Diagnostic Benchmark

Endoscopic visual question answering (VQA) increasingly asks complex questions that combine several endoscopic answer components rather than isolated factual queries. Such complex answers may be scored as correct even when the same model fails on associated atomic questions. We introduce EndoCA, a paired complex-atomic answer consistency benchmark for evaluating whether complex answers remain consistent with same-image atomic answers. EndoCA contains two suites: EndoCA-Core evaluates compact question-complexity patterns commonly seen in practical endoscopic VQA, and EndoCA-Diagnostic supports controlled analysis across increasing question complexity. We evaluate 11 VLMs spanning open, medical, endoscopy-adapted, and closed-source models on EndoCA. Some VLMs achieve high complex-answer accuracy, yet their atomic-answer accuracy and complex-atomic answer consistency remain substantially lower. To reduce this complex-atomic inconsistency, we introduce Atomic-Support Reconciliation (ASR), a training-free mechanism that uses model-generated atomic answers as contextual premises for answer revision and consistency-guided selective answering. On four selected publicly available models, ASR-Revise improves paired complex-atomic correctness with modest changes in complex-answer accuracy, while ASR-Selective improves accuracy on answered cases by allowing the model to abstain from less reliable cases. Together, EndoCA and ASR provide a consistency-aware benchmark and a training-free mechanism for answer reconciliation and selective answering in endoscopic VQA.

Large language models achieve strong scores on medical benchmarks, yet these benchmarks evaluate each question in isolation, providing no measure of whether a system can distinguish clinically similar presentations requiring different interventions. We introduce MamaBench, the first counterfactual benchmark for maternal and paediatric AI: 434 expert-authored clinical narratives in 217 pairs across 371 pathologies, evaluated via the Bias Trap Rate (BTR), the conditional probability that a model fails the counterfactual given success on the base case. We propose Evidence-Anchored RAG (EA-RAG), a three-stage retrieval method that replaces aggregate similarity with an evidence coverage objective through clinical parameter extraction, coverage auditing, and contrastive sub-queries. Across eight configurations of four frontier LLMs, base accuracy overstates robust accuracy by 16-28 percentage points in every model. EA-RAG achieves 20.3% BTR and 65.0% robust accuracy on Claude Sonnet 4.6, a 5.5 percentage point BTR reduction without degrading base accuracy. The residual 20% BTR confirms that counterfactual robustness in clinical AI remains an open challenge. Keywords: counterfactual evaluation, clinical AI, maternal healthcare, retrieval-augmented generation, diagnostic robustness

Frontier language models are increasingly evaluated on biomedical benchmarks, but two problems undermine most published evaluations: legacy benchmarks are near-saturated, and open-ended responses are graded by other language models. We evaluate Claude Fable 5, Anthropic's most capable publicly available model, across eight biomedical benchmarks, four text and four multimodal, using deterministic scoring against fixed answer keys throughout. We include two Claude predecessors and GPT-5 as baselines. Refusal is tracked as a distinct outcome in every result table. That decision produces the paper's central finding. Fable 5 refuses between 8.0% and 99.4% of questions depending on the benchmark, a pattern absent in both predecessors and in GPT-5. Once refused items are excluded from the denominator, Fable 5's accuracy exceeds or meets every other model on every benchmark in this study. We identify two distinguishable refusal patterns: one concentrating in basic-science and mechanism content across MedQA and MedXpertQA MM, confirmed independently on two benchmarks using each benchmark's own category labels; and a separate disease-domain pattern on RareBench, where inborn metabolic disease presentations are refused near-universally while adult-onset autoimmune presentations are not. The primary constraint on Fable 5's biomedical usefulness is willingness to engage, not capability once it does.

Large language models achieve high scores on medical knowledge assessments, yet clinical reasoning requires actively deciding what to investigate under uncertainty. We developed an agentic evaluation framework in hematologic oncology in which models must proactively request clinical data across three sequential rounds before committing to a diagnosis and treatment plan. Across 32 frontier models, the best achieved only 68% overall accuracy. Information utilization, the fraction of available data actually requested, was the strongest predictor of diagnostic accuracy (R = 0.69, P < 0.001), yet utilization collapsed from 57% to 26% in the final round, leaving molecular and cytogenetic data critical for treatment selection unexamined. Reasoning traces scored high on a clinical reasoning rubric (91% above threshold) but decorrelated from accuracy, revealing a gap between locally coherent rationales and globally correct conclusions. Error analysis identified search satisficing, anchoring and premature closure as the dominant failure modes, the same cognitive biases that characterize novice clinicians under dual-process models of diagnostic reasoning. These findings demonstrate that the primary limitation of current models in clinical oncology is not insufficient medical knowledge but a systematic failure of information-seeking under uncertainty.

Motivation: Rare disease (RD) diagnosis is frequently delayed due to the similarities in symptoms to common disease variants. Machine Learning Algorithms applied to Electronic Health Records show promise for accelerating the diagnosis; however, legal and privacy concerns pose significant barriers. To address these issues, Synthetic Data Generation is an alternative method for obtaining Electronic Health Records and can be applied with any Machine Learning algorithm for benchmarking and development purposes. Despite the availability of Synthetic Data Generation algorithms, support for generating a subset of patients that differ in a definable degree from the majority to simulate patients with RD is often lacking. Results: We present SYNRARE, a graphical user interface based on the Synthea framework that enables easier modification and generation of synthetic Electronic Health Records of RD patients, which differ only to a definable degree from patients with common diseases, thereby enabling the benchmarking and testing of algorithms under controlled technical conditions. SYNRARE enables researchers to rapidly benchmark their Machine Learning algorithms across any scenario. Availability and implementation: SYNRARE, including detailed instructions for installing, is available at https://gitlab.sdu.dk/screen4care/synrare.

Recent benchmarks for VLMs largely assess single- or limited-view perception, leaving untested the core cognitive ability to integrate observations across viewpoints into a coherent, world-centric (allocentric) 3D mental model. We introduce MultiView-Bench, a diagnostic benchmark expressly designed to evaluate multi-view integration for holistic 3D scene comprehension. Unlike existing datasets that focus on pixel-level mapping or camera-relative navigation, MultiView-Bench requires models to decouple object positioning from transient perspectives and ground them in a fixed global coordinate system. This capability serves as a prerequisite for VLMs before being deployed for downstream tasks such as mechanical part assembly. Our systematic evaluation of frontier VLMs reveals consistent failure modes: strong performance on 2D planar relations from a single image, but marked difficulty with 3D spatial relations and with aggregating information across views. We further identify biases in VLMs, such as struggles with unconventional axis directions and sensitivity to object colorways and texture variations. Acknowledging these limitations, we propose ViewNavigator, a multi-agent framework that actively selects informative viewpoints, perceives, and fuses multi-view evidence, improving diverse base models on MultiView-Bench even under a strict budget-matched comparison (and by 3-5x for the full agent).

Quantum Architecture Search (QAS) automates the design of parameterized quantum circuits for variational quantum algorithms, yet existing benchmarks organize instances by molecular identity or qubit count -- criteria agnostic to Hamiltonian structure -- and rely solely on energy accuracy, which cannot detect structural failures such as over-parameterization on near-product ground states. We introduce HamQASBench, a Hamiltonian-informed diagnostic benchmark organizing 11 molecules into five structural tiers via fingerprints derived from the Pauli operator basis, computational basis representation, and ground-state entanglement. A post-hoc critical-structure extraction procedure identifies minimal circuits consistent with each tier's requirements, complementing energy-based evaluation with per-qubit entanglement analysis and pairwise state fidelity. Benchmarking five QAS methods across four paradigms reveals failure modes invisible to conventional metrics: over-parameterization in the minimalism regime, eigenstate commitment under degeneracy, a representation bottleneck in strongly correlated systems, topology-induced routing failure, and circuit search space growth as a scalability bottleneck.

Plasma diagnostic models for tokamak fusion devices are almost universally evaluated on clean, complete sensor data. In practice, fusion diagnostics fail regularly: acquisition systems start late, individual sensors die, and signal dropouts cluster precisely when a plasma disruption is approaching. We present the first systematic robustness benchmark for plasma diagnostic ML using the TokaMark dataset of 11,573 MAST shots, evaluating XGBoost, LSTM, Transformer, and the TokaMark CNN baseline across six physically-grounded failure scenarios and three imputation strategies. We introduce the Robustness Score (RS) for standardized cross-architecture comparison. Our central finding is that disruption-proximate sensor failure (corruption injected in the final window timesteps) collapses sequence model performance (LSTM +212% NRMSE) while a statistical feature model remains comparatively stable (XGBoost +37%). Forward-fill imputation eliminates nearly all degradation from random dropout for sequence models (LSTM +57% to ~0%), but offers little help when the end of the window is corrupted. Shot-level alarm evaluation using ground-truth disruption timestamps reveals that LSTM alarm detection collapses to TPR=0.00 under proximate sensor failure, while mean-fill imputation recovers it to TPR=1.00, a reversal of the pattern observed in NRMSE. Plasma current emerges as the single most critical diagnostic across all architectures (+73% to +140% upon removal). Code, data, and trained checkpoints are available at https://github.com/Neerav-Gupta/tokamark-robustness.

Materials phase diagrams are a core knowledge representation in materials science, encoding temperature,composition, phase stability, and phase transformation pathways, with their full understanding requiring thermodynamic mechanism analysis and scientific reasoning. Although VLMs have shown promise in scientific image understanding, their systematic evaluation on such logically complex images demanding deep mechanistic interpretation remains limited, and phase diagrams provide a challenging testbed for this purpose. We introduce MatPhaseBench, a high-quality, high-reliability benchmark for complex scientific image understanding, focused on materials phase diagrams. MatPhaseBench is constructed from 3681 papers in classical materials science journals, from which 200 high-quality diagram-text pairs were selected, covering 189 material systems and 70 elements. The benchmark has three key features: (1)targeting complex scientific image understanding-it moves beyond simple objective tests to open-ended tasks requiring deep comprehension; (2)comprehensive image-text alignment-semantic information associated with images is fully preserved during literature mining and matching; (3) high-quality human-supervised text acquisition-all descriptions undergo strict manual validation. Experimental results show that current VLMs remain substantially behind expert-level understanding: they are largely limited to surface visual perception, lack deep reasoning grounded in thermodynamic mechanisms, have limited domain awareness and expert analytical experience, and perform poorly in distinguishing fine-grained differences in composite or multi-diagram settings. Overall, MatPhaseBench constitutes a challenging research-grade benchmark, providing a foundational platform for complex scientific image understanding, phase diagram analysis, and trustworthy multi-modal AI in science.

Vision Language Models (VLMs) are increasingly applied to software engineering artifacts, especially UML class diagrams whose meaning depends on visual notation. Yet, it is unclear whether VLMs actually read such diagrams or instead answer from pretrained priors about how classes typically relate. We introduce a controlled UML benchmark in which each prior-conforming diagram is paired with its prior-conflicting counterpart that (1) preserves the same class names and layout while (2) reverses only the relation arrow. We evaluate eight open-source VLMs from two model families, InternVL3.5 and Qwen3, alongside two closed-source frontier models GPT-5.4 and GPT-5.4 Mini. Across the eight open-source models, reversing the arrow reduces relation-direction accuracy by 33.48% on average, while GPT-5.4 Mini retains a 10% gap. In the harder three-class condition, accuracy drops sharply by 45.28% for open-source models, and even 18.62% for the GPT-5.4 family on average. Scaling provides only limited improvements and is family-dependent. Our benchmark presents a diagnostic prior-driven failure in diagram-grounded software understanding. Our artifact is available at https://anonymous.4open.science/r/UMLKnowledgeConflict-8461.

Vision-Language Models (VLMs) are increasingly applied in medical tasks such as pathology description, report generation, and visual question answering. Medical Image Quality Assessment (MIQA) supports diagnostic accuracy and patient safety by determining whether images meet the standards required for clinical decision-making. Automating MIQA with VLMs may reduce workload, but their behavior under real-world conditions, where images may be degraded or textual context may affect judgments, should be further explored before deployment. We benchmark VLMs on medical image quality using the MediMeta-C dataset zero-shot across seven corruption types and five severity levels. We evaluate sensitivity to degradation patterns, the effect of corruptions on embedding geometry, and whether textual attributes (demographics, expertise, infrastructure, institution) alter scores. Across 16 VLMs and seven modalities, pixelation produced the largest score reductions (mean -20.58%, up to -34.4% for OCT), whereas brightness had limited effect (-0.81%). Embedding displacement was associated with score changes. Same-family models showed correlations of 0.67-0.83; some produced increases up to +31% for corrupted mammography. Textual attributes affected scores: institutional prestige raised them +17.15%, and equipment age lowered them -14.7%. The largest changes were +95.62% (InternVL-8B) and -37.7% (MedGemma). Current VLMs show limitations for medical image quality assessment. Pixelation, a privacy-preserving transformation, reduces performance, indicating a trade-off between patient privacy and reliability. Sensitivity to contextual metadata indicates limited objectivity and marks metadata as a privacy and bias source. Privacy protection and objective quality assessment are related requirements for use.

Existing medical video benchmarks primarily evaluate whether a model produces the correct answer, but rarely assess whether it answers at the right time. In real clinical settings, AI systems must decide not only what to predict, but also when to answer, defer judgment, or proactively raise alerts. This creates a critical gap between benchmark evaluation and deployment requirements. We present MedStreamBench, a benchmark for time-aware medical video understanding. MedStreamBench integrates 22 medical datasets and 5,419 QA instances across four temporal settings: retrospective, present, future, and proactive. Unlike conventional benchmarks that assume full-video access, MedStreamBench restricts models to temporally bounded evidence windows and supports both single-turn and streaming evaluation. We further introduce a proactive monitoring setting that requires models to determine whether and when clinically relevant alerts should be triggered. Beyond answer correctness, MedStreamBench evaluates temporal behavior through responsiveness and post-evidence stability. Experiments on leading general-purpose and medical vision-language models reveal a substantial gap between offline recognition and temporally grounded decision-making, with performance dropping markedly in streaming and proactive settings. Our benchmark is available at https://huggingface.co/datasets/Venn2024/MedStreamBench.

Large language model agents are increasingly connected to scientific software, yet it remains unclear when tool access makes scientific computation more reliable rather than merely more complex. We introduce PHREEQC-MCQ-200, a benchmark for evaluating tool-augmented agents on deterministic aqueous-geochemistry simulations. The benchmark contains 200 multiple-choice questions derived from 21 validated PHREEQC scenarios, requiring agents to construct simulator inputs, execute PHREEQC, inspect structured outputs, and commit to final answers. Across multiple frontier and mid-tier model families, simulator access substantially improves aggregate accuracy, confirming that grounded execution is necessary for many scientific-computation tasks. However, the gains are not monotonic: tool-augmented agents also lose items they answered correctly without tools, revealing regressions that average accuracy alone hides. We further show that output-access protocol matters. A table-of-contents interface can reduce token cost while preserving or improving accuracy for stronger models, but it degrades performance for mid-tier models that cannot reliably navigate structured simulator outputs. PHREEQC-MCQ-200 therefore frames scientific tool use as an end-to-end diagnostic problem rather than a simple tool-calling capability. We argue that evaluations of scientific agents should report not only accuracy, but also item-level retention, output-access sensitivity, trajectory failures, and where the computation chain breaks.

Rare disease differential diagnosis is a critical yet arduous clinical task, requiring physicians to identify precise phenotypes from complex, unstructured patient symptoms and execute intricate reasoning within a vast search space. However, existing AI approaches typically rely on pipeline-based phenotype extraction or retrieval-augmented generation, which suffer from critical information loss due to predefined ontologies, retrieval bottlenecks, and a lack of diagnostic logic. To address these challenges, we introduce RareDxR1, an end-to-end reasoning-centric large language model designed for open-domain rare disease diagnosis directly from unstructured clinical notes. We design a progressive end-to-end training framework by synergizing knowledge internalization with autonomous evolutionary learning, thereby bypassing reliance on structured phenotypes and closed-set decision-making. To overcome the limitations of RAG and phenotype restriction, we enabled the deep internalization of fragmented rare-disease knowledge directly into the model's parameters. Moreover, to bridge the gap between model generation and expert reasoning, we propose Reflection-Enhanced Reasoning Sampling (RERS), a strategy that synthesizes expert-level diagnostic trajectories by learning from failures without human annotation. Additionally, we propose a dual-level curriculum reinforcement learning approach for gradually mastering rare disease diagnosis. Experimental results demonstrate that RareDxR1 achieves state-of-the-art accuracy across different benchmarks, marking a significant breakthrough in open-domain rare disease diagnosis. Our code and dataset will be publicly available.

Recent music audio-language models achieve high accuracy on instrument question-answering benchmarks, but it remains unclear whether this reflects robust audio grounding or benchmark-specific shortcuts. In this paper, we introduce an OpenMIC-derived diagnostic benchmark sequence for instrument grounding in music audio-language models, extending binary instrument-presence QA to genre-prior-reduced examples, confusable instrument discrimination, longer audio context, and temporal localization. Across these settings, high binary QA accuracy often fails to predict model behavior: models can exhibit option-position bias, confusable-instrument errors, and temporal response bias. These results suggest that instrument grounding should be evaluated with multi-axis diagnostic benchmarks rather than a single aggregate accuracy.

Current evaluation protocols for Vision-Language Models (VLMs) in Radiology Report Generation (RRG) rely on report-level metrics that measure lexical overlap or aggregate clinical correctness. However, such metrics do not test whether individual diagnostic statements stem from the actual pathological evidence visible in the image. This allows models to achieve competitive scores by exploiting learned priors or spurious correlations, a failure mode we refer to as vision shortcut. We introduce SHOVIR, a benchmark for evaluating vision shortcut behavior in RRG. SHOVIR extends two spatially annotated chest X-ray datasets, MIMIC-CXR and PadChest-GR, with per-box CheXpert labels, and defines image-level and disease-level occlusion experiments that contrast baseline performance on clean images against localized, region-specific perturbations. Comparing predictions across these conditions isolates two failure modes at the disease-class level: direct shortcuts, where a finding persists after its visual evidence is removed, and contextual shortcuts, where detection degrades once co-occurring pathologies are occluded despite the target region remaining intact. Benchmarking eight state-of-the-art VLMs, we find that shortcut behavior varies substantially across architectures and datasets. Models achieving the highest baseline report quality do not necessarily rank highest in spatial grounding, revealing that clinically fluent generation can coexist with shallow reliance on visual evidence. These findings expose a blind spot in current RRG evaluation and motivate region-aware assessment protocols.

Modern large language models (LLMs) reach 60-70% diagnostic accuracy on complex clinical case benchmarks, but accuracy alone cannot distinguish stable clinically-grounded reasoning from pattern matching. We introduce clinical reasoning graphs, structured graph representations extracted from free-text LLM diagnostic traces using a domain-grounded ontology with 5 node types and 7 edge types. We apply this pipeline to 750 traces from five LLMs across 50 New England Journal of Medicine Clinicopathological Conference cases and three prompt conditions, and test whether diagnostic traces show stable structured reasoning patterns, or diagnostic schemas, for clinically similar cases. We operationalize this as higher graph similarity among clinically similar cases than among clinically dissimilar ones. Across 15 model-condition comparisons, within-cluster and between-cluster composite similarity are nearly equal, and no comparison survives multiple-testing correction; a component-level analysis finds any residual content signal far below schema scale. Graph similarity is also nearly identical for pairs of models that are both correct (0.488) and both incorrect (0.484), suggesting that graph structure captures a dimension not reflected in diagnostic accuracy. Structured reflection prompting increases explicit discriminating-feature analysis within traces (+33%) but does not increase cross-case consistency. These results show diagnostic competence without schema-scale reasoning consistency, and indicate that final-answer accuracy should be complemented by process-level evaluation. We release the ontology, extraction pipeline, validation protocol, and the extracted reasoning graphs and similarity artifacts as resources for structured evaluation of LLM clinical reasoning.

The verbose context problem occurs when structured concepts have token-inefficient textual representations. This bottleneck is acute in population health: cohort-level analysis of longitudinal patient records requires reasoning over thousands of medically-coded events, often exceeding 400K tokens in total. We present PopMedQA, a benchmark isolating this problem through computational tasks on groups of longitudinal patient records. We construct the benchmark using neopatient, a new library for language-controlled generation of artificial patient records. Through extensive ablations -- including prompting strategies, prompt compression, and agentic decomposition -- we find that domain-independent methods fail to alleviate the verbose context problem. There remains significant opportunity to exploit domain-specific structure in language model inputs for population-scale reasoning.

Physicians now pose millions of clinical questions to AI tools each week, yet these tools are evaluated largely on hypothetical or exam-style questions, not those actually asked in practice. We report a blinded evaluation built on 620 Real-world Point-Of-Care Queries (Real-POCQi) submitted to the OpenEvidence (OE) platform by physicians spanning 30 specialties, as well as 187 questions from HealthBench. 149 practicing physicians across 36 states made head-to-head comparisons between answers from three frontier general-purpose models (Claude Opus 4.8, Gemini 3.1 Pro, and GPT-5.5) and a specialized clinical tool (OE), with graders matched to each question's specialty. When comparing answers along five dimensions relevant to clinical decision support -- accuracy, clinical utility, source quality, verifiability, & completeness -- physicians scored the specialized tool highest on all axes; in the primary analysis on Real-POCQi, win differences (margins between win and loss rates) ranged from 25 to 39 percentage points (p<0.001). Results remained consistent in sensitivity analyses stratifying by citation display, answer length, OE-user status, and Real-POCQi versus HealthBench. In parallel, LLM judges were found to systematically differ from expert judges, though both generally agreed on the best model. These findings underscore two conclusions: (i) AI tool evaluations should reflect real-world query distributions and use expert judges that mirror the specialization defining modern medicine and (ii) the consistent advantage of the specialized tool over general-purpose models does not necessarily mean that the latter cannot serve similar purposes, but that targeted engineering and customization can yield meaningful gains in performance for its users. We release Real-POCQi as a public benchmark, as well as the prespecified statistical analysis for reproducing results of this study.

Recent interest in multimodal large language models (MLLMs) raises a central question: can they reason over dynamic visual evidence rather than merely recognize objects or events in individual frames? This ability, which we refer to as video temporal-logical reasoning, requires models to maintain, update, and compose evidence as visual states evolve across frames. Existing video benchmarks often conflate this capability with scene complexity, static recognition, or uncontrolled temporal variation. To isolate this capability, we introduce Video-MME-Logical, a controlled benchmark organized around five temporal-logical operations: state tracking, sequential counting, temporal ordering, dynamic spatiality, and structural composition. The benchmark contains 25 fine-grained task categories generated with controlled object states, transitions, temporal dependencies, and logical compositions. It enables difficulty-controlled final-answer evaluation by varying temporal horizon and reasoning complexity, and supports intermediate-state diagnostics by verifying whether models recover the required logical reasoning trace before producing the final answer. Experiments with state-of-the-art MLLMs reveal a substantial human-model gap, especially as temporal-logical complexity increases. Supervised fine-tuning on up to 500K generated samples improves performance but remains insufficient to close the reasoning gap, positioning Video-MME-Logical as a scalable testbed for analyzing and improving temporal-logical reasoning in MLLMs.

Reasoning in multimodal large language models (MLLMs) has shown strong promise in medical imaging. However, this reasoning is usually free-form text judged only by its final answer, making it hard to interpret and verify, especially in 3D radiology, where a diagnosis should be traceable to evidence in the scan. Existing chest CT question-answering datasets compound this by reducing expert radiology reports to answer-only pairs, dropping the reasoning that links findings to conclusions and omitting the patient history clinicians rely on. As a result, reasoning-capable 3D chest CT MLLMs remain out of reach, as neither the structured supervision needed to train them nor the protocol needed to verify their reasoning yet exists. We introduce CORTEX (Clinically Organized Reasoning and sTructured EXplanation), a structured reasoning benchmark for 3D chest CT. For each question, CORTEX restores the missing reasoning as a four-stage diagnostic trace mirroring a radiologist's workflow: task understanding, visual observation, diagnostic reasoning, and answer synthesis. We generate these traces using frontier large language models with broad medical and general-domain knowledge, then filter and verify them with a stage-level evaluation protocol combining automated rubric scoring with expert radiologist review. Crucially, both the reasoning structure and evaluation rubrics are designed in close collaboration with clinicians. Built on CT-RATE, a large, publicly available chest CT dataset without reasoning annotations, CORTEX comprises 76,177 validated reasoning traces across open-ended VQA, closed-ended VQA, and report generation, providing both the structured supervision and the stage-level evaluation protocol needed to build and evaluate trustworthy reasoning models for 3D chest CT. Our dataset and evaluation code is available at https://huggingface.co/datasets/aneesurhashmi/cortex

Rare diseases affect millions of individuals worldwide, yet timely diagnosis remains a major public health challenge due to scarcity of specialized clinical expertise. While large language models (LLMs) show promise to support rare disease diagnosis, current models are constrained by insufficient clinical deployability, limited clinically grounded evidence, and scarcity of training data. Here we present RaDaR (Rare Disease navigatoR), an open-source, compact reasoning LLM (32B parameters) for rare disease diagnosis. RaDaR was trained with 49,170 publicly available free-text cases and 104,666 synthetic cases with reasoning-enhanced training. RaDaR showed the strongest performance among evaluated open-source models, including the 671B DeepSeek-R1, across public benchmarks and four external validation centers. In a retrospective cohort, RaDaR prioritized the final diagnosis before documented clinical suspicion in 61.06 percent of cases, corresponding to a potential lead time of 1.87 months and 50.18 percent of the within-center interval. In a randomized physician-assistance trial, RaDaR assistance improved physicians' rare-disease diagnostic accuracy by 21.44 percentage points compared with internet search alone. Synthetic-data ablations suggested that phenotype-anchored narratives provide useful training signal for long-tail rare diseases, with a monotonic scaling trend within the tested data range. Together, RaDaR and its development and validation framework provide a deployable rare-disease reasoning model and a reproducible development framework for diagnostic AI under data scarcity.

Existing medical AI benchmarks lack process visibility, atomic skill evaluation, and integrated hallucination detection. We introduce MedBench v5, a redesigned benchmark for clinical multimodal models (language, vision-language, and agent systems) that moves from static QA to dynamic, process-oriented evaluation. MedBench v5 features: (1) a dual-dimensional framework combining Clinical Cognitive Responsiveness (13 sub-dimensions) and Medical Atomic Skills (4 agent environments), covering 63 tasks; (2) three switchable information-flow stressors (omission, contradiction, evidence delay) for factorized degradation analysis; (3) a dynamic process audit protocol with five reasoning nodes that produces model-specific failure fingerprints; (4) hallucination propagation monitoring across initiation, propagation, anchoring, and contradiction interaction-capturing silent hallucination. Experiments on frontier models show that strong overall task performance does not guarantee process stability: stressors mainly disrupt contradiction detection, diagnosis updating, hallucination propagation, and contradiction-based self-correction, while final evidence grounding can remain superficially stable. MedBench v5 provides a unified infrastructure for capability profiling, controllable stress testing, process auditing, and hallucination trajectory analysis in clinical AI evaluation.

Large language models (LLMs) can produce clinically fluent recommendations for type 2 diabetes while failing to satisfy guideline constraints or explicitly justify lifestyle-related glycemic claims. We present T2D-Bench, a reproducible benchmark and evidence-gated evaluation framework for testing whether LLM outputs satisfy explicit, graph-checkable evidence requirements. T2D-Bench is built on a multi-layer clinical-lifestyle knowledge graph that combines a biomedical spine (UMLS, DrugBank, SIDER), computable ADA Standards of Care rules, and lifestyle knowledge connected through a mechanistic bridge to glycemic laboratory effects. Across 100 structured vignettes spanning diagnosis, medication safety, and adversarial lifestyle conflicts, baseline outputs failed benchmark-defined evidence-path checks in 35% of cases for GPT-4o-mini and 33% for GPT-4o. The evidence gate detects unsupported omissions and uses constrained revision to bring outputs into verifier-level compliance with benchmark-defined evidence requirements. These results show that computable evidence constraints can make unsupported clinical omissions explicit, measurable, and correctable in diabetes-focused LLM outputs.

Clinical agents promise to democratize access to electronic health records (EHRs), yet existing benchmarks fail to reflect the complexity of practical EHR analysis, e.g., often operating on idealized, clean EHRs via static SQL generation rather than interactive execution. In this work, we introduce EHR-Complex, a large-scale benchmark designed for interactive clinical database reasoning. Built on the large MIMIC-IV substrate (365K patients, 31 tables, 500M+ records), EHR-Complex comprises about 52K tasks spanning six clinical intents, supporting both patient-level and population-level queries, where each task requires an agent to interact with a sandboxed environment by executing SQL queries or Python code. Notably, EHR-Complex considers the real-world SQL task complexity for longitudinal multi-table aggregation and compositional reasoning, resulting in 31.93 SQL structural components per query on average. Evaluation results on EHR-Complex reveal the clinical difficulty of these EHR reasoning scenarios, with the top-performing model achieving only 62.3% exact-match accuracy. Pass^k consistency drops below 50% for nearly all evaluated models at k=4, exposing broad stochastic fragility. A fine-grained analysis of more than 3,800 failed trajectories for representative LLMs reveals three dominant failure modes: SQL logic errors, medical-code lookup failures, and semantic misunderstandings. EHR-Complex provides a rigorous testbed for clinical agents and highlights remaining gaps in robust reasoning for large-scale EHR analysis.

The evaluation of vision-language models (VLMs) for chest X-ray (CXR) analysis has largely been limited to disease-presence classification without visual grounding. Such evaluations fail to verify the expert-level lesion perception necessary to ensure the clinical reliability of VLMs. To address these limitations, we introduce CheXpercept, a sequential, multi-level perception benchmark that mirrors a radiologist's cognitive workflow across coarse-level detection, fine-level contour evaluation and revision, and semantic-level attribute extraction. To ensure high clinical fidelity at scale, we construct the dataset using a semi-automated generation pipeline paired with a review by six medical experts. CheXpercept contains 10,400 QA items derived from 2,100 CXRs, covering seven clinically critical pulmonary and cardiac lesions. To demonstrate the current landscape of VLM perception, we benchmark 14 general and medical VLMs on CheXpercept. The models achieve adequate performance only at the coarse level, with accuracy degrading precipitously on deeper visual tasks. Notably, medical VLMs show almost no perceptual advantage over their general-domain counterparts, highlighting a systemic flaw in current domain adaptation. The code and dataset will be publicly available.

Recent text-to-image generation models have demonstrated remarkable capabilities in synthesizing highly realistic images from text inputs alone. Although existing benchmarks can evaluate the generation capabilities of various models to some extent, they struggle to comprehensively and accurately measure performance across multiple dimensions, often failing to reveal the inherent deficiencies of models in specific categories. To address these limitations, we propose WeGenBench, a novel benchmark designed for the comprehensive, multi-perspective evaluation of text-to-image generation capabilities. Our benchmark comprises a total of 4,000 test prompts across two primary categories, meticulously balanced between Chinese and English to evaluate bilingual and cross-cultural generation capabilities. Beyond macroscopic scene classification, we annotate each prompt with multi-dimensional tags tailored to the distinct content and challenges of each language, thereby refining the generation tasks into more specific sub-categories. Through a cross-dimensional evaluation mechanism leveraging both scene classifications and multi-dimensional tags, WeGenBench can precisely pinpoint model shortcomings in specific generation categories. Furthermore, to measure generation quality more accurately, we design and validate several novel evaluation metrics by integrating Vision-Language Models (VLMs), which assess model performance on domain-specific tasks from three core aspects. Crucially, our approach yields both the assessment outcomes and the detailed reasoning trajectories, facilitating a rigorous verification of the accuracy and soundness of the evaluation results. Finally, we conduct systematic benchmarking on current state-of-the-art methods and provide an in-depth analysis of the limitations present in existing models.

Recent advancements in Large Vision-Language Models (LVLMs) have demonstrated remarkable multimodal perception and reasoning capabilities. While numerous benchmarks have evaluated LVLMs from holistic or task-specific perspectives, their capabilities on fine-grained image tasks-fundamental to computer vision-remain insufficiently understood. To address this gap, we introduce FG-BMK, a comprehensive fine-grained evaluation benchmark containing 1.01 million questions and 0.28 million images, covering diverse scenarios from common object-centric domains to specialized domains. FG-BMK jointly evaluates dialogue-level fine-grained semantic recognition and feature-level visual discriminability through human-oriented and machine-oriented paradigms, enabling diagnostic analysis of whether LVLM failures arise from insufficient visual representations, weak visual-to-semantic grounding, or limited fine-grained knowledge. Through extensive experiments on a diverse set of representative LVLMs/VLMs, we find that current LVLMs remain inadequate fine-grained recognizers, with failures arising from intertwined bottlenecks in visual representations, semantic grounding, modality alignment, and category-level knowledge. We further analyze training design factors for improving fine-grained capabilities and examine how visual and linguistic perturbations affect LVLM predictions. These findings provide diagnostic insights into the limitations of current LVLMs and offer guidance for future data construction and model design in developing more reliable LVLMs for fine-grained visual tasks. Our code is open-source and available at https://fg-bmk.github.io/.

The most plausible near-term role of medical LLMs is to assist rather than replace physicians, yet current evaluations often test isolated capabilities: clinical knowledge, EHR system interaction, or patient communication. Physician assistance instead requires coordinating these capabilities within the same interaction, where physicians issue underspecified requests, patients describe symptoms ambiguously, and EHR systems demand precise tool use. We introduce PhysAssistBench, a benchmark for interactive doctor-patient-EHR assistance. Built from real MIMIC-IV cases, PhysAssistBench uses a scalable pipeline to construct agentic patients: interactive, record-grounded agents that turn static EHR records into multi-turn clinical scenarios while preserving clinical factuality. PhysAssistBench provides a curated bilingual evaluation set of 1,296 manually reviewed and physician-validated turns. Experiments with leading LLMs show that current models remain unreliable in this setting, which exposes a key bottleneck for clinical LLMs: reliable assistance requires coordination across knowledge, communication, and systems, not isolated gains in any of them.

Language models increasingly serve as advisory systems in maintenance operations. To prevent hallucination, recent systems ground these models in procedural documentation to constrain them to approved steps. In practice, however, operator queries frequently stray from this path, requiring models to recognise out-of-scope inputs mid-conversation, a dynamic that current benchmarks rarely prioritise. We introduce DiagFlowBench, a dataset of 50 industrial diagnostic flowcharts from a consumer manufacturer converted into 1,676 multi-turn conversations that contrast compliant with out-of-scope utterances. Evaluating a panel of ten commercial and open-weight models reveals high variability in abstention rates, with models commonly selecting a real but contextually inadequate step rather than fabricating facts. The inherent plausibility and authority of this mapped but wrong advice exposes a challenging vulnerability for grounding systems.

Generalist embodied agents require more than object recognition: they must reason about spatial relations, actions, procedures, human intentions, environmental constraints, and commonsense consequences from situated visual observations. Yet existing visual and embodied question answering benchmarks often provide limited control over the reasoning dependencies being tested, making it difficult to distinguish grounded embodied reasoning from shortcut-driven visual or linguistic pattern matching. We present ERQA-Plus, a diagnostic benchmark for reasoning in embodied AI. ERQA-Plus contains 1,766 question-answer instances grounded in 711 robot-centric images and organized according to a structured taxonomy spanning perceptual, action-centric, social-interaction, navigation-environmental, and contextual commonsense reasoning. The dataset is constructed using a multi-stage generation and validation pipeline that combines taxonomy-guided question generation, automatic quality judging, iterative revision, and human assessment to improve visual grounding, answer validity, and reasoning quality. We benchmark representative general-purpose vision-language models and embodied models, including LLaVA-NeXT-8B, Prismatic-7B, MiniCPM-V-4.5-8B, Qwen3-VL, RoboRefer-8B, and RoboBrain2.5-8B. Although the strongest model, Qwen3-VL-32B, achieves 83.4% overall accuracy and 61.4 SBERT score, category-level results reveal persistent weaknesses in spatial reasoning, procedural reasoning, event prediction, and intention inference. ERQA-Plus therefore provides a fine-grained evaluation framework for measuring not only whether embodied agents answer correctly, but also which forms of embodied reasoning they can and cannot perform reliably. The dataset is available https://huggingface.co/datasets/huggingdas/erqa-plus and the project page at https://github.com/LUNAProject22/erqa-plus.

Safe deployment of clinical vision-language models (VLMs) requires reliable uncertainty estimation (UE): a signal indicating when predictions should be trusted or escalated to a clinician. We test whether current UE methods actually deliver this signal. Benchmarking 8 methods across 12 VLMs on clinical visual question-answering (VQA), we find that UE quality is not an intrinsic property of the UE method: it tracks model accuracy, degrading precisely where the model performance is weakest, and therefore where reliability is most needed. When we stress-test models by hiding the correct option among the multiple-choice answers (NOTA perturbations), accuracy collapses while uncertainty barely changes, leaving models systematically miscalibrated. Yet, we find that uncertainty on the unperturbed input reliably anticipates which predictions will collapse under NOTA, indicating that UE in current VLMs carries diagnostic information about model fragility. Our results position UE as a diagnostic tool for identifying fragile predictions and motivate perturbation-based evaluation as a path toward safe clinical deployment.

Rare disease diagnosis depends on expert reasoning that is scarce and difficult to transfer. Large language models rank the correct disease first in only 35.4% of benchmark cases and often rely on learned phenotype-disease associations rather than reusable diagnostic reasoning strategies. We developed liteOdyssey through Policy Iteration with Human Feedback, a process in which model failures and expert corrections are iteratively consolidated into a clinician-gated, natural-language policy executed by a language model. Across 1,243 public benchmark cases spanning 722 rare diseases, liteOdyssey ranked the correct disease first in 59.3% of cases versus 26.5% without the policy, with comparable gains in cases involving diseases excluded from policy development. The same policy transferred across model families and sizes without retraining. Adaptation of the policy to the Undiagnosed Diseases Network (UDN) improved diagnostic accuracy among 515 UDN patients, with gains confirmed by blinded physician adjudication. These results show that expert reasoning can be externalized into an inspectable and revisable natural-language policy that generalizes across rare diseases, transfers across model backbones, and adapts to a real-world patient cohort.

Building trustworthy medical multimodal large language models (MLLMs) is critical for reliable clinical decision support. Existing medical hallucination benchmarks mainly focus on data collection, but often ignore where hallucinations originate within the reasoning process. We find that hallucination sources vary across samples: errors may arise from visual misrecognition, incorrect medical knowledge recall, or flawed reasoning integration. To enable source-level hallucination diagnosis, we introduce ClinHallu, a benchmark for stage-wise hallucination diagnosis in medical MLLM reasoning. ClinHallu contains 7,031 validated instances, where each instance is augmented with a structured reasoning trace decomposed into Visual Recognition, Knowledge Recall, and Reasoning Integration. We also use stage-replacement interventions to measure how correcting specific stages affects the final answer. Beyond evaluation, we show that trace-supervised fine-tuning reduces stage-wise hallucinations. ClinHallu provides a fine-grained hallucination testbed for diagnosing and mitigating reasoning failures in medical MLLMs. The benchmark is publicly available at https://github.com/alibaba-damo-academy/ClinHallu.

Large language models (LLMs) now reach expert-level scores on medical licensing exams, encouraging the assumption that high scores imply safe medical judgment while patients increasingly use them for health advice. We show this assumption is fragile: when misleading context is injected into questions that LLMs originally answer correctly, they abandon the correct answer. We call the ability to maintain correct judgment under adversarial context epistemic resilience, and introduce MedMisBench to measure it. MedMisBench contains 10,932 medical question items and 48,889 misleading context-option pairs spanning medical reasoning, agentic capability, and patient-journey evaluation. Across 11 model configurations, mean accuracy falls from 71.1% on original questions to 38.0% under focused misleading context, with 51.5% attack success. The most damaging injections are formal, rule-like fabrications: authority-framed falsehoods reach 69.5% attack success and exception-poisoning claims reach 64.1%. A 14-member clinical panel from 7 countries identified serious potential harm in 38.2% of reviewed cases. MedMisBench exposes a structural blind spot in LLM evaluation in medical settings: existing benchmarks measure what models know, but not whether they preserve correct medical judgment under misleading context.

Diagnosing pulmonary diseases requires integrating heterogeneous evidence amid phenotypic variability and cross-disease overlap. Although large language models (LLMs) have shown progress on pulmonary knowledge question answering (QA) and information-processing tasks, reliable pulmonary diagnosis requires patient-specific, relation-aware reasoning over electronic medical record (EMR) evidence rather than isolated knowledge recall. We define this gap between pulmonary knowledge and case-level diagnostic reasoning as the Pulmonary Knowledge-to-Diagnosis Gap. To address it, we introduce LungKG, the first structured pulmonary knowledge graph for diagnostic knowledge organization and record-grounded reasoning. LungKG contains 59,038 nodes and 164,308 edges across 15 entity types and 112 relation types, serving as both a reusable pulmonary knowledge resource and the foundation for LungKG-guided model adaptation. Built on LungKG, we propose Lung-R1, a LungKG-guided pulmonary LLM trained through KG-constrained reasoning-chain construction and KG-guided reinforcement learning. In a 20-system evaluation, Lung-R1-14B achieves state-of-the-art performance across Choice, Pulmonary-QA, and EMR Diagnosis, reaching an EMR Diagnosis score of 4.3583 and surpassing the strongest non-Lung-R1 baseline by 0.1476 points. These results demonstrate the value of LungKG-guided training for EMR-based pulmonary diagnosis.

Strabismus is a common ocular disorder that requires fine-grained subtype diagnosis for individualized treatment planning. However, existing deep learning methods mainly provide diagnostic predictions without transparent reasoning, while recent large vision-language models (LVLMs), although promising for joint image understanding and report generation, remain highly prone to hallucination in this evidence-sensitive and rule-driven medical task. To address these challenges, we propose MAGIS, an evidence-based Multi-AGent reasoning for Interpretable Strabismus diagnosis framework. MAGIS transforms black-box end-to-end generation into a structured diagnostic process consisting of candidate hypothesis generation, dual-evidence constrained context, evidence-based corrective verification, and report generation. Specifically, we introduce a Dual-Evidence Constrained Context (DECC) mechanism that jointly organizes visual evidence from the photograph of the nine cardinal positions of gaze and evidence-based clinical diagnostic rules into a constrained context for reliable diagnostic reasoning. We further develop an Evidence-Based Corrective Verification (EBCV) mechanism that verifies whether the current diagnostic hypothesis is supported by visual evidence, heatmap-based visual cues, and evidence-based clinical diagnostic rules. Hypothesis refinement is triggered when inconsistency is detected. Experiments on a fine-grained strabismus benchmark demonstrate that MAGIS not only significantly outperforms other state-of-the-art diagnostic systems, improving the weighted F1 score from 72.0% to 91.3%, but also substantially improves the clinical reliability (consistency, alignment, and completeness) of generated diagnostic reports. These results demonstrate that MAGIS provides an effective solution for building accurate, evidence-based, and clinically interpretable strabismus diagnosis systems.

Clinical diagnosis requires flexible use of multiple reasoning paradigms under incomplete patient information. Existing LLM-based medical agents show strong medical reasoning ability, but single-paradigm or naively mixed dialogue supervision makes these paradigms difficult to learn without interference. We propose \textbf{PACT} (Periodic Anchor Consensus Training), a framework that couples supervised multi-paradigm dialogue synthesis with consensus-based Branch training. At the data level, \textbf{DPS} (Doctor-Patient-Supervisor) uses complete electronic medical records (EMRs) for quality control while keeping the doctor agent restricted to patient-visible information. This produces validated dialogues under four diagnostic reasoning paradigms without leaking hidden clinical answers. At the training level, PACT trains one paradigm-specific LoRA Branch per paradigm and periodically aggregates Branches into a shared Anchor through sign consensus. We further construct a dynamic multi-turn Chinese medical diagnosis benchmark for interactive consultation. Experiments show that PACT achieves state-of-the-art performance among compared proprietary, medical-specialized, and task-adapted baselines on diagnostic outcome and consultation-process metrics.

Planning is central to LLM agents: before acting, an agent must decompose goals, select tools, reason over constraints, and decide when a task is infeasible. Yet existing agent evaluations often report only end-to-end success, making it difficult to determine whether failures stem from planning or execution. We introduce Agent Planning Benchmark (APB), a planning-specific diagnostic benchmark with 4,209 multimodal cases across 22 domains and five settings, covering holistic planning, feedback-conditioned step-wise planning, and robustness under extraneous tools, broken tools, and unsolvable tasks. Across 12 MLLMs, APB reveals systematic weaknesses in long-horizon planning, tool-noise robustness, calibrated refusal, and inference-time refinement. We further validate APB on 200 ToolSandbox tasks and 200 $τ^2$-bench tasks, where APB-guided refinement consistently improves plan correctness, plan grade, and downstream execution metrics across three representative models. APB thus serves as an upstream diagnostic complement to execution benchmarks. The APB benchmark and code are available in \href{https://github.com/Mikivishy/AgentPlanningBenchmark}{this URL}.

Many real-world questions over business, legal, and scientific corpora are natural-language versions of database-style queries over records latent in text. Existing retrieval-augmented generation (RAG) systems are optimized primarily for semantic relevance, but retrieving plausible passages does not guarantee correct query execution. We introduce QO-Bench, a diagnostic benchmark for query-operator question answering over typed event tuples. The benchmark covers 22,984 news articles and 614 corporate events, with 18 query templates instantiating 785 questions. Each gold answer is deterministically computed from typed event tuples and scored by recall, with answers matched to the gold tuples by exact match rather than an LLM judge. This design enables operator-level diagnosis such as joins and intersection. We evaluate RAG, ReAct RAG, GraphRAG, and information-extraction-to-SQL under matched conditions, with a long-context oracle ceiling to isolate retrieval failure. A two-axis framework -- index-time preservation versus query-time execution -- predicts where each paradigm fails, and the results bear it out: systems retrieve relevant text but discard the typed values operators need, and the deployable paradigm ranking inverts across operators, with similarity retrieval leading on filter/project and extraction-to-SQL on intersection and counting. Even given the gold evidence, a long-context oracle stays far from saturated, so operator execution -- not retrieval alone -- is a core bottleneck that a stronger answer model does not remove. QO-Bench reframes the goal from passage relevance to query-operator-preserving retrieval. The benchmark, predictions, and code are released at https://github.com/ZHANG-MENGAO/qo-bench.

Progress in genomic foundation models is difficult to assess due to fragmented benchmarks, incompatible evaluation protocols, and task-specific reporting. As a result, claims of superiority or generality across models are often not directly comparable. We introduce GENEB, a large-scale diagnostic benchmark that evaluates frozen representations from 40 genomic foundation models across 100 tasks spanning 13 functional categories under a unified probing-based protocol, including few-shot regimes. GENEB enables controlled comparison across model scale, architecture, tokenization, and pretraining data while explicitly exposing task-level trade-offs. Our analysis shows that aggregate leaderboards are unstable: model rankings vary sharply across task categories, scale provides only modest and inconsistent gains, and architectural and pretraining alignment frequently outweigh parameter count. These results highlight limitations of current evaluation practices and position GENEB as a reference framework for principled comparison and category-aware model selection in genomic machine learning.

Large language models (LLMs) are increasingly used for health-related decision support. Yet most evaluations treat diagnosis as a single-shot task with complete information provided upfront, often as a multiple-choice selection. This diverges from clinical practice, where diagnosis is interactive and open-ended, involving sequential hypothesis refinement through targeted questioning. We address this gap. We build MeDxBench, a large-scale benchmark of 4,421 clinical cases across 20 specialties. We further propose MeDxAgent, a multi-agent consultation system for interactive diagnosis, and systematically study its prompt-, flow- and agent-level design choices. MeDxAgent achieves a 10.3% accuracy gain over the baseline on MeDxBench, closing 52.3% of the gap to a full-information oracle. We find that specific design choices: collecting demographics first, passing summarized dialogue for diagnosis, and feeding candidate diagnoses for targeted questioning, improve accuracy, mirroring how physicians reason, though their effect emerges fully only in combination. Code and dataset will be released upon publication.

Engineering diagrams pose a distinct challenge for vision-language models: unlike natural images or general documents, they encode information through dense spatial layouts, domain-specific symbols, and cross-references between visual callouts and structured parts tables. Despite their centrality to service, repair, and design workflows, there is no public benchmark for measuring VLM capabilities in this domain; existing datasets primarily focus on flowcharts, scientific figures, or business documents. To address this gap, we introduce Enginuity, the first open dataset and benchmark for evaluating VLMs on complex engineering diagrams. We define two tasks over a corpus of U.S. military service and repair manuals: structured parts-table extraction (Task 1) and free-form visual diagram question answering (VQA)(Task 2) for benchmarking. We evaluate four frontier VLMs (GPT-5.2 Chat, Claude Opus 4.7, Gemma 4, Qwen3-VL-32B-Instruct) under zero-shot and chain-of-thought prompting. On Task 1, models reach Recall@all of 0.61-0.87 but Token F1pen of only 0.03-0.18, exposing a systematic gap between part identification and description fidelity. Task 2 reveals a consistent factual-reasoning gap across all models. A supporting analysis shows that token-overlap metrics under-report model capability on technical descriptions by 2-6x relative to semantic similarity, motivating LLM-as-judge calibration for domain-specific evaluation. We release the dataset, annotations, evaluation harness, and per-sample model outputs to support a reproducible study of VLM capability on engineering content.

Evaluating vision-language models (VLMs) on medical images requires benchmarks that are clinically grounded, scalable, and controlled for evaluation confounds. Existing public benchmarks are limited in scale, manually annotated, or potentially leaked into VLM pretraining corpora. We present an automated agent-driven pipeline that generates multiple-choice VQA datasets directly from paired private radiology reports and 3D oncology imaging, producing two complementary question types: RADS-style questions deterministically derived from clinician-defined reporting schemas, and radiology report-derived questions generated by an LLM from radiologist findings and verified against the source report. Applied to four in-house cancer cohorts, the pipeline yields an instance-contamination-controlled benchmark without per-question human annotation. Zero-shot evaluation of six VLMs reveals no dominant model and substantial headroom across all cells. A blind ablation reveals that visual reliance is highly dataset-specific: liver Report-derived questions genuinely require the image, while Lung CT is essentially solvable without it - the leading closed model exceeds its sighted accuracy on Lung CT when blinded - indicating that even private clinical data does not guarantee a contamination-controlled read of visual capability. The pipeline is released as an open agent skill for in-house redeployment.

Continuous episodic memory is a core capability for autonomous agents operating in dynamic, real-world environments, yet current streaming video benchmarks provide limited tools for diagnosing what models remember and for how long. We introduce Egostream, a diagnostic benchmark for streaming episodic memory evaluation in egocentric vision. \egostream organizes 2,250 curated questions along seven cognitive dimensions: detail, spatial, temporal, event, social, causal, and prospective memory. We introduce the Answer Validity Window (AVW), which specifies the temporal span an answer remains valid as the observed scene evolves. This allows us to expand the questions into 8,528 recall-conditioned evaluations, enabling controlled testing from instant to ultra-long-term recall while separating genuine model forgetting from natural world-state changes. We rigorously establish baseline performance through a unified streaming MLLM framework that compares several state-of-the-art memory-management mechanisms, covering sliding windows, attention sinks, KV-cache pruning, merging, and offloading. Experiments within a unified Qwen3-VL backbone reveal that comparable aggregate accuracies mask starkly different memory profiles. For instance, token pruning preserves fine-grained details and temporal structure significantly better than token merging, while quantized offloading rescues ultra-long-term recall. Ultimately, all mechanisms operate well below real-time (>1s per frame), and top performing methods ceil at about 45% accuracy, exposing critical gaps in current architectures. Egostream provides the diagnostic testbed needed to close these gaps. Project website, news and updates at: https://saroo25.github.io/Egostream/

Multimodal large language models (MLLMs) often know the rule but pick the wrong answer: on abstract visual reasoning (AVR) tasks, a model can describe what it sees and name the underlying pattern, yet still fail to choose the matching candidate. Existing AVR benchmarks cannot detect this because they collapse perception, rule induction, and answer selection into a single right-or-wrong signal. We introduce StemBind, a shared-stem diagnostic benchmark that probes the same visual stem with three aligned questions: Perception (what is in the image), Rule (what pattern governs it), and Full (which option completes it), so a final-answer error can be attributed to a specific sub-step on the same evidence. StemBind contains 2,298 curated knowledge-light stems across nine auditable visual operations, totaling 19,533 P/R/F tasks, with each full item annotated by Sternberg's four reasoning stages (S1 Encode, S2 Infer, S3 Map, S4 Apply). Evaluating 24 frontier MLLM configurations yields four findings. (i) The R-F chasm: rule accuracy exceeds full-item accuracy on 22 of 24 models, so most failures happen after the rule is identified. (ii) A persistent binding gap: even when P and R are both correct on the same stem, models still answer F incorrectly 51.2% of the time. (iii) The bottleneck is S3: process diagnostics and Stage-wise Stimulus Augmentation localize the dominant failure to rule-to-instance mapping. (iv) Scaling and thinking do not help: neither larger models nor explicit thinking mode reliably closes the gap, and thinking even lowers rule and full-item accuracy. StemBind reframes AVR evaluation from final-answer ranking to locating where abstract visual reasoning breaks down, identifying rule-to-instance binding as a concrete next target for vision-grounded reasoning.

Clinical decision-making (CDM) is central to real-world clinical workflows, where clinicians infer diagnoses, select treatments, or anticipate future health outcomes under incomplete evidence. LLMs are increasingly used to support these decisions due to strong language capabilities, broad biomedical knowledge, and efficiency, yet the reliability of LLMs on real-world clinical decision tasks remains insufficiently understood. To evaluate CDM models, especially LLM-based models, an ideal and practical medical decision benchmark should be constructed via an automated yet reliable pipeline to ensure both scale and quality. Moreover, the grounding of a CDM benchmark in real patient EHRs can better support evaluation on practical CDM tasks that require substantive biomedical knowledge and clinical inference. To fill the gaps, we introduce EHRBench, an automated and reliable EHR-grounded benchmark for evaluating LLM-based clinical decision-making at scale. To ensure scalability and reliability, EHRBench is constructed through an EHR-LLM-KB(knowledge-base) interaction pipeline. For efficiency, we use a specialized LLM to automatically convert encounter-level EHR trajectories into structured templates and deterministically instantiate the templates into QA items. In parallel, we apply systematic KB-based verification and enrichment to filter hallucinated or ambiguous relations and to improve reliability. Using this pipeline, we construct nearly 1M (960,067) QA items spanning three core inference-required clinical decision tasks: diagnosis, treatment, and prognosis. We benchmark more than 30 representative LLMs on EHRBench and provide detailed analyses of performance and robustness. The results show consistent capability trends across settings, further validating the reliability of EHRBench and highlighting actionable gaps toward clinically reliable LLM systems.

Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited. Existing benchmarks often rely on static datasets or unstructured inputs that do not reflect the interoperable data formats used in clinical systems. We introduce a reusable pipeline for generating terminology-grounded HL7 FHIR R4 bundles from unstructured text, enabling controllable evaluation of clinical decision support systems over structured inputs. The pipeline combines staged LLM generation with terminology-grounded validation and repair to eliminate hallucinated codes and enforce structural and semantic consistency. Applying this approach to MedCaseReasoning, we construct MedCase-Structured, a synthetic dataset of 1,732 FHIR bundles derived from clinician-authored diagnostic cases, producing complete, valid bundles for 97.1% of attempted cases. Evaluation on MedCase-Structured reveals consistently lower diagnostic accuracy for LLMs on structured FHIR inputs than with plain text, highlighting the importance of deployment-aligned benchmarking.

Long-form video generation is rapidly moving from short, single-scene synthesis toward minute-long, multi-shot creation with narrative structure, cinematic control, audio, and cross-modal synchronization. However, evaluating such videos remains challenging, since existing benchmarks largely focus on local visual quality, short-horizon temporal consistency, or generic prompt alignment, and provide limited diagnosis of workflow failures and user-dependent preferences. We introduce DirectorBench, a personalized multi-agent diagnostic benchmark for long-form video generation. DirectorBench evaluates generated videos with respect to 80 structured metadata entries, 7 user profiles, and 40 checkpoint criteria across 5 dimensions: script, visual, audio, cross-modal, and stability. Instead of reducing quality to a single aggregate score, DirectorBench localizes checkpoint-level bottlenecks and supports profile-aware evaluation. We evaluate 4 long-form video generation workflows, 6 base LLMs, and 7 user profiles. Across workflows, DirectorBench reveals a between-unit bottleneck: transition quality averages only 0.256 and reaches 0.356 for the best workflow, while prompt-level user demand fulfillment averages 0.71. We further conduct human evaluation with 14 annotators to validate the alignment between DirectorBench and human judgment. The results show that DirectorBench captures human-perceptible quality differences and reveals workflow- and profile-dependent failure modes that are hidden by aggregate scoring. These findings highlight the importance of diagnostic and profile-aware benchmarking for long-form video generation.

As large language models (LLMs) are increasingly applied in social contexts such as emotional companionship and customer service, measuring their social intelligence has become critical to the quality and safety of human-AI interaction. However, existing social intelligence benchmarks lack a unified framework that organizes social abilities into a unified structure, and therefore cannot enable fine-grained diagnosis. To build the first holistic diagnostic evaluation grounded in social theory, we first construct a social intelligence framework through a literature review and multi-stage expert validation guided by psychometric principles. The resulting framework includes 4 categories and 11 dimensions, each further specified by fine-grained capability facets. Building on this framework, we introduce NICE (Norm, Interaction, Cognition, Experience), a diagnostic benchmark of 137 items operationalized through representative Chinese contexts. Across 5 frontier LLMs and a human reference group, models score higher in aggregate accuracy yet show a consistent weakness in Communication, which the framework localizes to 3 specific capability facets: multi-turn communication, nonverbal communication, and synchrony. NICE thus reframes social intelligence evaluation toward theory-grounded diagnosis of socially consequential weaknesses in LLMs.

General-purpose machine translation benchmarks such as FLORES-200 have reached a saturation regime on Chinese-English pairs, where modern large language models cluster within a narrow band of high scores. Across 22 systems, FLORES-200 zh-en GEMBA scores fall in a 7.87-point range with a standard deviation of 2.29, which compresses the separation between systems on knowledge-intensive domains such as finance, healthcare, law, and science and technology. We introduce HardMTBench, a difficulty-aware diagnostic benchmark for bidirectional Chinese-English domain translation. HardMTBench covers 12 domains and contains 10,000 hand-curated source sentences with reference translations, packaged as 20,000 directional test items. A three-stage construction pipeline builds a domain-balanced candidate pool of 84{,}566 pairs, applies an LLM-based multi-signal judge over knowledge density, translation difficulty, terminology load and reference correctness, and assembles the final test set under a hardness fusion rule with per-domain quotas. Across 22 systems spanning general LLMs, commercial engines and specialised MT models, HardMTBench widens the cross-system GEMBA range by roughly a factor of two over FLORES-200, induces visible rank reorderings, and exposes domain-specific terminology and knowledge weaknesses that quality-only metrics tend to flatten. All data and code are open-sourced at https://github.com/jasonNLP/HardMTBench.

Point cloud quality plays a critical role in 3D acquisition, reconstruction, rendering, and perception, yet existing point cloud quality assessment (PCQA) research remains largely centered on scalar score prediction. In practical inspection scenarios, quality assessment often involves identifying defects, characterizing dominant issue types, assessing downstream usability, and providing evidence-supported descriptions, which are not explicitly evaluated by current benchmarks. We introduce PointQ-Bench, a benchmark designed to extend PCQA from scalar scoring toward comprehensive quality understanding. PointQ-Bench consists of 3,083 point clouds spanning authentic scans, simulated distortions, and AI-generated content, covering eight major issue types. Each sample is annotated with mean opinion scores (MOS), quality levels, issue tags, expert-grounded descriptions, and 12,332 question-answer pairs. The benchmark supports three perception-oriented tasks: anomaly sensing, defect diagnosis, and usability grading, as well as a cognition-oriented task of open-ended quality reporting. To evaluate free-form quality descriptions, we further propose SSFRQ-5D, a five-dimensional evaluation protocol validated through human-AI agreement analysis. Extensive experiments on 14 vision-language models and traditional PCQA baselines reveal a consistent perception-diagnosis gap: while current models exhibit emerging abilities in coarse defect perception, they struggle with grounded diagnosis and quality calibration. Strong 2D MLLMs generally outperform existing 3D VLMs, and the benefit of additional views or point-level inputs is non-uniform, varying across tasks, data sources, and models, particularly under boundary-ambiguous conditions. Overall, PointQ-Bench provides a diagnostic testbed for advancing reliable and interpretable point cloud quality understanding.

Clinical diagnosis of meniscus injuries requires radiologists to integrate volumetric MRI evidence with patient context (e.g., sex, age, BMI) and to produce structured diagnostic reports. Existing knee MRI benchmarks are typically unimodal and rely on coarse labels, limiting their ability to evaluate holistic clinical reasoning. We introduce MeniOmni, a structured multimodal benchmark for meniscus injury assessment, consisting of 746 multi-center MRI studies with tri-planar volumetric inputs, Clinical Priors, and expert-annotated clinical text. MeniOmni supports two tasks: (1) fine-grained Stoller severity grading and (2) diagnostic report generation. We further propose risk-aware ordinal evaluation and a semantic consistency metric (Meni-Score) to better reflect clinical relevance. Baseline experiments show that incorporating Clinical Priors improves grading performance and reduces severe errors, highlighting the value of multimodal context for safer assessment. Code and data are available at https://github.com/ShuruiXu/MeniOmni.

Chart-to-data extraction with vision-language models (VLMs) is increasingly evaluated on benchmarks that show diminishing headroom (frontier VLMs exceed 89% on ChartQA) and with metrics that treat extracted points as unordered key-value pairs, ignoring the temporal structure of time series and penalizing small alignment shifts as catastrophic failures. We address both gaps with EpiCurveBench, a benchmark of 1,000 real-world epidemic curve images curated from diverse public-health sources, and EpiCurveSimilarity (ECS), an evaluation metric that aligns predicted and ground-truth series via dynamic programming, tolerating local temporal shifts and gaps while penalizing them proportionally. Evaluating six methods--three frontier closed VLMs, one open VLM, and two specialized chart-extraction systems--we find the strongest model reaches only 52.3% ECS, and that ECS spreads the four general-purpose VLMs over a 25-point range where key-value metrics (RMS, SCRM) compress them into a 5-point band. We further validate ECS against four downstream epidemiological summary statistics, finding that higher ECS predicts smaller errors in total counts, peak timing, and peak magnitude, and higher growth-rate fidelity; across all four, ECS correlates 1.5--3.6 times more strongly than Dynamic Time Warping, which lacks a gap penalty and therefore cannot distinguish a truncated prediction from a temporally faithful one. EpiCurveBench targets a high-impact public-health application--unlocking decades of outbreak data trapped in published figures--but the benchmark and metric apply directly to any structured time-series chart-extraction setting.

Large language model (LLM) agents increasingly rely on external memory systems to remain consistent across long-horizon interactions, but little empirical work has been done to understand the specific failure modes and design choices that these systems present. Existing benchmarks report aggregate question-answering accuracy and treat memory systems as black boxes, making it impossible to attribute an incorrect answer to a particular failure mode of the system. We introduce MemFail, a diagnostic benchmark that isolates the failure modes of modern LLM memory systems. We begin by formalizing memory systems as the composition of three canonical operations -- summarization, storage, and retrieval -- and identify the potential failure modes induced by each. Based on these hypothesized failure modes, we construct five datasets spanning four tasks, each adversarially designed to test a specific operation of a memory system. Using these datasets, we evaluate four state-of-the-art memory systems on MemFail and demonstrate how MemFail can be used to empirically understand the tradeoffs induced by differences in memory system architectures.

Data consistency between unstructured clinical notes and structured tables in Electronic Health Records (EHRs) is essential for patient safety and clinical decision-making. However, existing work on note-table consistency verification mainly relies on surface-level matching of numeric values or simple events. Such approaches fail to capture the reasoning underlying real-world EHR documentation, including clinical interpretation, event relations, and temporal changes. To address this gap, we introduce EHR-ReasonCon, a reasoning-intensive benchmark for note-table consistency verification. Built on MIMIC-III with expert-guided annotations, it comprises 8,048 entities derived from clinical notes and provides high-quality ground-truth labels. The annotation protocol is supported by specialized table-exploration tools to ensure systematic evidence retrieval and reliable consistency assessment. We also propose EHR-Inspector, an LLM-based framework that segments notes, extracts anchor entities and temporal references, and uses table-exploration tools to verify consistency against structured tables. Evaluated using expert-validated LLM-as-a-judge metrics under harsh and lenient criteria, EHR-Inspector achieves state-of-the-art performance across multiple model backbones. Analyses further demonstrate the effectiveness of its components and highlight differences from human verification.

Evidence construction--the stage that determines which passages reach the language model before generation begins--is evaluated paradigm by paradigm, leaving practitioners with no principled way to diagnose which organization strategy fails, where, or why. We introduce AuthTrace, a diagnostic benchmark built on thematically dense single-author corpora where near-miss distractors share style, topic, and vocabulary with the required evidence. AuthTrace provides explicit quoted evidence, exact fan-in annotation, and a unified pack-level protocol measuring evidence recall, evidence precision, and answer correctness. A fan-in gradient--the number of source documents required to support the answer--serves as the primary diagnostic axis, enabling controlled comparison across retrieval, memory, graph, and structured-evidence paradigms. Evaluating eight systems across two QA models, we find that evidence recall is the strongest observed predictor of answer correctness under the primary reader-judge pair (r = 0.96); most failures stem from missing evidence rather than answer synthesis. Fan-in further exposes paradigm-specific collapse patterns: flat retrieval degrades 2-3x faster than thematically organized evidence construction. These results show fan-in decomposition to be a reusable diagnostic lens for identifying where evidence-construction systems fail and which paradigm best serves a given workload.

While large language models (LLMs) hold transformative potential for medicine, their reasoning robustness and safety in real-world clinical scenarios remain critically underexplored, particularly in dentistry. Here we introduce GlobalDentBench, the first multinational dental benchmark, featuring a taxonomy that encompasses 14 dental specialties across 88 countries and regions spanning six continents. The benchmark comprises 8,978 expert-validated questions across three formats (multiple-choice, short-answer, and case-based questions) and assesses three progressive reasoning levels: knowledge recall (L1), routine reasoning (L2), and individualized reasoning (L3). To ensure data quality, the automated construction framework was calibrated by six senior dentists, achieving expert agreement rates of 99.98% for multiple-choice and short-answer questions and 96.78% for the more complex case-based questions. Evaluation of 12 frontier LLMs on GlobalDentBench revealed a sharp, stepwise performance degradation with increasing reasoning complexity. Specifically, accuracy plummeted from 81.34% on multiple-choice to 64.53% on short-answer and 22.34% on case-based questions, while declining markedly from 74.01% at L1 to 55.64% at L2 and 35.71% at L3. More critically, risk analysis of real-world dental cases demonstrated an alarming overall unsafe rate of 31.01% in LLM-generated clinical recommendations, with 4.51% posing risks of irreversible patient harm and risks particularly pronounced in specialties such as orthodontics. These findings expose fundamental limitations in the medical reasoning and safety of current LLMs. Consequently, GlobalDentBench provides a scalable foundation for trustworthy clinical AI evaluation, underscoring the urgent need for rigorous validation before the safe deployment of these models in healthcare.

Vision-language models have demonstrated impressive capabilities in general medical visual question answering, yet due to limited interpretability, it remains unclear whether their predictions reflect evidence-grounded clinical reasoning or reliance on spurious priors. We introduce Med-R2 Bench, a hierarchical benchmark aligned with the clinical workflow to evaluate adversarial robustness with visual grounding. We design stepwise QA tasks to assess whether reasoning chains are strictly grounded in visual evidence across the four clinical stages, and employ adversarial perturbations to test robustness against misleading cues. Med-R2 comprises 42,432 images, 31 task categories, and 110,406 QA pairs. Evaluation across 14 VLMs reveals a sequential performance degradation along the four-stage clinical workflow. Adversarial experiments show that models rely heavily on correct prompts to guess answers. Even when provided with explicit visual cues, the models struggle to accurately align textual descriptions. Finally, we demonstrate stepwise fine-tuning using our hierarchical data significantly improves reasoning robustness, highlighting its potential to drive future improvements in evidence-based medical AI.

Medical diagnosis is not a single prediction from a fully specified vignette. It is a sequential workup: clinicians decide what evidence to obtain, revise a differential diagnosis, and stop when the diagnosis is sufficiently supported. Most medical AI benchmarks instead reveal the relevant context upfront and score only the final answer, making unsupported correct guesses, premature closure, inefficient workups, and poor uncertainty updating invisible. We introduce DDX-TRACE, a physician-adjudicated benchmark for multimodal neuroradiology that evaluates diagnostic trajectories under hidden evidence over 211 challenging cases. Each case begins with limited clinical history; models request imaging studies in free form, receive matched image bundles when available, update a probabilistic differential diagnosis after each turn, and stop with a localized final diagnosis. Evaluating state-of-the-art VLMs, we find that final diagnosis scores can substantially misrepresent workup quality: models may guess plausible diagnoses without essential evidence, request useful studies but misinterpret raw images, or acquire evidence inefficiently while updating uncertainty poorly. Controlled evidence variants isolate bottlenecks in planning, visual evidence extraction, and downstream differential reasoning. DDX-TRACE shifts medical AI evaluation from final answers to evidence-supported diagnostic trajectories.