healthcare data engineers

Abstract: Synthetic data is an important data source in the AI era. This paper studies the generation of mixed-type tabular synthetic data in federated settings, where two key challenges arise: ensuring distributional fidelity and effectively handling mixed-type data. We propose Federated Integrative Two-Step Synthesis (FITS), a framework for mixed-type tabular data synthesis. At its core is a two-step federated algorithm for estimating conditional cumulative distribution functions (CDFs) using local linear regression. Building on this algorithm, we develop a federated synthesis procedure based on the probability chain rule to ensure distributional fidelity. To handle mixed-type data, FITS introduces a continualization method that lifts discrete variables into a continuous space and recovers their discrete distributions without loss at both the density-function and CDF levels. This transformation provides a unified continuous representation of mixed-type variables, facilitating the application of local linear regression and synthetic data generation. Our theoretical analysis characterizes the conditional density and cumulative distribution functions of the continualized mixed-type variables and establishes the uniform convergence of the resulting federated conditional CDF estimators. Experiments demonstrate that FITS-generated synthetic data improves downstream task performance for all clients, with the benefits depending on how the synthetic data is used.

Abstract: Automated radiology report generation requires models to do more than produce fluent clinical narratives: they must explicitly state supported diagnoses while avoiding unsupported ones. However, existing medical vision-language models (MedVLMs) are typically trained with token-level maximum likelihood objectives, which prioritize text agreement over diagnostically critical terms. As a result, models can miss key diagnoses and introduce wrong ones. We identify this as an objective misalignment between conventional language modeling and the asymmetric diagnostic requirements of radiology reporting. To encode these requirements, we introduce Diagnostic Loss (DLoss), a differentiable, architecture-agnostic objective that operates directly on decoder token probabilities. DLoss separately aggregates probability mass over vocabularies associated with diagnoses supported by the reference report and with unsupported alternatives. Using asymmetric pooling across token positions in the report, it encourages supported diagnoses to receive sufficient probability in at least one position while suppressing spurious probability spikes for unsupported diagnoses across all positions during training. The loss can be applied to existing 3D MedVLMs without modifying their vision backbones, language decoders, or inference procedures, and introduces no additional inference-time computation. We train and evaluate DLoss on 50,000 abdominal CT scans across several 3D MedVLM architectures on both in-distribution and out-of-distribution report-generation benchmarks. Across these settings, DLoss improves diagnostic faithfulness while maintaining competitive performance on conventional language-generation metrics, showing the value of asymmetric sequence-level supervision for radiology report generation. The code for DLoss is available at https://github.com/gmum/DLoss.

Abstract: Whole slide image (WSI) analysis enables computational diagnosis and prognosis, but gigapixel images and limited annotations make slide-level learning challenging. Multiple instance learning addresses this task by aggregating patch representations from frozen pretrained encoders. Recently, Mamba has enabled efficient modeling of long patch sequences. However, task supervision alone does not explicitly constrain information recovery during feature adaptation, while Mamba couples local processing with long-range propagation rather than retaining separate representations for fusion. Motivated by these challenges, we introduce LEAF-Mamba, a framework that jointly addresses latent evidence adaptation and fusion for frozen-feature WSI analysis. A reconstruction-regularized adapter learns compact, task-specific representations while reconstructing the input features. Parallel Mamba and convolutional streams then capture long-range dependencies and sequence-local interactions, with an input-dependent gate modulating their joint representation before slide-level pooling. Experiments across feature extractors demonstrate improved average performance over strong MIL baselines in both diagnostic classification and survival prediction. Component analyses further support the contributions of adaptation and fusion. These findings highlight the value of jointly designing feature transformation and contextual aggregation to translate pretrained representations into effective slide-level predictions.

Abstract: Time series are ubiquitous across different domains, and the growing use of synthetic data for privacy-preserving sharing, data augmentation, and stress testing makes time series generation increasingly important. Early generative approaches are predominantly autoregressive, which can suffer from low sample diversity, error accumulation, and difficulty modeling long-range dependencies. In this paper, we introduce FracTS, a hierarchical, coarse-to-fine autoregressive model for multivariate time series generation. Inspired by fractal generative modeling developed for images, FracTS adapts the paradigm from 2D to 1D sequences by learning a multi-scale representation that captures global trajectory structure at coarse scales and local dynamics at fine scales while following the autoregressive nature of time series. In contrast to unstructured images, time series are structured, allowing easy automated or designated temporal feature processing optimized for the model, and global (static) feature extraction describing the instances that generate the corresponding time series in the collection. We incorporate them in the generation process to further improve the generation quality. The design naturally handles multivariate dependencies and improves long-horizon temporal coherence without requiring fixed-length inputs. Experiments on five datasets (two conditional, three unconditional) conducted against seven baselines show that FracTS consistently outperforms baselines across marginal distribution and predictive ML utility, and correlation preservation in the unconditional setting. In particular, the predictive ML utility is averagely improved by 100.0% and 75.0-81.0% for unconditional and conditional time series datasets compared to the best baseline (relative error computed on dataset-averaged raw values). Code is available at: https://github.com/BetterdataLabs/fracts.

Abstract: Electrocardiogram (ECG) beat classifiers lose accuracy on new patients and devices, and source-free adaptation methods that assume class-balanced target batches fail on real recordings, whose label-free prefix is 87.9--98.6% normal beats. We propose Normal-Anchored Geometric Transport (NAGT, GA_NS), which estimates a closed-form symmetric positive-definite congruence map from label-free normal anchors in the first 5 min of each recording and applies it only to the normal and supraventricular prototypes, keeping the ventricular and fusion prototypes fixed. The score offsets and decision rules were set on MIT-BIH only; the rate-invariant RR head (relA) was adopted after the development databases (INCART, SVDB) had been opened; the frozen model was then evaluated once on Icentia11k chest-patch recordings under a pre-registered protocol. In 493 patients (973 recordings, 3,615,388 evaluated beats), NAGT reached an arrhythmia macro-$F_1$ $J = \frac{1}{2}(\text{S-}F_1 + \text{V-}F_1) = 48.7\%$ [95% CI 42.1, 54.7] versus 34.5% without adaptation ($ΔJ = +14.1$ [+8.6, +19.3] pp; 59.8% versus 43.9% in non-AF) and outperformed all five Holm-adjusted comparators, including AdaBN, Tent and T3A. In the 75-patient test subgroup of the historical split (73 analyzed), the gain was not significant (+6.1 [-8.5, +23.4] pp). Adaptation takes a median of 5.8 ms per record without back-propagation.

Abstract: Retrieval-Augmented Generation (RAG) enhances the capabilities of large language models (LLMs) by querying external structured knowledge. However, it can also introduce privacy risks by leaking sensitive information from the retrieval datastore. We propose a simple method to preserve datastore privacy in RAG systems via random projection. By applying the same projection to both datastore embeddings and query embeddings, our method provably preserves semantic similarity between queries and retrieved items while substantially mitigating data extraction attacks. Across multiple RAG architectures and datasets, we show that this lightweight approach achieves superior retrieval and generation performance compared to prior methods which leverage formal differential privacy (DP) guarantees, while exhibiting comparable empirical privacy under strong attack models. Our results for the first time suggest that random projection can serve as a competitive and practical baseline for privacy-preserving RAG systems.

Abstract: Heterogeneous medical image data motivate domain-specialized diffusion experts, but expert specialization alone does not determine how their predictions should be combined during sampling. Learning a global router is particularly challenging when the server has limited, potentially unrepresentative images. We study two router-learning strategies for a fixed expert pool. Server-Only learns input- and timestep-dependent expert assignments from server images with component labels. Anchor-Delta (AD) uses the same images and frozen experts to obtain additional evidence from denoising losses. It distills targets that combine this evidence with the current router's assignments, while a proxy gate controls a subsequent refinement step. Component labels describe data origin; expert losses measure empirical prediction performance. We evaluate these distinct signals through routing analyses and paired medical image generation. An AD-trained router improves generation metrics over Server-Only in a heterogeneous four-domain setting, and a separate server-data study shows gains in held-out routing over a corrected-routing comparator. Additional paired evaluations show that the effect of inference-time evidence mixing varies across benchmarks. These findings establish server-data availability and expert performance as distinct considerations in learning routers for multi-domain diffusion models.

Abstract: Biomedical Named Entity Linking (BioNEL) is the task of mapping mentions extracted from biomedical texts to canonical entities or concepts in the standardized knowledge base. Although existing methods have achieved remarkable performance in mapping accuracy, most rely on training with domain-specific datasets, which fundamentally limits their cross-domain adaptability. To address this limitation, we propose BioNEL-RAG, a novel training-free framework that combines retrieval-augmented generation (RAG) with large language models (LLMs). Within this framework, the RAG module focuses on retrieving candidate entities, while the large language model module plays the role of selecting the most appropriate candidate for entity normalization, which is based on the analysis of the mention's context, with the aid of its remarkable text comprehension capabilities. Experimental results demonstrate that BioNEL-RAG achieves performance comparable to existing methods without requiring training on subdomain datasets, whereas these methods necessitate fine-tuning on specific subdomains such as genes, diseases, or chemical compounds.

Abstract: Fault diagnosis in asset-intensive industries requires multiclass models trained on noisy, sensitive data collected across geographically distributed client sites. Federated learning enables collaborative training without centralizing data, but most approaches do not provide formal privacy guarantees for individual records stored at client sites and can degrade under label noise. To address these limitations, we develop a differentially private, distributionally robust framework for federated multiclass classification that provides sample-level privacy for records stored at each client. We build on a federated Wasserstein distributionally robust multiclass objective with the Crammer-Singer loss, solved using an Alternating Direction Method of Multipliers (ADMM)-based algorithm. To protect the released client updates, our method injects calibrated Gaussian noise into the proximal linearized client updates of both the local model and the local distributionally robust variable before aggregation at the central server, and we quantify the cumulative privacy loss using the moments accountant. We provide per-round sample-level $(ε,δ)$-differential privacy guarantees and an overall composed privacy guarantee across all training rounds, together with convergence results and an explicit privacy-utility tradeoff. Experiments on simulated industrial fault data and UCI benchmark datasets show that our method outperforms differentially private federated empirical risk minimization and stochastic gradient descent baselines in most tested settings, with the largest gains under strong privacy-induced noise.

Abstract: Self-supervised multimodal representation learning has achieved remarkable success across diverse domains, yet capturing synergistic information remains challenging due to the complexity of cross-modal interactions. Unlike the shared information across individual modalities, synergy arises when task-relevant signals emerge only from the joint configuration of multiple modalities and cannot be recovered from any modality in isolation. This work focuses on how to preserve the information capacity for such synergistic signals in multimodal representations. The key observation is that synergistic information is reflected in higher-order statistical dependence among modalities, which provides a principled target for explicitly modeling joint interactions. Motivated by this insight, we propose Higher-order Representation and Information Learning (HRIL), which constructs an empirical cross-moment tensor over modality embeddings to represent multi-way interactions. HRIL employs Tucker decomposition to obtain a core tensor, complemented by a synergy-aware regularizer that prevents energy concentration and preserves higher-order coupling capacity for synergistic information capture. Experiments on the controlled synergy task and real-world benchmarks demonstrate consistent improvements over existing multimodal contrastive methods, with notable gains on tasks dominated by synergistic interactions. Code is released at https://github.com/brightest66/HRIL.

Abstract: Medical question answering spans specialties and clinical operations that may benefit from different adaptation directions. We propose ARBOR, a parameter-efficient method that selects rank-one components from a shared low-rank basis for each question. An additive gate combines question representations, specialty tags, operation tags, and their interaction; a learned coefficient scales the adapter residual. An illustrative separation under orthogonal, equiprobable subtasks shows how conditional selection can avoid an approximation floor faced by a fixed update with the same active rank. This result motivates the design without asserting a corresponding bound for medical corpora. On Qwen3-8B across CMB, CMExam, MedQA, and MedMCQA, five-seed experiments yield 69.69% mean accuracy across benchmarks, exceeding LoRA r16 and MoELoRA by 1.26 and 1.30 percentage points, respectively. The reported advantage over LoRA r16 increases from 0.08 to 1.94 points as training expands from one to seven specialties. Tag perturbations and atom masking support the usefulness of clinical routing, while atom clusters align with the supplied specialty labels (adjusted Rand index 0.62). Calibration, transfer, and measured costs further characterize the method. These findings support structured conditional adaptation for medical QA, while leaving clinical safety and broader deployment untested.

Abstract: While medical multimodal large language models (Med-MLLMs) advance medical visual question answering (VQA), existing clinical workflow-inspired multi-agent frameworks suffer from interaction patterns and excessive computational overhead caused by redundant communication topologies. In this paper, we propose MedPrune, an efficient medical multimodal multi-agent collaboration framework that dynamically prunes both nodes and edges from the communication topology to enhance reasoning ability and token efficiency. Specifically, we first formulate the diagnostic process as a heterogeneous communication graph, where nodes represent specialist agents from various departments and edges capture intra- and inter-departmental interactions. Building on this graph, we introduce two sparsification mechanisms to enable adaptive collaborative evolution: (1) Heterogeneous Node Sparsification, which eliminates task-irrelevant specialist agents irrelevant to the current multimodal question via reinforcement learning-driven topological optimization, and (2) Heterogeneous Edge Sparsification, which selectively retains only the most diagnostically salient intra- and inter-departmental connections by jointly optimizing task performance and topological complexity. Extensive medical VQA experiments under full-set and few-shot training settings prove MedPrune surpasses multi-agent baselines and boosts token efficiency with strong adversarial robustness.

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: Large language models (LLMs) are increasingly explored for clinical reasoning, but whether they appropriately revise judgments as patient evidence evolves remains unclear. We evaluated longitudinal belief updating using matched intensive-care trajectories from electronic health records. Across diverse LLMs, conditioning on a preceding judgment more often increased than reduced prediction error when estimates changed, replicated for a second endpoint. Controlled interventions revealed two failure modes. First, with preceding assessment fixed, models responded more strongly to worsening than matched improving respiratory evidence; this asymmetry persisted after headroom normalization at moderate and strong evidence levels. Second, with current evidence fixed, increasing prior risk from 10% to 90% shifted estimates by 26.2 percentage points, demonstrating causal influence of prior model beliefs. Prompting did not restore reliable updating. Evidence-Validated Longitudinal Update (EVLU) identified fewer, more reliable revisions, revealing a reliability-coverage trade-off. These findings establish longitudinal belief updating as a distinct dimension of LLM reliability.

Abstract: In hospital workflows, electronic health records (EHRs) are often noisy, and may not contain the evidence needed to confirm events or measurements referenced in a clinical query. Even when database retrieval succeeds, clinical agents can overlook such discrepancies and return plausible but unsupported answers. We introduce EHR-RobustGym, a scalable and interactive environment for evaluating and training robust clinical agents grounded in noisy EHRs. Built on MIMIC-IV hospital records (365K patients, 31 tables, and over 500M records), EHR-RobustGym comprises 5,486 Clean-Noise pairs spanning six clinical intents and both patient-level and population-level queries. The pairs test robustness to Record-level, Value-level, and Query-level noise, while interactive SQL/Python execution and outcome verification support trajectory collection and training. Evaluating multiple LLMs reveals substantial robustness gaps: average task success across proprietary and large-scale open-weight models drops from 62.2% on Clean questions to 37.9% on Noise questions. At k=4, pass^k consistency falls below 50% for most evaluated models, exposing instability in clinical task completion. Supervised fine-tuning and reinforcement learning in EHR-RobustGym improve performance, with gains generalizing to five external EHR benchmarks. Together, these results position EHR-RobustGym as a testbed for evaluating and improving the evidence-grounded robustness of clinical agents.

Abstract: Recent advances in generative modeling have substantially improved time series generation, yet most existing methods either assume a regular temporal grid or focus on feature dynamics under a given sampling structure. This makes them illsuited for generating irregular time series in their native form, where a model must capture not only feature values, but also how many observations occur, when they occur, and which features are observed together. To address this heterogeneous generation problem, we propose ChronoFlow, a unified hierarchical flow matching framework organized by statistical granularity. Following a coarse-to-fine hierarchy, ChronoFlow first generates observation counts and feature-wise frequencies, then jointly generates observation times and feature co-observation patterns, and finally generates values conditioned on the realized pattern. This turns a complex joint generation problem into structurally aligned subproblems while preserving their dependencies. To evaluate complete irregular time series generation, we introduce complementary metrics spanning sample realism, sampling structure, value fidelity, and temporal and cross-feature dependencies, and validate them through controlled corruptions. Across five benchmarks, ChronoFlow achieves strong improvements in generation fidelity over existing baselines, while factorization studies support the proposed hierarchy. Our code is available at https://anonymous.4open.science/r/ChronoFlow.

Abstract: Multimodal large language models (MLLMs) can now interpret a standard ten-second, twelve-lead electrocardiogram (ECG) with clinically grounded, reward-verified reasoning. Real cardiac monitoring is different. Ambulatory (Holter) and telemetry recordings span hours to days and are read as they stream in, and their clinically decisive findings are paroxysmal, brief episodes buried in an otherwise unremarkable trace. Such a recording cannot be held in one context at diagnostic resolution, and its future has not yet happened, so a reader must work online, deciding what to measure now, committing evidence to memory as it passes, and reporting events as they occur. We recast long-duration ECG interpretation as a long-horizon, online (streaming, causal) sequential decision process and introduce ECG-Scroll. As a benchmark, long ambulatory recordings are streamed to an agent chunk by chunk, and it must localize, quantify, and promptly flag paroxysmal events without access to future signal; because the underlying signal is retained, every answer is checkable against objective ground truth, giving rule-based rather than judge-based rewards, and the streaming formulation adds a metric batch evaluation cannot express, the detection latency between an event's onset and the moment the agent records it. As an agent environment, it is a fixed, gym-style interaction layer that exercises three competencies single-glance ECG models never touch: Memory, Tool use through signal-grounded measurement rather than reading pixels, and Planning of what to measure now and when to commit. We release 390 whole-recording instances spanning 2,536 hours of two-lead ambulatory ECG and evaluate a signal-threshold rule agent alongside off-the-shelf LLM agents online, characterizing how they use memory, tools, and planning and where the benchmark's head-room lies.

Abstract: Dermoscopy classifiers built on Vision Transformers process all image patches uniformly, although diagnostic evidence is concentrated in the lesion region. Existing token pruning methods reduce tokens using generic saliency or similarity signals, but rarely ask whether the retained subset still contains the lesion. This paper introduces MedTokenBudget, a supervised post-backbone token routing framework that learns to construct compact lesion-enriched representations when auxiliary lesion masks are available. Its Lesion-Aware Token Scoring (LATS) module fuses attention entropy, feature norm, and local feature contrast through a learned scorer, then routes the top-$K$ patches under a target budget. LATS is trained with budget curriculum learning, diversity regularization, attention distillation, and lesion-mask supervision. The trained router is evaluated with a lesion retention rate that directly measures how much ground-truth lesion evidence survives the token budget. On ISIC 2019, mask-supervised LATS consistently outperforms Random and ToMe at headline budgets while retaining substantially more lesion patches. Code is provided for reproducibility, and complete tabulated results are included in the supplementary material.

Abstract: Pathology foundation models (PFMs) have transformed computational pathology through powerful representation learning from histopathological images. PFMs provide rich, discriminative representations for whole slide image (WSI) analysis, enabling tasks such as slide-level classification under multiple instance learning (MIL). However, these representations may also encode non-biological signals associated with acquisition centers, potentially introducing spurious shortcuts into downstream predictions. In this work, we evaluate center-associated robustness in WSI classification using a controlled training setting with increasing class-center correlations quantified by Cramér's V. We benchmark six PFMs across four datasets and two MIL aggregators, while evaluating ComBat as a robustification strategy. We further introduce the Area Under the Cramér's V Curve (AUCC) to jointly capture absolute classification performance and its degradation as spurious correlation increases. Results show that center-related information encoded by PFMs propagates to WSI-level predictions, with robustness depending on both the PFM representation and MIL aggregation strategy. Additionally, ComBat harmonization does not provide consistent robustness gains across datasets.

Abstract: We propose Low-Rank Quantile Surfaces (LRQS), a bivariate causal model in which, in the causal direction, an unknown monotone transformation of the conditional quantile surface admits a low-rank functional decomposition. LRQS subsumes location-scale noise models and post-nonlinear heteroscedastic noise models, while allowing multiple quantile bases to represent changes beyond location-scale effects. We prove generic identifiability of LRQS: the transformed quantile surface is low rank in the causal direction, whereas reverse representability under the corresponding constraints occurs only for exceptional, fine-tuned cause marginals. We provide a simple-yet-powerful causal score using a nonparametric fitting procedure that alternates between rank-constrained approximation of discretized quantile surfaces and isotonic estimation of the unknown monotone transformation. Experiments on synthetic mechanisms with higher-rank distributional shape variation and strong nonlinear distortions, together with standard bivariate benchmarks, show that LRQS is especially effective when conditional distributional shape or observation distortion goes beyond existing location-scale assumptions.

Abstract: Generative augmentation is a standard remedy for label scarcity in physiological signal classification, but existing quantum generative models start from uninformative noise, ignoring class structure that is already available. We propose Conditional Quantum Flow Matching (CQFM): a single 306-parameter circuit, conditioned on both flow time and class label, transports a compact class-conditional prior toward the target distribution. Quantum flow matching as published is unconditional, so this is to our knowledge the first conditional one, and the first EEG augmentation on a parameterized quantum circuit. A nonnegative spectral embedding removes the need for tomography at readout. On BCI Competition IV-2a, starting from a prior rather than noise is worth $+5.1$ accuracy points over QuDDPM (9/9 subjects), though at that operating point a class-conditional Gaussian matches CQFM. Where the prior fails the transport earns its keep: given one transferred from other subjects it regains $+7.2$ TSTR points (9/9).

Abstract: Question-answering often requires reasoning across multiple connected facts rather than retrieving a single isolated relation. Knowledge graphs (KGs) provide a structured way to represent such facts, but training large language models (LLMs) only on isolated KG head-relation-tail triples may limit their ability to learn the surrounding context needed for multi-hop reasoning. In this work, we propose a context-augmented training framework for multi-hop question-answering. Although generally applicable, we validate the framework in the context of disease-specific KGs, extracted using a reliable KG extraction framework called GraphMERT, for Gastroparesis and Diabetes. For each primary KG triple, we attach supporting triples extracted from the same source text chunk to form a context graph (CG). This creates two supervision settings: KG-grounded supervision, which uses only the target KG triple or path, and CG-grounded supervision, which uses the target KG triple or path together with supporting context triples. We train the Qwen3-14B model using supervised fine-tuning (SFT) under both settings, producing KGModel and CGModel variants. To strengthen the lower-hop factual foundation of the models, we introduce an LLM-judged, history-aware adaptive repair pipeline that identifies unresolved one-hop failures, continually fine-tunes on targeted repair examples, and removes or quarantines problematic noisy triples. This repair stage enables the models to reach 100% accuracy on the cleaned retained one-hop validation sets. Finally, we employ reinforcement learning (RL) using lower-hop question-answer items and evaluate generalization on harder 3-hop, 4-hop, and 5-hop tasks. Across both diseases, context-augmented supervision consistently improves multi-hop performance over KG-only supervision. RL initialized from repaired SFT checkpoints yields larger and more stable gains.