clinical software developers

Abstract: Medical workflows often require selecting among predefined options. We compared 13 decision models with 15 generative large language model configurations, including different reasoning settings, using 1,273 four-option MedQA questions under text-only conditions. Accuracy ranged from 67.71% to 89.08% for decision models and from 78.32% to 96.86% for generative configurations. Among the tested configurations, Mercury Decide had the lowest mean final-attempt cost (USD 0.0069 per 1,000 questions), while Clef Omni had the shortest median request duration (0.291 seconds). Decision-model probabilities distinguished correct from incorrect answers, but error rates among answers assigned probabilities of at least 0.90 ranged from 1.71% to 12.77%. Answer agreement across three runs ranged from 92.30% to 100%, while probability repeatability varied. Decision models offered resource advantages alongside lower peak accuracy; selecting models for medical workflows requires considering probability quality and repeatability together with accuracy and the resources needed to detect and correct errors.

Abstract: Deformable image registration relies on accurate anatomical correspondences. However, explicitly coupling local matching reliability with spatial context selection and deformation update strength remains insufficiently explored in learning-based registration. This challenge is particularly pronounced in homogeneous, weakly textured, and severely deformed regions, where ambiguous matches may induce erroneous deformation updates. We propose ReliMorph, a reliability-routed symmetric framework for 3D deformable registration that couples correspondence assessment with spatial context selection and update strength.Local correlation distributions characterize correspondence ambiguity using shared anatomical features with modality-specific adaptation. These reliability cues guide spatial expert fusion and gate residual velocities during coarse-to-fine refinement. Updated inverse-inconsistency feedback guides routing and gating at finer pyramid levels. To our knowledge, ReliMorph is the first 3D deformable registration framework to jointly condition spatial expert routing and residual velocity gating on correspondence reliability. Extensive experiments demonstrate that ReliMorph consistently outperforms competing methods in anatomical overlap, highlighting its effectiveness across unimodal and multimodal registration tasks.

Abstract: Whole Slide Image (WSI) analysis serves as the fundamental method for the clinical diagnosis of cancer in digital histopathology. Recent advances in Multimodal Large Language Models (MLLMs) have enabled state-of-the-art (SOTA) automated histopathology report generation. However, MLLMs reason purely through distributions encoded in their neural parameters, limiting the amount of knowledge and reasoning logic they can contain given the model scale. Their black-box reasoning poses another challenge to the human interpretation of intermediate reasoning. We address these issues by utilizing knowledge graphs to inject external structured knowledge for MLLMs to reason over, while making this reasoning component visible. Knowledge graphs are capable of partially externalizing the containment of medical knowledge, an area that remains underexplored in pathology report generation. We introduce PathKGen, a knowledge graph-assisted MLLM for histopathology report generation. PathKGen has two main branches: (1) a visual path that learns visual token inputs to the MLLM using pathology foundation models, and (2) a knowledge path that learns knowledge token inputs by extracting key morphological features of WSIs through querying a pathology-specific knowledge graph. A comprehensive evaluation on WSI-Bench dataset shows that PathKGen surpasses previous SOTA methods while revealing diagnostic reasoning as visually intuitive graphs. Due to its modular design, the proposed knowledge path is complementary to vision-aligned MLLMs and can be extended to other applications by curating domain-specific knowledge graphs to generate knowledge tokens.

Abstract: Computed tomography (CT) and magnetic resonance (MR) imaging provide complementary information for the brain, but acquiring both modalities is not always possible. The cycle-consistent adversarial network (CycleGAN) enables unpaired CT-to-MR synthesis, but because the standard L1-norm cycle?consistency penalty grows linearly with the residual magnitude, the network tends to focus on large residuals. This paper introduces an L0-norm-based cycle?consistency term, in which the L0-norm is approximated by a smooth and bounded function. This approximation not only increases sensitivity to small residuals but also effectively suppresses the influence of large residuals. The proposed model and an otherwise identical L1-norm baseline were trained on 102 images and evaluated on 9 test images. The proposed model achieves a lower mean squared error (0.02746 versus 0.03464, a 20.7% reduction), a higher mean peak signal-to-noise ratio (15.80 versus 14.77 dB), and a higher mean structural similarity index (0.5689 versus 0.5407). It also has a lower maximum MSE and higher minimum PSNR and SSIM than the baseline. These results indicate that modifying the cycle-consistency penalty can improve reconstruction accuracy on this dataset.

Abstract: AI models already inform clinical decisions and draft notes in Australian clinical software, usually without the practitioner being told which model is used. Existing medical benchmarks are written for other jurisdictions. We wrote 142 questions from Australian guidelines and schedules across five domains (PBS authority, MBS billing, Ahpra obligations, triage red flags, immunisation and screening), each with one verifiable answer scored by exact match. Each question ran blind and with the governing clause supplied, which separates failure to recall the current rule from failure to apply it. We tested 28 models between July and October 2026. Blind accuracy ranged from 51.5% to 92.7%, and the highest-scoring models could not be separated. Of 791 failed model-question pairs, 684 (86%) were wrong blind and right with the clause. Confident-error rates ranged from 6.6% to 47.8%. On five immunisation questions where the guideline gives no directive, 82% of answers stated one. On 20 Aboriginal and Torres Strait Islander health questions, models did no worse overall, but on a few the wrong answers gave the rule for the general population, an older rule or another country's rule. We propose treating the model as an ingredient of a clinical product, with a minimum standard on local rules that sits beside product evaluation. The keys are one general practitioner's and are not yet independently reviewed. The benchmark measures base models, not clinical products, and does not license any model for clinical use.

Abstract: Deep learning has become the default tool for medical image analysis, driven by the open-source movement. However, achieving the best performance on a given task remains difficult, with architecture selection and hyperparameter optimization (HPO) still considered "more of an art than a science". Automated machine learning (AutoML) automates parts of model training, yet helps little in medical imaging: general-purpose approaches lack medical architectures and preprocessing, and medical-focused ones demand engineering expertise and remain confined to narrow tasks such as 3D segmentation. We introduce MedicalMLOmni, a multi-agent AutoML framework that automates model training for diverse single- and multi-modal medical tasks through a natural language interface. Specifically, MedicalMLOmni performs evidence-based planning by retrieving published results to guide model selection and configuration, and employs parallel HPO where multiple agents explore adjustment strategies concurrently. MedicalMLOmni achieves the best score on 19 of 20 benchmarks; PMC-VQA is the exception, where a vision-language model with broader pre-training leads. Backbone-matched controls attribute the gains to the framework, not the backbone. By removing coding requirements, MedicalMLOmni lowers the barrier for domain experts with rich datasets but limited engineering expertise.

Abstract: Autonomous agents are increasingly capable of developing machine learning (ML) models end to end. In medical practice, however, strong performance on the target metric does not fully characterize how good the models are in real-world use cases. For example, medical ML models should also provide well-calibrated risk estimates and remain robust across patient populations. Yet autonomous model development is typically guided by task objectives that emphasize simple predictive discrimination (e.g. AUROC). This raises a key question: are these objectives sufficient to guide agents toward models that meet the broader requirements of real-world medical use? In this study, we introduce Auto-MD-bench, a benchmark of 15 real-world medical tasks from 10 clinical datasets, spanning survival analysis, classification and sequential prediction, with external validation across cohorts, hospitals and time periods. We evaluate four agents: AIDE, AI Scientist v2, Codex, and Autoresearch. The strongest agents achieve competitive primary scores, yet their predicted risks are less calibrated than those of the simple baseline models, which could lead to severe medical accidents. Moreover, models with nearly identical primary scores can exhibit markedly different calibration, while performance varies substantially across population shifts. These findings show that primary task performance alone is insufficient to assess autonomous clinical modeling and multiple different metrics widely used in healthcare practice need to be taken into consideration.

Abstract: Raw image intensities are a poor surrogate for similarity across images in correspondence problems. Further, while auxiliary segmentation labels can provide semantic identification and improve matching, they can assign only coarse identities to fine-grained anatomy and often cover only a subset of structures, particularly in whole-body settings. We present an approach that instead establishes correspondence using complementary representations of anatomy and demonstrate its utility for longitudinal whole-body PET/CT registration in the Learn2Reg 2026 PSMAReg Challenge. Our 3D foundation model, anatomix, is used to derive fine-grained, per-voxel semantic representations that are consistent across volumes, and we further employ off-the-shelf segmentation models to obtain coarse anatomical identities. Together, these representations drive a GPU-accelerated iterative registration solver (FireANTs) in a hybrid multistage framework: the first stage estimates alignment from dense multi-channel features, after which a second refines the deformation using both anatomix- and segmentation-based losses. Lastly, because registration should not introduce non-biological tumor volume changes across time, we develop lesion-specific component-wise volume preservation schemes. Without any task-specific training, our system won first place in the PSMAReg Challenge leaderboard. Code and interactive visualizations are available at http://www.neeldey.com/reps-for-reg.

Abstract: ScienceBuddy-PV adapts the ScienceBuddy recursive-in-recursive design to panvascular intervention research through a structured evidence ledger, device-vessel ontology, abstention contract and retained failure bank. Recursive harness optimization and outer-loop model learning, including reinforcement learning, are specified but not executed. We audit a fixed component, rather than the complete agent system, using separate ARCADE syntax and stenosis tasks (1,000 training, 200 validation and 300 test images per task). A shared task-masked convolutional model was trained once per representation setting; its parameters and the heuristic support gate were then held fixed, with the stenosis threshold selected on validation data. On the locked test sets, syntax Dice was 0.475 (95% CI 0.459-0.490) and stenosis Dice was 0.231 (95% CI 0.214-0.249). Stenosis pixel AUROC was 0.957 and AUPRC was 0.180 at prevalence 0.00975. The gate accepted 76.7% of stenosis-frame outputs versus 100% for a score-only comparator. In a constructed mask audit, it accepted 44.3% of reference candidates and rejected 55.7%, exposing the cost of abstention. Acceptance does not establish correctness or clinical safety. This public-data component audit makes support and abstention measurable and provides a reproducible protocol for future collaborative agent studies. It does not demonstrate recursive improvement, patient-level validity or clinical device recommendations.

Abstract: Chronic ischemic stroke lesions are difficult to segment on T1-weighted MRI. Their appearance overlaps with healthy tissue, and their volumes span four orders of magnitude, so voxel-level and lesion level metrics often disagree. We build an eleven-member nnU-Net ensemble that covers five design axes: a baseline dice + top-K loss, heavy augmentation, per-lesion volume loss re-weighting, stochastic weight averaging, and a sampling-and-architecture block that pairs cohort-balanced sampling with a residual-encoder backbone. Weighted soft-map fusion of the members feeds a tuned decision layer, SADL, that estimates lesion volume, applies an adaptive per-lesion-size threshold, prunes components by voxel count and peak probability, and adds a never-empty rescue. All fusion weights and per-bucket parameters are fitted on out-of-fold (OOF) predictions, so tuning never touches the held-out test set. On a site-disjoint 91-case holdout, SADL reaches Dice 0.7322, lesion-F1 0.7461 and PR-AUC 0.8430 when scored online with the challenge's released evaluation code. A paired non-parametric bootstrap against a reference single ensemble member confirms the lesion-F1 gain at p=0.024, and the gain is largest in the small-lesion regime, where the rescue step recovers cases that a fixed threshold would silently discard.

Abstract: Widely reused preprocessing pipelines for electronic health records can encode assumptions about when information became available, what clinical episode a label represents, and what missingness means. These assumptions are rarely audited systematically and may propagate across subsequent studies when preprocessing pipelines are reused or adapted. Using MIMIC-IV as a case study, we identify and quantify violations of three complementary forms of preprocessing alignment, i.e., temporal, semantic, and population alignment, which manifest as temporal leakage, feature-task misalignment, and biased imputation. We show how ambiguities in timestamp semantics, episode definitions, endpoint construction, modality selection, and missingness handling can alter the information available to a model and affect the interpretation of its predictions. Through analyses of MIMIC-IV data and empirical case studies, we demonstrate that such choices may remain largely invisible in aggregate predictive performance while changing the signals on which models rely. We derive practical recommendations for temporally valid, clinically aligned, and reproducible preprocessing of MIMIC-IV and related electronic health record datasets. The code for our experiments, including our proposed preprocessing, is available at: https://github.com/m2l-lab/mimic-iv-preprocess.

Abstract: Reliable liver segmentation in contrast-enhanced MRI is essential for quantitative hepatic assessment, treatment planning, and longitudinal disease monitoring. However, limited annotated data and scanner- or vendor-dependent intensity variations can cause overfitting and poor generalization to unseen acquisition domains. Moreover, simultaneously achieving robust global localization and precise boundary delineation remains challenging, while predictions may contain isolated false-positive regions outside the main liver component. To address these challenges, we propose CIRSeg, a coarse-to-fine, intensity-robust liver segmentation framework based on nnU-Netv2. CIRSeg combines 3D CutMix with stochastic intensity transfer using either Nyul augmentation or histogram matching to improve robustness to heterogeneous MRI intensities. Its cascaded architecture decouples low-resolution anatomical localization from full-resolution boundary refinement. At inference, source-free test-time adaptation based on confidence-filtered predictions and probability-prior regularization further improves robustness to out-of-distribution inputs. As a final deterministic post-processing step, largest connected component filtering removes isolated false-positive regions. On the CARE 2026 test set, CIRSeg achieves Dice scores of 97.13\% and 97.93\% on the in-domain and unseen-domain subsets, with corresponding HD95 values of 20.18 mm and 11.30 mm, respectively. These results demonstrate consistently accurate segmentation across both in-domain and unseen acquisition settings. The code is available at https://github.com/jingkunchen/MICCAI_CARE_2026

Abstract: Artificial Intelligence (AI) tools are widely used to support decision making in tasks and domains where no immediate performance feedback is available. In these settings, users cannot learn to adjust their reliance behavior over time through trial and error. However, little is known about how novice users calibrate reliance on AI when external feedback is unavailable, or whether AI explanations can support calibration in its absence. We introduce reliance calibration as an organizing construct for studying how novice users dynamically adjust reliance behavior, and examine how AI explanations and meta-cognitive self-assessment shape it. Through a between-subjects study with 110 participants completing a clinical entity extraction task with AI assistance and limited performance feedback, we observe that novice users exhibit systematic drift toward over-reliance in the presence of explanations, while higher self-reported task understanding is associated with more selective reliance behavior. These results extend reliance calibration research into human-AI collaboration contexts without real-time performance signals and present actionable guidelines on designing AI tools that must support appropriate reliance in these settings.

Abstract: Automated neurodevelopmental assessment increasingly combines computer vision, speech, eye tracking, physiology, and machine learning, yet multimodality and discrimination do not establish construct validity, clinical usefulness, or appropriate interpretation of behavioral variation. We propose a testable architecture for neurodiversity-aware multimodal affective computing in which population-relative deviation is not treated as sufficient evidence of adverse functioning. This conceptual article reports neither a new participant-level study nor a trained predictive system, and no predictive or clinical superiority is claimed. The framework keeps observable signals, modality quality and availability, context, population-relative information, pooled within-person references and, when sufficiently supported, context-conditioned within person references, and predictive uncertainty distinguishable throughout inference. It defines structured decision-support outputs and auditable requirements for target validity, temporal integrity, contextual leakage, missing-modality robustness, calibration, subgroup evaluation, interpretability, privacy, and human decision boundaries. The contribution is architectural rather than algorithmic: it specifies empirically testable constraints that can be instantiated with different multimodal learning methods. Autism provides the principal motivating evidence base, without assuming unchanged transfer to other neurodevelopmental conditions.

Abstract: Accurate colon segmentation from CT images is essential for colorectal disease analysis, yet deep learning based methods often produce disconnected predictions due to complex anatomy. This study introduces a three-stage, topology-preserving segmentation pipeline to address this issue. The first stage performs initial deep learning-based segmentation, followed by centreline bridging to reconnect disjoint regions and a reconstruction stage to refine continuity. Evaluations on TotalSegmentator and RAOS datasets using overlap, distance and topology-based metrics demonstrate improved structural consistency while maintaining segmentation accuracy. The proposed method enhances topological integrity, enabling more reliable colon segmentation for clinical and research applications.

Abstract: Multi-cancer segmentation in computed tomography (CT) is fundamentally limited by the scarcity of tumor masks across different organs. We present Merlin Plus, the first large-scale CT dataset with radiologist-created tumor masks across 9 organs. Merlin Plus extends the Merlin dataset by adding 1,153 per-voxel tumor masks and longitudinal metadata. To create these tumor masks, we developed a report-based active-learning framework in which radiology reports identify tumor cases for annotation and support training of a tumor segmentation model. The model generates initial masks, which radiologists review and correct to produce the final masks, reducing annotation burden while maintaining high-quality annotations. Besides tumor masks, the longitudinal metadata in Merlin Plus enables temporal modeling of cancer progression. By directly addressing the major bottleneck of limited multi-cancer segmentation masks, Merlin Plus supports scalable multi-organ cancer detection, segmentation, and longitudinal analysis in CT. Dataset is available at: https://github.com/MrGiovanni/MerlinPlus

Abstract: Developmental screening videos show how children perform specific behaviors, but clinical records usually contain outcomes rather than descriptions of what happened. We present SemReward-VL, which learns to describe item-specific behavior from these outcomes. A vision-language model generates a description, and a frozen language model scores its agreement with the clinical outcome, relevance to the item, abstention on unrelated video-item pairs, and clarity. Group relative policy optimization (GRPO) updates LoRA adapters using this semantic reward. On 13,379 videos covering 41 items, the method improves aggregate accuracy and the number of items with recall above 0.5. Errors remain in temporal direction, duration, and age-specific interpretations of behavior.

Abstract: Speech therapists often face difficulties diagnosing impairments due to the lack of efficient tools for transcribing speech into the International Phonetic Alphabet (IPA). This work addresses this challenge with Broca, a Conformer-based deep learning system pretrained on 8 days of adult speech and fine-tuned on a 165-minute dataset of Italian child speech collected through a range of standardized diagnostic tests for children aged 3.5-6.5. Broca was optimized to handle phonetic variability in children's speech, including tone, accent, and speech errors, and achieved a state-of-the-art weighted Phoneme Error Rate of 13.36% on Italian speech. Remarkably, this performance was obtained using less than three hours of child-specific data, underscoring the model's efficiency and robustness in low-resource clinical settings. This work demonstrates that accurate, vocabulary-independent speech-to-IPA transcription can be achieved with minimal data, paving the way for more accessible, data-efficient tools to support speech assessment and diagnosis.

Abstract: Large Language Models (LLMs) perform well on medical examinations and question-answering benchmarks, but remain unreliable on medical calculation tasks that require exact numerical outputs. These calculations support high-stakes decisions such as medication dosing, organ-function assessment, and prognostic scoring, for which even small errors can have serious clinical consequences. We introduce MedCode, a framework that improves medical calculation by training LLMs to generate embedded executable code. Given a clinical context, the model identifies the relevant calculator, extracts its input variables, and produces a script that delegates arithmetic operations to a deterministic interpreter. Executing the script returns the calculated value together with an explanation and the appropriate unit. We construct supervised fine-tuning (SFT) and preference datasets from the MedCalc benchmark and additionally curate a dataset for calculation tasks in Intensive Care Unit (ICU) scenarios. We further propose weighted Direct Preference Optimization (wDPO), which adaptively emphasizes preference pairs that are difficult for the model to distinguish. Experiments with LLaMA3-8B, Qwen2.5-7B, and Mistral-7B show absolute accuracy gains of 20--30 percentage points, demonstrating the effectiveness of embedded code generation for medical calculation.

Abstract: Accurate brain tumor segmentation from Magnetic Resonance Imaging is essential for diagnosis, treatment planning, and surgical guidance. Although Convolutional Neural Networks, particularly UNet, have achieved significant success in medical image segmentation, they often struggle to capture the long-range spatial dependencies required to model tumors with irregular shapes and complex boundaries. This paper proposes a lightweight Vision Transformer UNet that combines the hierarchical feature extraction capability of UNet with the global context modeling of Vision Transformers. The proposed architecture incorporates a compact ViT bottleneck within a U-Net encoder-decoder framework, enabling effective learning of both local and global features while maintaining computational efficiency with only 2.6 million trainable parameters. The model was evaluated on the TCGA LGG MRI Segmentation dataset, achieving a mean Intersection over Union of 0.8100 and a Dice score of 0.8446, outperforming the baseline UNet by 3.75% and 3.15%, respectively. Extensive quantitative and qualitative analyses, including confusion matrix evaluation, precision recall curves, per-image performance distribution, and tumor size dependency analysis, demonstrate the effectiveness and robustness of the proposed method for brain tumor segmentation.

Abstract: Medical agents increasingly combine general reasoning models with specialized clinical tools, yet their capabilities remain largely fixed by what clinicians and engineers design before deployment. Recursive self-improvement (RSI) offers a different paradigm in which agents learn from their own failures and autonomously expand their capabilities, but directly applying RSI to medicine introduces fundamental safety challenges. We introduce MedRSI, the first recursive self-improvement framework for medicine, which continuously transforms diagnostic failures into new clinical capabilities through tool composition and task-specific model training. Inspired by clinical practice, MedRSI introduces two mechanisms for clinically aligned self-evolution. Clinical-cost-aware failure prioritization directs improvement toward errors according to their potential clinical consequences rather than frequency alone. Fast discovery with slow registration separates rapid capability invention from conservative adoption, allowing new tools to enter the persistent agent only after demonstrating sustained benefit across subsequent patient cohorts. Across public glaucoma and heart disease benchmarks and two private clinical tasks, MedRSI progressively develops segmentation, measurement, prediction, multimodal reasoning, and generative capabilities, surpasses manually engineered medical agents, and autonomously discovers solutions to clinical problems not anticipated by its original designers. Our results show that medical agents need not remain constrained by capabilities specified before deployment: with clinically grounded mechanisms governing what to improve and what to retain, they can continuously construct, validate, and accumulate new capabilities from diagnostic experience. Code is available at https://github.com/ImprintLab/MedRSI.

Abstract: Medical image segmentation models typically rely on large amounts of densely annotated volumetric data, limiting their scalability across tasks and imaging modalities. This work addresses the challenge of predicting entire 3D anatomical structures from extreme annotation sparsity. An annotation-efficient student-teacher framework is proposed for automatic 3D medical segmentation that requires only a set of point prompts on a single 2D slice per volume, as input. A foundation model serves as an offline teacher, utilizing the provided point prompts from the selected slice to full-volume pseudo-annotations alongside their corresponding spatial confidence scores prior to student training. To mitigate the error propagation of noisy pseudo-annotations, a task-specific 3D student network is trained using a confidence-aware optimization strategy. By leveraging the teacher's pre-computed confidence scores, this strategy explicitly excludes statically uncertain regions of the pseudo-annotations from the loss calculation, while simultaneously emphasizing regions with higher confidence. Evaluated on 3D cardiac MRI datasets, our framework outperforms state-of-the-art semi-supervised methods, improving segmentation performance by up to 43.6%. Furthermore, it drastically reduces the manual annotation burden to just a few positive point prompts per volume, while improving surface boundary precision by up to 14.7% over the teacher and successfully recovering up to 34.1% of the performance gap toward the fully supervised upper bound.

Abstract: Background: Molecular testing for NPM1 and FLT3-ITD mutations guides critical early treatment decisions in acute myeloid leukemia (AML), but results can take weeks, long after these decisions must be made. Flow cytometry, already performed within hours of admission as part of routine care, may carry enough signal to predict these mutations directly, without added cost or delay. Methods: We developed an interpretable multi-instance learning classifier based on a decision tree, in which each patient sample is modeled as a collection of individual cells and mutation status is inferred from cell-level predictions. The model was benchmarked against a random forest trained on clinical variables and a deep convolutional neural network adapted for multitube flow cytometry data. Performance was assessed by cross-validation on a discovery cohort of 197 patients and tested on an independent cohort of 161 patients, using the area under the receiver operating characteristic curve (AUROC) and positive predictive value. Results: In cross-validation on the discovery cohort, the MIL model achieved mean AUROCs of 0.96 (SD=0.05) for NPM1 and 0.86 (SD=0.10) for FLT3-ITD, outperforming the clinical baseline and matching deep learning approaches. The model then successfully generalized to the independent test cohort of 161 patients, reaching AUROCs of 0.90 (NPM1) and 0.82 (FLT3-ITD), with positive predictive values of 0.87 and 0.68, respectively. Cell-level interpretation recovered established immunophenotypic signatures (CD33${}^{+}$ /CD34___ for NPM1-mutated cases, CD33${}^{+}$ /low side-scatter for FLT3-ITD), directly linking model predictions to known biology. Conclusions: These results show that an interpretable model applied to data already collected in routine care can predict AML molecular status within hours, offering a practical route to earlier, biology-informed treatment decisions.

Abstract: Automated depression screening from clinical interviews requires attribution of utterances to the clinician or patient. We evaluate two datasets: DAIC-WOZ, where participant-only recordings require re-synthesizing both sides for controlled two-party evaluation, and PDCH-HAMD, comprising voice-converted real Chinese interviews for cross-lingual validation. Cascaded systems combine speaker diarization with role-assignment heuristics, so errors can propagate across stages. We propose an end-to-end model, which we named DiaWhisper, that fine-tunes Whisper-large-v3 with LoRA and an auxiliary frame-level role head for transcription and attribution, together with DiaWhisper-DPO, a failure-mined refinement that uses genuine decoding failures as DPO rejected completions without human preference annotation. On 29 DAIC-WOZ test sessions, DiaWhisper-DPO achieves 0.973 role accuracy and 0.119 DER, 72% below the strongest cascaded baseline, and reduces seed variation from σ = .205 to .002. Retrained on PDCH-HAMD, it achieves 0.757 role accuracy and improves all 78 session-seed pairs.

Abstract: Modelling how a disease progresses over time requires longitudinal imaging cohorts, which are scarce and small, whereas cross-sectional data -- one image per participant -- is abundant. Self-supervised pre-training on such data offers a way to bridge this gap, but it is unclear which strategy best supports progression modelling, or how that answer depends on the amount of labelled longitudinal data. We study this for age-related macular degeneration (AMD), pre-training encoders on the large cross-sectional NAKO cohort and predicting time to late AMD on the longitudinal AREDS dataset. We compare in-house self-supervised encoders against a general-purpose (DINOv2) and a domain-specific (RETFound) foundation model, across contrastive, masked-autoencoding, and self-distillation objectives, under frozen and fine-tuned protocols, and across labelled training sets from 100 to 32,250 examples. Which model performs best depends on how the encoder is used. When the encoder is frozen and labels are few -- the regime typical of longitudinal cohorts -- pre-trained representations reach clinically reasonable discrimination from a few hundred labelled samples, while models trained from scratch do not; this advantage fades under fine-tuning. Transfer is governed by the self-supervision objective rather than corpus scale or domain match, so that an encoder pre-trained on a modest cross-sectional cohort matches or exceeds a far larger in-domain foundation model. Together, these results offer a practical recipe for building progression models where longitudinal data is scarce: a frozen self-supervised encoder with a lightweight survival head.

Abstract: Post-treatment MRI in patients with glioma provides serial observations for updating patient-specific tumor-state proxy estimates, but variable appearances and trajectories complicate forecasting. We formulate forecasting as an observation-aware digital-twin update in which an intermediate observation anchors the patient-specific state. Among 203 patients and 594 follow-up time points, a predefined no-new-treatment criterion retained 120 of 236 candidate triplets, split into 81/24/15 training/validation/test triplets at the patient level. Each time point was represented by a continuous voxel-wise tumor-state proxy map in [0,1] derived from MRI lesion labels. A SegMamba-based single-step forecaster predicted update proposals from multimodal source-state tensors. Observation-Anchored Selective Assimilation (OASA) retained the observed intermediate proxy as the state anchor and selectively applied updates through a validation-selected tiered case-level rule and voxel-wise soft gate. We compared initial-scan forecasting, rollout without assimilation, latest-observation persistence, direct prediction, OASA, OASA + calibration, and morphological dilation. Checkpoints, OASA rules, and calibration thresholds were selected using validation data only. Across three seeds on 15 held-out test triplets, OASA maintained Dice at $τ$ = 0.2 comparable to persistence (0.6071 $\pm$ 0.0025 vs. 0.6070) while yielding numerically higher Dice at $τ$ = 0.5 (0.4269 $\pm$ 0.0079 vs. 0.3981), with a small RMSE increase. Calibration increased Dice at $τ$ = 0.2 to 0.6178 $\pm$ 0.0025, increased false-positive (FP) support (11,836$\rightarrow$18,663), and reduced false-negative (FN) support (22,107$\rightarrow$17,536). This reflects near-threshold support calibration rather than improved biological predictive capability. Code is publicly available at https://github.com/jsudg436/longitudinal-proxy-forecasting.

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.

Abstract: The same underlying computational problem is solved across unrelated fields under different names: recursive Bayesian state estimation appears as a "Kalman filter" in control, "Bayesian forecasting" in pharmacokinetics, and "data assimilation" in geoscience. Topical and citation-based scientific embeddings cannot see this shared problem. We distill each paper once into a domain- and method-name-stripped faceted computational fingerprint, a free-text mechanism skeleton plus controlled computational facets. We define a tunable, facet-selectable distance over it. The goal is solution import: surface cross-field pairs solving the same problem, so a bespoke implementation can be swapped for another field's standard, specialized solver. On a benchmark of 18 method families across 109 papers, the skeleton lifts cross-domain retrieval average precision over the abstract from 0.222 to 0.513, and the whole fingerprint reaches 0.557. Strikingly, four trained scientific embedders all fall below plain abstract+TF-IDF: they encode topical and citation similarity, the wrong signal for this task. The gain is the representation: the abstract-to-skeleton swap lifts every embedder, and the pipeline is one cached LLM call per paper plus a cheap embedder. An interventional re-skin / math-edit test shows the fingerprint tracks the computation, not the field. On a 501-paper wild corpus, known twins dominate the top of the ranking (23 of the top 30); with planted pairs excluded from the results, three blind LLM judges rate 3 of the top 5 and 8 of the top 30 pairs genuine import candidates, and 0 of 30 random ones. The human verification is the four executed imports: in one, an open standard solver reproduces a bespoke clinical dosing engine's output. We release the benchmark, the code, and the distillation prompt.

Abstract: Biomedical tables often combine thousands of measured variables with only tens or hundreds of labelled samples, a regime that is poorly represented in general-purpose tabular benchmarks. We introduce TabBench-Bio, a living and interactive benchmark of 43 biomedical datasets spanning multiple domains. Under a shared cross-validation protocol, we compare classical estimators, neural networks, and tabular foundation models across 28 feature-by-sample operating points. At the reference cell of 10,000 features and 100 training samples, RealTabPFN v2.5 has the highest point estimate, followed by Logistic Regression and TabDPT, whose point estimates are nearly identical. A paired bootstrap over the target pool separates RealTabPFN v2.5 from Logistic Regression by 145 Elo (95% interval [59, 232]). Tabular foundation models generally occupy the leading ranks, while the strongest configuration depends on the operating point and biomedical modality. The AutoML framework AutoGluon, using its one-hour "extreme" preset, is configured as a separate resource-intensive reference and is reported here at the reference cell. Fold-level predictions, run status, and deterministic aggregations make every reported result reproducible and reusable. We invite the community to contribute: TabBench-Bio is designed to grow, and we welcome submissions of new biomedical tabular datasets, particularly from underrepresented assays and clinical endpoints, for inclusion in future releases. The interactive leaderboard is available at: https://tabbench-bio.eu