medical informatics teams

Abstract: In the age of data-driven decision-making, deep learning models have become powerful tools for uncovering patterns and making predictions that influence many aspects of society. However, their broader adoption in scientific and business applications is often limited by a lack of interpretability. Feature weighting methods, which assess the relevance of individual features, are among the most widely studied approaches for improving interpretability. While post hoc techniques have advanced significantly, especially in modeling nuanced relationships between features and labels in multiclass problems, embedded methods typically fall short in this regard. Embedded techniques integrate feature relevance learning directly into the model training process, but they are often unable to capture label-specific relationships. To address the limitation, we propose multiple extensions to the Feature Selection Layer, an embedded feature weighting mechanism for neural networks. Through extensive experimentation, we identify the most effective extension and benchmark it against established feature weighting methods. Our results show that the proposed method matches existing techniques in identifying globally relevant features and outperforms them in capturing label-specific relevance. By leveraging the internal dynamics of the trained neural network, it reveals how individual features contribute to the prediction of specific labels, requiring no post-processing beyond the training process.

Abstract: Sampling multiple reports creates an inference problem: how should sampled evidence be converted into a final decision, and does a better structured decision yield a better report? We study these questions through a framework that separates the decision signal, scoring objective, and feasible decision set, followed by text realization. On MIMIC-CXR and IU-Xray, controlled comparisons across 13 generator configurations per benchmark under grouped development/test evaluation reveal three findings. First, changing the objective under fixed evidence and rule capacity changes predictions and their held-out metric trade-offs. Second, relaxing candidate constraints has objective-dependent effects under shared signals and frozen scores. Diagnostics connect the IU macro-oriented assertion increase to near-zero label thresholds and show that limited candidate coverage coexists with selection headroom. Third, a controlled realization study with SFT-Qwen3-VL-8B shows that decision-level gains can be attenuated, amplified, or reversed. Change decomposition reveals that realization can remove incorrect assertions while losing correct findings, so target fidelity and reference accuracy need not improve together. Finding gains also do not consistently improve reference-based report quality. These results motivate separate evaluation of decision rules, candidate constraints, and realized reports.

Abstract: Retrieval-Augmented Generation (RAG) systems are increasingly used for biomedical Question Answering (QA). However, evaluating their effectiveness remains challenging due to the lack of reliable reference resources and the frequent misalignment between automatic evaluation metrics and human judgments. One practical question is how evaluation results should be used to guide development decisions, especially when they correlate weakly with human judgments and may even lead to different conclusions. We explore how to use a small amount of human preference signals to calibrate direct assessment evaluation metrics, and show that calibrated metrics consistently outperform baselines that either treat all metrics equally or rely on a single best metric across multiple datasets.

Abstract: Scientific agents can retrieve relevant passages yet still lose functional order, mix evidence across sources, or state conclusions that exceed the retrieved record. We introduce PathAnchor, a bounded scientific reasoning system built on path-structured evidence workspaces. Instead of treating passages or extracted concepts as independent units, the system retrieves source-linked Material-Sensor-Signal-System trajectories that preserve role, direction, and the evidence supporting each transition. A controller uses three read-only tools to search paper-specific trajectories, trace paths across candidate sources, and open exact evidence before producing a claim-cited answer and an explicit evidence boundary. On 120 single- and cross-paper flexible-sensor questions, PathAnchor scores 82.6% and leads six evaluated systems. Under a matched controller, corpus, and six-call budget, replacing unordered concept graphs with path-structured records raises source recall from 61.3% to 82.9%, increases answers whose claims all cite opened evidence from 69.2% to 90.0%, and reduces tool calls. These results show that evidence organization affects retrieval and citation completeness under fixed agent resources.

Abstract: Verifying multi-step LLM reasoning requires more than determining whether a trace is correct: a useful verifier should identify where the reasoning first goes wrong. However, existing holistic methods provide little positional evidence, while forward sequential verification often treats the first rejected step as the error source. Under error propagation, this assumption can fail, since an earlier mistake may remain locally plausible and become observable only through its downstream consequences. We therefore rethink reasoning verification as a progression-aware error-source localization problem: rather than asking only where a reasoning trace first appears inconsistent, we ask which earlier step best explains how that inconsistency emerges along the trajectory. Based on this view, we propose Progression-aware Reasoning Origin (PRO), a training-free framework for first-error localization. PRO jointly models incoming support from the preceding context and outgoing compatibility with subsequent reasoning, selectively refines regions where these signals disagree, and finally performs detector-conditioned source attribution with intervention-based evidence to distinguish the true error origin from its propagated manifestations. We further formalize the gap between forward rejection and structural exposure, showing why incoming-side evidence alone is insufficient for reliable localization under error propagation. Experiments across open-form, medical, and structured reasoning tasks demonstrate consistent improvements over strong verification baselines, supporting progression-aware source attribution as a more faithful formulation of reasoning verification.

Abstract: Querying clinical trial registries remains a manual and error-prone process, requiring researchers to navigate large volumes of semi-structured data without support for natural language interaction or cross-source synthesis. To address this, we introduce ClinAgent, a conversational system based on agentic Retrieval-Augmented Generation (RAG) that enables clinicians and researchers to query clinical trial information in plain language and receive grounded, up-to-date responses across multi-turn interactions. The system centers on a Large Language Model (LLM) agent following the ReAct paradigm, which iteratively reasons over queries, selects among a set of integrated tools, and refines its actions based on intermediate outputs. These tools include a ClinicalTrials.gov search interface, a PubMed module, and a Python-based analyzer operating on a locally cached structured dataset of clinical trials. We evaluate the system using a three-phase framework assessing operational effectiveness, planning quality, tool-use efficiency, and expert qualitative judgments, comparing three LLM backends: Gemini 3.0 Flash and two variants of DeepSeek V3.2 (thinking and non-thinking). Results reveal complementary strengths, with DeepSeek (thinking mode) excelling in planning quality, while Gemini achieves the highest overall performance and strongest expert ratings. Overall, our findings highlight the potential of agentic AI systems to improve the accessibility and synthesis of clinical trial information, supporting more efficient and user-centered biomedical research workflows.

Abstract: Pretrained diabetic retinopathy (DR) prediction models differ in their input fields, serialization formats, preprocessing requirements, and output semantics. Making these models accessible through a common clinical interface therefore requires explicit coordination between the user interface and the inference service. We designed and implemented DR-LabStack, a React-Flask web system integrating four externally developed pretrained models: RuleFit, Pruned RuleFit, Elaborative XGBoost, and Two-level Ensemble. A shared form retrieves ordered model features, renders model-specific numerical and categorical controls, and constructs a positional input vector. Backend adapters load heterogeneous artifacts and apply the ensemble's accompanying scaler, while a common JSON response supports binary classification display alongside method and source information. Functional evaluation on September 8, 2026 used copied application files and real model artifacts in a documented isolated environment. All four models loaded and exposed their 14-, 6-, 8-, and 25-field contracts. Sixty-two Flask test-client requests characterized service behavior; 12 limited-vector checks confirmed invocation-path and threshold consistency. Twenty-four browser-component scenarios with mocked transport verified input ordering and result rendering and characterized input-validation behavior. The resulting system demonstrates a reusable interaction and serving workflow for heterogeneous DR models. The contribution is web-system design, integration, and software functionality; clinical effectiveness and clinician usability require separate evaluation.