitable for high-performance image analysis. To make deployment of CNNs user-friendly and feasible on low-end machines, we have developed a new platform, FastPathology, using the FAST framework and C++. It minimizes memory usage for reading and processing WSIs, deployment of CNN models, and real-time interactive visualization of results. Runtime experiments were conducted on four different use cases, using different architectures, inference engines, hardware configurations and operating systems. Memory usage for reading, visualizing, zooming and panning a WSI were measured, using FastPathology and three existing platforms. FastPathology performed similarly in terms of memory to the other C++ based application, while using considerably less than the two Java-based platforms. The choice of neural network model, inference engine, hardware and processors influenced runtime considerably. Thus, FastPathology includes all steps needed for efficient visualization and processing of WSIs in a single application, including inference of CNNs with real-time display of the results. Source code, binary releases and test data can be found online on GitHub at https://github.com/SINTEFMedtek/FAST-Pathology/.

  • 6 authors
·
Nov 11, 2020

Two Case Studies of Experience Prototyping Machine Learning Systems in the Wild

Throughout the course of my Ph.D., I have been designing the user experience (UX) of various machine learning (ML) systems. In this workshop, I share two projects as case studies in which people engage with ML in much more complicated and nuanced ways than the technical HCML work might assume. The first case study describes how cardiology teams in three hospitals used a clinical decision-support system that helps them decide whether and when to implant an artificial heart to a heart failure patient. I demonstrate that physicians cannot draw on their decision-making experience by seeing only patient data on paper. They are also confused by some fundamental premises upon which ML operates. For example, physicians asked: Are ML predictions made based on clinicians' best efforts? Is it ethical to make decisions based on previous patients' collective outcomes? In the second case study, my collaborators and I designed an intelligent text editor, with the goal of improving authors' writing experience with NLP (Natural Language Processing) technologies. We prototyped a number of generative functionalities where the system provides phrase-or-sentence-level writing suggestions upon user request. When writing with the prototype, however, authors shared that they need to "see where the sentence is going two paragraphs later" in order to decide whether the suggestion aligns with their writing; Some even considered adopting machine suggestions as plagiarism, therefore "is simply wrong". By sharing these unexpected and intriguing responses from these real-world ML users, I hope to start a discussion about such previously-unknown complexities and nuances of -- as the workshop proposal states -- "putting ML at the service of people in a way that is accessible, useful, and trustworthy to all".

  • 1 authors
·
Oct 20, 2019

Clone What You Can't Steal: Black-Box LLM Replication via Logit Leakage and Distillation

Large Language Models (LLMs) are increasingly deployed in mission-critical systems, facilitating tasks such as satellite operations, command-and-control, military decision support, and cyber defense. Many of these systems are accessed through application programming interfaces (APIs). When such APIs lack robust access controls, they can expose full or top-k logits, creating a significant and often overlooked attack surface. Prior art has mainly focused on reconstructing the output projection layer or distilling surface-level behaviors. However, regenerating a black-box model under tight query constraints remains underexplored. We address that gap by introducing a constrained replication pipeline that transforms partial logit leakage into a functional deployable substitute model clone. Our two-stage approach (i) reconstructs the output projection matrix by collecting top-k logits from under 10k black-box queries via singular value decomposition (SVD) over the logits, then (ii) distills the remaining architecture into compact student models with varying transformer depths, trained on an open source dataset. A 6-layer student recreates 97.6% of the 6-layer teacher model's hidden-state geometry, with only a 7.31% perplexity increase, and a 7.58 Negative Log-Likelihood (NLL). A 4-layer variant achieves 17.1% faster inference and 18.1% parameter reduction with comparable performance. The entire attack completes in under 24 graphics processing unit (GPU) hours and avoids triggering API rate-limit defenses. These results demonstrate how quickly a cost-limited adversary can clone an LLM, underscoring the urgent need for hardened inference APIs and secure on-premise defense deployments.

  • 4 authors
·
Aug 31

Optimizing Retrieval-Augmented Generation: Analysis of Hyperparameter Impact on Performance and Efficiency

Large language models achieve high task performance yet often hallucinate or rely on outdated knowledge. Retrieval-augmented generation (RAG) addresses these gaps by coupling generation with external search. We analyse how hyperparameters influence speed and quality in RAG systems, covering Chroma and Faiss vector stores, chunking policies, cross-encoder re-ranking, and temperature, and we evaluate six metrics: faithfulness, answer correctness, answer relevancy, context precision, context recall, and answer similarity. Chroma processes queries 13% faster, whereas Faiss yields higher retrieval precision, revealing a clear speed-accuracy trade-off. Naive fixed-length chunking with small windows and minimal overlap outperforms semantic segmentation while remaining the quickest option. Re-ranking provides modest gains in retrieval quality yet increases runtime by roughly a factor of 5, so its usefulness depends on latency constraints. These results help practitioners balance computational cost and accuracy when tuning RAG systems for transparent, up-to-date responses. Finally, we re-evaluate the top configurations with a corrective RAG workflow and show that their advantages persist when the model can iteratively request additional evidence. We obtain a near-perfect context precision (99%), which demonstrates that RAG systems can achieve extremely high retrieval accuracy with the right combination of hyperparameters, with significant implications for applications where retrieval quality directly impacts downstream task performance, such as clinical decision support in healthcare.

  • 4 authors
·
May 13 2

Tiny-BioMoE: a Lightweight Embedding Model for Biosignal Analysis

Pain is a complex and pervasive condition that affects a significant portion of the population. Accurate and consistent assessment is essential for individuals suffering from pain, as well as for developing effective management strategies in a healthcare system. Automatic pain assessment systems enable continuous monitoring, support clinical decision-making, and help minimize patient distress while mitigating the risk of functional deterioration. Leveraging physiological signals offers objective and precise insights into a person's state, and their integration in a multimodal framework can further enhance system performance. This study has been submitted to the Second Multimodal Sensing Grand Challenge for Next-Gen Pain Assessment (AI4PAIN). The proposed approach introduces Tiny-BioMoE, a lightweight pretrained embedding model for biosignal analysis. Trained on 4.4 million biosignal image representations and consisting of only 7.3 million parameters, it serves as an effective tool for extracting high-quality embeddings for downstream tasks. Extensive experiments involving electrodermal activity, blood volume pulse, respiratory signals, peripheral oxygen saturation, and their combinations highlight the model's effectiveness across diverse modalities in automatic pain recognition tasks. The model's architecture (code) and weights are available at https://github.com/GkikasStefanos/Tiny-BioMoE.

  • 3 authors
·
Jul 29

HumanAgencyBench: Scalable Evaluation of Human Agency Support in AI Assistants

As humans delegate more tasks and decisions to artificial intelligence (AI), we risk losing control of our individual and collective futures. Relatively simple algorithmic systems already steer human decision-making, such as social media feed algorithms that lead people to unintentionally and absent-mindedly scroll through engagement-optimized content. In this paper, we develop the idea of human agency by integrating philosophical and scientific theories of agency with AI-assisted evaluation methods: using large language models (LLMs) to simulate and validate user queries and to evaluate AI responses. We develop HumanAgencyBench (HAB), a scalable and adaptive benchmark with six dimensions of human agency based on typical AI use cases. HAB measures the tendency of an AI assistant or agent to Ask Clarifying Questions, Avoid Value Manipulation, Correct Misinformation, Defer Important Decisions, Encourage Learning, and Maintain Social Boundaries. We find low-to-moderate agency support in contemporary LLM-based assistants and substantial variation across system developers and dimensions. For example, while Anthropic LLMs most support human agency overall, they are the least supportive LLMs in terms of Avoid Value Manipulation. Agency support does not appear to consistently result from increasing LLM capabilities or instruction-following behavior (e.g., RLHF), and we encourage a shift towards more robust safety and alignment targets.

  • 4 authors
·
Sep 10 2

EXPEREPAIR: Dual-Memory Enhanced LLM-based Repository-Level Program Repair

Automatically repairing software issues remains a fundamental challenge at the intersection of software engineering and AI. Although recent advancements in Large Language Models (LLMs) have demonstrated potential for repository-level repair tasks, current methodologies exhibit two notable limitations: (1) they often address issues in isolation, neglecting to incorporate insights from previously resolved issues, and (2) they rely on static and rigid prompting strategies, which constrain their ability to generalize across diverse and evolving issue scenarios. Inspired by the dual memory systems of human cognition, where episodic and semantic memories work synergistically to support human reasoning and decision-making, we propose ExpeRepair, a novel LLM-based approach that continuously learns from historical repair experiences through dual-channel knowledge accumulation. ExpeRepair organizes historical repair experiences into two complementary memories: an episodic memory that stores concrete repair demonstrations, and a semantic memory that encodes abstract reflective insights. At inference time, ExpeRepair activates both memory systems by retrieving relevant demonstrations from episodic memory and recalling high-level repair insights from semantic memory. It further enhances adaptability through dynamic prompt composition, synergistically integrating both memory types to replace static prompts with context-aware, experience-driven prompts. Experiments on the SWE-bench Lite benchmark demonstrate that ExpeRepair achieves a pass@1 score of 49.3% with Claude 3.7 Sonnet, outperforming all state-of-the-art open-source methods.

  • 6 authors
·
Jun 12

Securing AI Agents: Implementing Role-Based Access Control for Industrial Applications

The emergence of Large Language Models (LLMs) has significantly advanced solutions across various domains, from political science to software development. However, these models are constrained by their training data, which is static and limited to information available up to a specific date. Additionally, their generalized nature often necessitates fine-tuning -- whether for classification or instructional purposes -- to effectively perform specific downstream tasks. AI agents, leveraging LLMs as their core, mitigate some of these limitations by accessing external tools and real-time data, enabling applications such as live weather reporting and data analysis. In industrial settings, AI agents are transforming operations by enhancing decision-making, predictive maintenance, and process optimization. For example, in manufacturing, AI agents enable near-autonomous systems that boost productivity and support real-time decision-making. Despite these advancements, AI agents remain vulnerable to security threats, including prompt injection attacks, which pose significant risks to their integrity and reliability. To address these challenges, this paper proposes a framework for integrating Role-Based Access Control (RBAC) into AI agents, providing a robust security guardrail. This framework aims to support the effective and scalable deployment of AI agents, with a focus on on-premises implementations.

  • 1 authors
·
Sep 14

Clinical Decision Support System for Unani Medicine Practitioners

Like other fields of Traditional Medicines, Unani Medicines have been found as an effective medical practice for ages. It is still widely used in the subcontinent, particularly in Pakistan and India. However, Unani Medicines Practitioners are lacking modern IT applications in their everyday clinical practices. An Online Clinical Decision Support System may address this challenge to assist apprentice Unani Medicines practitioners in their diagnostic processes. The proposed system provides a web-based interface to enter the patient's symptoms, which are then automatically analyzed by our system to generate a list of probable diseases. The system allows practitioners to choose the most likely disease and inform patients about the associated treatment options remotely. The system consists of three modules: an Online Clinical Decision Support System, an Artificial Intelligence Inference Engine, and a comprehensive Unani Medicines Database. The system employs advanced AI techniques such as Decision Trees, Deep Learning, and Natural Language Processing. For system development, the project team used a technology stack that includes React, FastAPI, and MySQL. Data and functionality of the application is exposed using APIs for integration and extension with similar domain applications. The novelty of the project is that it addresses the challenge of diagnosing diseases accurately and efficiently in the context of Unani Medicines principles. By leveraging the power of technology, the proposed Clinical Decision Support System has the potential to ease access to healthcare services and information, reduce cost, boost practitioner and patient satisfaction, improve speed and accuracy of the diagnostic process, and provide effective treatments remotely. The application will be useful for Unani Medicines Practitioners, Patients, Government Drug Regulators, Software Developers, and Medical Researchers.

  • 5 authors
·
Oct 24, 2023

From Questions to Clinical Recommendations: Large Language Models Driving Evidence-Based Clinical Decision Making

Clinical evidence, derived from rigorous research and data analysis, provides healthcare professionals with reliable scientific foundations for informed decision-making. Integrating clinical evidence into real-time practice is challenging due to the enormous workload, complex professional processes, and time constraints. This highlights the need for tools that automate evidence synthesis to support more efficient and accurate decision making in clinical settings. This study introduces Quicker, an evidence-based clinical decision support system powered by large language models (LLMs), designed to automate evidence synthesis and generate clinical recommendations modeled after standard clinical guideline development processes. Quicker implements a fully automated chain that covers all phases, from questions to clinical recommendations, and further enables customized decision-making through integrated tools and interactive user interfaces. To evaluate Quicker's capabilities, we developed the Q2CRBench-3 benchmark dataset, based on clinical guideline development records for three different diseases. Experimental results highlighted Quicker's strong performance, with fine-grained question decomposition tailored to user preferences, retrieval sensitivities comparable to human experts, and literature screening performance approaching comprehensive inclusion of relevant studies. In addition, Quicker-assisted evidence assessment effectively supported human reviewers, while Quicker's recommendations were more comprehensive and logically coherent than those of clinicians. In system-level testing, collaboration between a single reviewer and Quicker reduced the time required for recommendation development to 20-40 minutes. In general, our findings affirm the potential of Quicker to help physicians make quicker and more reliable evidence-based clinical decisions.

  • 16 authors
·
May 15

AI Agents vs. Agentic AI: A Conceptual Taxonomy, Applications and Challenge

This study critically distinguishes between AI Agents and Agentic AI, offering a structured conceptual taxonomy, application mapping, and challenge analysis to clarify their divergent design philosophies and capabilities. We begin by outlining the search strategy and foundational definitions, characterizing AI Agents as modular systems driven by Large Language Models (LLMs) and Large Image Models (LIMs) for narrow, task-specific automation. Generative AI is positioned as a precursor, with AI Agents advancing through tool integration, prompt engineering, and reasoning enhancements. In contrast, Agentic AI systems represent a paradigmatic shift marked by multi-agent collaboration, dynamic task decomposition, persistent memory, and orchestrated autonomy. Through a sequential evaluation of architectural evolution, operational mechanisms, interaction styles, and autonomy levels, we present a comparative analysis across both paradigms. Application domains such as customer support, scheduling, and data summarization are contrasted with Agentic AI deployments in research automation, robotic coordination, and medical decision support. We further examine unique challenges in each paradigm including hallucination, brittleness, emergent behavior, and coordination failure and propose targeted solutions such as ReAct loops, RAG, orchestration layers, and causal modeling. This work aims to provide a definitive roadmap for developing robust, scalable, and explainable AI agent and Agentic AI-driven systems. >AI Agents, Agent-driven, Vision-Language-Models, Agentic AI Decision Support System, Agentic-AI Applications

  • 3 authors
·
May 15 2

Knowledge Graph Modeling-Driven Large Language Model Operating System (LLM OS) for Task Automation in Process Engineering Problem-Solving

We present the Process Engineering Operations Assistant (PEOA), an AI-driven framework designed to solve complex problems in the chemical and process industries. The framework employs a modular architecture orchestrated by a meta-agent, which serves as the central coordinator, managing an action generator and instruction-tuned small-scale language models (expert models). The action generator decomposes complex problems into sub-tasks and identifies suitable expert models to execute each, delivering precise solutions for multi-step problem-solving. Key techniques include advanced knowledge modeling using property graphs for improved information retrieval, facilitating more accurate and contextually relevant solutions. Additionally, the framework utilizes a teacher-student transfer-learning approach with GPT-4 (Omni) to fine-tune the action generator and expert models for domain adaptation, alongside an iterative problem-solving mechanism with sophisticated error handling. Custom datasets were developed to evaluate the framework against leading proprietary language models on various engineering tasks. The results demonstrate the framework effectiveness in automating calculations, accelerating prototyping, and providing AI-augmented decision support for industrial processes, marking a significant advancement in process engineering capabilities.

  • 3 authors
·
Aug 23, 2024

Beyond Benchmarks: Dynamic, Automatic And Systematic Red-Teaming Agents For Trustworthy Medical Language Models

Ensuring the safety and reliability of large language models (LLMs) in clinical practice is critical to prevent patient harm and promote trustworthy healthcare applications of AI. However, LLMs are advancing so rapidly that static safety benchmarks often become obsolete upon publication, yielding only an incomplete and sometimes misleading picture of model trustworthiness. We demonstrate that a Dynamic, Automatic, and Systematic (DAS) red-teaming framework that continuously stress-tests LLMs can reveal significant weaknesses of current LLMs across four safety-critical domains: robustness, privacy, bias/fairness, and hallucination. A suite of adversarial agents is applied to autonomously mutate test cases, identify/evolve unsafe-triggering strategies, and evaluate responses, uncovering vulnerabilities in real time without human intervention. Applying DAS to 15 proprietary and open-source LLMs revealed a stark contrast between static benchmark performance and vulnerability under adversarial pressure. Despite a median MedQA accuracy exceeding 80\%, 94\% of previously correct answers failed our dynamic robustness tests. We observed similarly high failure rates across other domains: privacy leaks were elicited in 86\% of scenarios, cognitive-bias priming altered clinical recommendations in 81\% of fairness tests, and we identified hallucination rates exceeding 66\% in widely used models. Such profound residual risks are incompatible with routine clinical practice. By converting red-teaming from a static checklist into a dynamic stress-test audit, DAS red-teaming offers the surveillance that hospitals/regulators/technology vendors require as LLMs become embedded in patient chatbots, decision-support dashboards, and broader healthcare workflows. Our framework delivers an evolvable, scalable, and reliable safeguard for the next generation of medical AI.

  • 21 authors
·
Jul 30

Contextual Bandits in Payment Processing: Non-uniform Exploration and Supervised Learning at Adyen

Uniform random exploration in decision-making systems supports off-policy learning via supervision but incurs high regret, making it impractical for many applications. Conversely, non-uniform exploration offers better immediate performance but lacks support for off-policy learning. Recent research suggests that regression oracles can bridge this gap by combining non-uniform exploration with supervised learning. In this paper, we analyze these approaches within a real-world industrial context at Adyen, a large global payments processor characterized by batch logged delayed feedback, short-term memory, and dynamic action spaces under the Empirical Risk Minimization (ERM) framework. Our analysis reveals that while regression oracles significantly improve performance, they introduce challenges due to rigid algorithmic assumptions. Specifically, we observe that as a policy improves, subsequent generations may perform worse due to shifts in the reward distribution and increased class imbalance in the training data. This degradation occurs de spite improvements in other aspects of the training data, leading to decreased performance in successive policy iterations. We further explore the long-term impact of regression oracles, identifying a potential "oscillation effect." This effect arises when regression oracles influence probability estimates and the realizability of subsequent policy models, leading to fluctuations in performance across iterations. Our findings highlight the need for more adaptable algorithms that can leverage the benefits of regression oracles without introducing instability in policy performance over time.

  • 2 authors
·
Nov 30, 2024

Progress Note Understanding -- Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 Shared Task

Daily progress notes are common types in the electronic health record (EHR) where healthcare providers document the patient's daily progress and treatment plans. The EHR is designed to document all the care provided to patients, but it also enables note bloat with extraneous information that distracts from the diagnoses and treatment plans. Applications of natural language processing (NLP) in the EHR is a growing field with the majority of methods in information extraction. Few tasks use NLP methods for downstream diagnostic decision support. We introduced the 2022 National NLP Clinical Challenge (N2C2) Track 3: Progress Note Understanding - Assessment and Plan Reasoning as one step towards a new suite of tasks. The Assessment and Plan Reasoning task focuses on the most critical components of progress notes, Assessment and Plan subsections where health problems and diagnoses are contained. The goal of the task was to develop and evaluate NLP systems that automatically predict causal relations between the overall status of the patient contained in the Assessment section and its relation to each component of the Plan section which contains the diagnoses and treatment plans. The goal of the task was to identify and prioritize diagnoses as the first steps in diagnostic decision support to find the most relevant information in long documents like daily progress notes. We present the results of 2022 n2c2 Track 3 and provide a description of the data, evaluation, participation and system performance.

  • 6 authors
·
Mar 14, 2023

The Ethics of ChatGPT in Medicine and Healthcare: A Systematic Review on Large Language Models (LLMs)

With the introduction of ChatGPT, Large Language Models (LLMs) have received enormous attention in healthcare. Despite their potential benefits, researchers have underscored various ethical implications. While individual instances have drawn much attention, the debate lacks a systematic overview of practical applications currently researched and ethical issues connected to them. Against this background, this work aims to map the ethical landscape surrounding the current stage of deployment of LLMs in medicine and healthcare. Electronic databases and preprint servers were queried using a comprehensive search strategy. Studies were screened and extracted following a modified rapid review approach. Methodological quality was assessed using a hybrid approach. For 53 records, a meta-aggregative synthesis was performed. Four fields of applications emerged and testify to a vivid exploration phase. Advantages of using LLMs are attributed to their capacity in data analysis, personalized information provisioning, support in decision-making, mitigating information loss and enhancing information accessibility. However, we also identifies recurrent ethical concerns connected to fairness, bias, non-maleficence, transparency, and privacy. A distinctive concern is the tendency to produce harmful misinformation or convincingly but inaccurate content. A recurrent plea for ethical guidance and human oversight is evident. Given the variety of use cases, it is suggested that the ethical guidance debate be reframed to focus on defining what constitutes acceptable human oversight across the spectrum of applications. This involves considering diverse settings, varying potentials for harm, and different acceptable thresholds for performance and certainty in healthcare. In addition, a critical inquiry is necessary to determine the extent to which the current experimental use of LLMs is necessary and justified.

  • 2 authors
·
Mar 21, 2024

Artificial intelligence in cyber physical systems

This article conducts a literature review of current and future challenges in the use of artificial intelligence (AI) in cyber physical systems. The literature review is focused on identifying a conceptual framework for increasing resilience with AI through automation supporting both, a technical and human level. The methodology applied resembled a literature review and taxonomic analysis of complex internet of things (IoT) interconnected and coupled cyber physical systems. There is an increased attention on propositions on models, infrastructures and frameworks of IoT in both academic and technical papers. These reports and publications frequently represent a juxtaposition of other related systems and technologies (e.g. Industrial Internet of Things, Cyber Physical Systems, Industry 4.0 etc.). We review academic and industry papers published between 2010 and 2020. The results determine a new hierarchical cascading conceptual framework for analysing the evolution of AI decision-making in cyber physical systems. We argue that such evolution is inevitable and autonomous because of the increased integration of connected devices (IoT) in cyber physical systems. To support this argument, taxonomic methodology is adapted and applied for transparency and justifications of concepts selection decisions through building summary maps that are applied for designing the hierarchical cascading conceptual framework.

  • 5 authors
·
Mar 11, 2019

Agentic Systems in Radiology: Design, Applications, Evaluation, and Challenges

Building agents, systems that perceive and act upon their environment with a degree of autonomy, has long been a focus of AI research. This pursuit has recently become vastly more practical with the emergence of large language models (LLMs) capable of using natural language to integrate information, follow instructions, and perform forms of "reasoning" and planning across a wide range of tasks. With its multimodal data streams and orchestrated workflows spanning multiple systems, radiology is uniquely suited to benefit from agents that can adapt to context and automate repetitive yet complex tasks. In radiology, LLMs and their multimodal variants have already demonstrated promising performance for individual tasks such as information extraction and report summarization. However, using LLMs in isolation underutilizes their potential to support complex, multi-step workflows where decisions depend on evolving context from multiple information sources. Equipping LLMs with external tools and feedback mechanisms enables them to drive systems that exhibit a spectrum of autonomy, ranging from semi-automated workflows to more adaptive agents capable of managing complex processes. This review examines the design of such LLM-driven agentic systems, highlights key applications, discusses evaluation methods for planning and tool use, and outlines challenges such as error cascades, tool-use efficiency, and health IT integration.

  • 11 authors
·
Oct 10

Mobile-Agent-v3: Foundamental Agents for GUI Automation

This paper introduces GUI-Owl, a foundational GUI agent model that achieves state-of-the-art performance among open-source end-to-end models on ten GUI benchmarks across desktop and mobile environments, covering grounding, question answering, planning, decision-making, and procedural knowledge. GUI-Owl-7B achieves 66.4 on AndroidWorld and 29.4 on OSWorld. Building on this, we propose Mobile-Agent-v3, a general-purpose GUI agent framework that further improves performance to 73.3 on AndroidWorld and 37.7 on OSWorld, setting a new state-of-the-art for open-source GUI agent frameworks. GUI-Owl incorporates three key innovations: (1) Large-scale Environment Infrastructure: a cloud-based virtual environment spanning Android, Ubuntu, macOS, and Windows, enabling our Self-Evolving GUI Trajectory Production framework. This generates high-quality interaction data via automated query generation and correctness validation, leveraging GUI-Owl to refine trajectories iteratively, forming a self-improving loop. It supports diverse data pipelines and reduces manual annotation. (2) Diverse Foundational Agent Capabilities: by integrating UI grounding, planning, action semantics, and reasoning patterns, GUI-Owl supports end-to-end decision-making and can act as a modular component in multi-agent systems. (3) Scalable Environment RL: we develop a scalable reinforcement learning framework with fully asynchronous training for real-world alignment. We also introduce Trajectory-aware Relative Policy Optimization (TRPO) for online RL, achieving 34.9 on OSWorld. GUI-Owl and Mobile-Agent-v3 are open-sourced at https://github.com/X-PLUG/MobileAgent.

  • 15 authors
·
Aug 20 3

Synthesizing mixed-integer linear programming models from natural language descriptions

Numerous real-world decision-making problems can be formulated and solved using Mixed-Integer Linear Programming (MILP) models. However, the transformation of these problems into MILP models heavily relies on expertise in operations research and mathematical optimization, which restricts non-experts' accessibility to MILP. To address this challenge, we propose a framework for automatically formulating MILP models from unstructured natural language descriptions of decision problems, which integrates Large Language Models (LLMs) and mathematical modeling techniques. This framework consists of three phases: i) identification of decision variables, ii) classification of objective and constraints, and iii) finally, generation of MILP models. In this study, we present a constraint classification scheme and a set of constraint templates that can guide the LLMs in synthesizing a complete MILP model. After fine-tuning LLMs, our approach can identify and synthesize logic constraints in addition to classic demand and resource constraints. The logic constraints have not been studied in existing work. To evaluate the performance of the proposed framework, we extend the NL4Opt dataset with more problem descriptions and constraint types, and with the new dataset, we compare our framework with one-step model generation methods offered by LLMs. The experimental results reveal that with respect to the accuracies of generating the correct model, objective, and constraints, our method which integrates constraint classification and templates with LLMs significantly outperforms the others. The prototype system that we developed has a great potential to capture more constraints for more complex MILPs. It opens up opportunities for developing training tools for operations research practitioners and has the potential to be a powerful tool for automatic decision problem modeling and solving in practice.

  • 3 authors
·
Nov 26, 2023

Towards MLOps: A DevOps Tools Recommender System for Machine Learning System

Applying DevOps practices to machine learning system is termed as MLOps and machine learning systems evolve on new data unlike traditional systems on requirements. The objective of MLOps is to establish a connection between different open-source tools to construct a pipeline that can automatically perform steps to construct a dataset, train the machine learning model and deploy the model to the production as well as store different versions of model and dataset. Benefits of MLOps is to make sure the fast delivery of the new trained models to the production to have accurate results. Furthermore, MLOps practice impacts the overall quality of the software products and is completely dependent on open-source tools and selection of relevant open-source tools is considered as challenged while a generalized method to select an appropriate open-source tools is desirable. In this paper, we present a framework for recommendation system that processes the contextual information (e.g., nature of data, type of the data) of the machine learning project and recommends a relevant toolchain (tech-stack) for the operationalization of machine learning systems. To check the applicability of the proposed framework, four different approaches i.e., rule-based, random forest, decision trees and k-nearest neighbors were investigated where precision, recall and f-score is measured, the random forest out classed other approaches with highest f-score value of 0.66.

  • 3 authors
·
Feb 20, 2024