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01.
arXiv (CS.CL) 2026-06-17

PACE-RAG: Patient-Aware Contextual and Evidence-Constrained RAG for Clinical Drug Recommendation

Drug recommendation requires a deep understanding of individual patient context, especially for complex conditions like Parkinson's disease. While LLMs possess broad medical knowledge, they fail to capture the subtle nuances of actual prescribing patterns. Existing RAG methods also struggle with these complexities because guideline-based retrieval remains too generic and similar-patient retrieval often replicates majority patterns without accounting for the unique clinical nuances of individual patients. To bridge this gap, we propose PACE-RAG (Patient-Aware Contextual and Evidence-Constrained RAG). Rather than directly copying frequent medications from retrieved patients, PACE-RAG personalizes recommendations by first extracting patient-specific clinical features, retrieving cases around these features, and then refining the final prescription using the patient's current symptoms, active medication history, and focus-specific prescribing tendencies. By analyzing treatment patterns tailored to specific clinical features, PACE-RAG generates patient-specific medication recommendations along with an explainable clinical summary. Evaluated on a Parkinson's cohort and the MIMIC-IV benchmark using Llama-3.1-8B and Qwen3-8B, PACE-RAG achieved state-of-the-art performance, reaching F1 scores of 80.84% and 47.22%, respectively. These results suggest that PACE-RAG is a robust and clinically grounded framework for personalized decision support. Our code is available at: https://github.com/ChaeYoungHuh/PACE-RAG.

02.
arXiv (CS.CL) 2026-06-18

Compact Geometric Representations of Hierarchies

Computing geometric representations of data is a cornerstone of modern machine learning, typically achieved by training dual encoders which map queries and documents into a shared embedding space. Recent work of You et al. [NeurIPS '25] has extended this approach to hierarchical retrieval, where relevance is determined by the ancestor-descendant relationships in a Directed Acyclic Graph (DAG). While previous work has shown that valid embeddings exist when the number of descendants is small, these bounds degrade significantly for deep hierarchies, requiring dimensions as large as the total number of nodes. In this paper, we investigate compact reachability embeddings for more general graph classes and provide theoretical guarantees for representing hierarchies using embeddings whose dimension depends on structural graph parameters. We prove that for any directed tree, there exists a reachability embedding in constant dimension 3, independent of the tree's size or depth. We generalize this result to graphs characterized by treewidth $t$, constructing embeddings of dimension $O(t \log n)$, where $n$ is the number of nodes. Complementing these upper bounds, we provide matching or near-matching lower bounds, showing that dimension $\Omega(n)$ is necessary for general DAGs and $\Omega(t/\log(n/t))$ is required for graphs of treewidth $t$. We also obtain upper and lower bounds parameterized by the number of cross-edges in the DAG. We additionally show that our embeddings can be constructed on real world datasets, and that they give much smaller dimensions in high recall regimes compared to prior embeddings with theoretical guarantees.

03.
arXiv (CS.LG) 2026-06-18

PACT: Preserving Anchored Cores in Task-vectors for Model Merging

arXiv:2606.18627v1 Announce Type: new Abstract: Model merging has emerged as a training-free alternative to multi-task learning, aiming to combine multiple task-specific fine-tuned models into a single multi-task model. Most existing model merging approaches follow the Task Arithmetic paradigm, which decomposes fine-tuned weights into pre-trained parameters and task vectors, and performs merging exclusively in the task-vector space. The effectiveness of this paradigm implicitly relies on the assumption that task-specific knowledge is encoded solely within task vectors. We argue that this assumption generally does not hold due to the intrinsic task preferences of pre-trained models. Specifically, we identify Load-Bearing Wall (LBW) dimensions, namely some task-critical knowledge that remains embedded in the pre-trained weights rather than being fully transferred into task vectors. We characterize LBW dimensions from both scalar-weight and subspace perspectives, thereby covering the major paradigms of existing model merging methods. Our analysis reveals that, by ignoring LBW dimensions, task-vector-based approaches fail to fully resolve task conflicts and may inadvertently damage task-specific knowledge encoded in the pre-trained model, leading to degradation. To address this issue, we propose PACT, which preserves the anchored task-specific cores (i.e., LBW dimensions) within task vectors by aligning their orthogonal complements with the subspace of the pre-trained weights. These aligned subspace components are then removed from the task vectors before applying existing model merging algorithms. Furthermore, we develop an efficient variant based on randomized SVD to improve scalability. PACT can be seamlessly integrated with existing methods. Extensive experiments across multiple benchmarks demonstrate that PACT consistently enhances mainstream model merging approaches and establishes new state-of-the-art performance.

04.
arXiv (math.PR) 2026-06-11

The $K$-th nearest neighbor random walk on a Poisson point process gets trapped

arXiv:2606.11271v1 Announce Type: new Abstract: The $K$-th nearest neighbor random walk $(X_n)_{n \geq 0}$ on a homogeneous Poisson point process $\chi$ on $\R^d$ ($d\geq 1$), starts at the origin and at each step picks its next Poisson point among its closest neighbors according to i.i.d. labels having the same distribution as $K$. Our main result (Theorem 1) states that the number of Poisson points visited by $(X_n)_{n \geq 0}$ admits an exponential decay whenever the random variable $K$ has a bounded support (BS). In particular, the $K$-th nearest neighbor random walk visits finitely many Poisson points if and only if $K$ satisfies Assumption (BS). To prove it, we introduce the key notion of pioneer point which allows us to deal with the region of $\R^d$ already explored by $(X_n)_{n \geq 0}$. Still under Assumption (BS), we also prove an exponential decay for the Euclidean length of the trajectory performed by $(X_n)_{n \geq 0}$ (Theorem 2). Finally, and quite surprisingly, we exhibit an example of label distribution with bounded support for which the $K$-th nearest neighbor random walk discovers new Poisson points after a number of steps whose tail distribution is at least polynomial (Theorem 3).

05.
arXiv (CS.AI) 2026-06-18

Guava: An Effective and Universal Harness for Embodied Manipulation

arXiv:2606.18363v1 Announce Type: cross Abstract: Language models trained on large-scale vision-language data have demonstrated strong potential for embodied agents. Harnessing models through embodied tools use offers a promising alternative to end-to-end vision-language-action systems by combining high-level reasoning with external modules for perception, planning, and control. However, it remains unclear what makes an effective harness for embodied manipulation, and to what extent such a harness can unlock embodied capabilities in a wide range of reasoning models. In this work, we present Guava, a harness framework for embodied tool use developed through systematic exploration of the design space of agent workflows, action spaces, and observation spaces. Our study identifies three key ingredients for effective embodied agents: iterative perception-reasoning-action loops, semantic action abstractions, and multimodal observations. To understand whether these design principles are universal even to small models, we develop an end-to-end training pipeline that distills embodied manipulation capabilities into a 4B open-source model using fewer than 2K trajectories collected entirely in simulation. Experimental results in both simulation and real-world environments show performance comparable to frontier proprietary models while exhibiting strong generalization to unseen objects, novel instructions, and long-horizon tasks. Results suggest that a well-designed harness can serve as a scalable, model-agnostic interface for embodied manipulation, enabling strong emergent embodied capabilities in compact open-source models with minimal training data.

06.
bioRxiv (Bioinfo) 2026-06-16

Physics-Driven Zero-Shot Reconstruction of Isotropic 3D Fluorescence Microscopy under Undersampled Acquisition

Three-dimensional (3D) imaging represents the development of next generation of fluorescence microscopy. However, routine axial down-sampling makes isotropic resolution unrealistic. Here, we propose DeepUI, a physical zero-shot framework designed to achieve isotropic 3D fluorescence images from a low axial sampling rate. DeepUI fully leverages the intrinsic characteristics of 3D images through physics-guided degradation, which incorporates spatial-frequency joint learning to generate a scaled optical transfer function, combined with noise degradation and an up-sampling branch. Typically requiring just 5 minutes for training and 0.5 minutes for high-throughput and fast prediction, we demonstrate the superior performance of DeepUI to get isotropic results, and the exclusivity to axial down-sampling conditions, even in more challenging conditions, including defocused background, noise, and resolution blur.

07.
arXiv (CS.CV) 2026-06-15

LiAuto-GeoX: Efficient Grounded Driving Transformer

Dense 3D reconstruction has demonstrated immense potential for spatial understanding, yet its viability as a real-time, onboard representation for autonomous driving remains an open challenge. Existing large-scale visual geometry models typically require substantial computational resources and lack the long-range geometric fidelity, surround-view consistency, and real-time efficiency demanded by dynamic driving environments. To bridge this gap, we present LiAuto-GeoX, an efficient grounded driving transformer designed for deployable, ego-centric 3D scene understanding. Our approach begins by learning a high-capacity driving geometry model from large-scale surround-view data, utilizing sparse LiDAR priors to provide robust geometric grounding in distant, ambiguous, or structure-sparse regions. We then instantiate this capability into a highly compact 155M-parameter onboard model through a novel geometry-preserving distillation framework. This framework employs mask-guided depth-aware distillation to retain fine-grained metric structures by emphasizing geometrically informative regions, and relative-pose relational distillation to enforce cross-view spatial consistency through pose-induced geometric relations. Extensive evaluations reveal that LiAuto-GeoX runs at 220 FPS on KITTI while maintaining high-fidelity dense reconstruction, enabling real-time deployment. The learned geometry transfers seamlessly to downstream autonomy tasks, achieving 90.6 PDMS in trajectory prediction, 24.63 mIoU in occupancy prediction, and 47.67 IoU in future-frame prediction. These all demonstrate that efficient dense 3D reconstruction can transcend its traditional role as a perception target to serve as a scalable, foundational geometric representation for next-generation autonomous driving.

08.
arXiv (CS.LG) 2026-06-11

MASK: Multi-Agent Semantic K-Scheduling for Risk-Sensitive 6G Robotics

arXiv:2606.11249v1 Announce Type: cross Abstract: Realizing the vision of 6G connected robotics requires reconciling high-performance collaborative control with the rigid spectral limitations of physical wireless channels. In realistic collaborative sensing scenarios, spectral resources are quantized into finite physical resource blocks or orthogonal subcarriers, rendering simultaneous transmission by all agents infeasible. To address this, we propose Multi-Agent Semantic K-Scheduling (MASK), a control architecture designed to sustain robust, risk-aware coordination under strict instantaneous bandwidth caps. We introduce Arbiter-Assisted Semantic Information Gating (A-SIG), a lightweight coordination mechanism that enforces hard access constraints by scheduling only the top-K agents based on locally computed semantic importance scores. By aggregating these prioritized observations into a compact latent state, a self-supervised global encoder enables a distributional policy to mitigate tail risks despite data sparsity. We evaluate MASK across diverse benchmarks, demonstrating that it matches the performance of communication-unconstrained baselines even when channel access is restricted to a small fraction of the swarm size. Furthermore, the framework exhibits inherent resilience to packet erasures, validating semantic scheduling as a critical enabler for resource-constrained 6G systems.

09.
arXiv (math.PR) 2026-06-18

Formation of clusters and coarsening in weakly interacting diffusions

arXiv:2510.17629v3 Announce Type: replace-cross Abstract: This paper studies the clustering behavior of weakly interacting diffusions under the influence of sufficiently localized attractive interaction potentials on the one-dimensional torus. We describe how this clustering behavior is closely related to the presence of discontinuous phase transitions in the mean-field PDE. For local attractive interactions, we employ a new variant of the strict Riesz rearrangement inequality to prove that all global minimizers of the free energy are either uniform or single-cluster states, in the sense that they are symmetrically decreasing. We analyze different timescales for the particle system and the mean-field (McKean-Vlasov) PDE, arguing that while the particle system can exhibit coarsening by both coalescence and diffusive mass exchange between clusters, the clusters in the mean-field PDE are unable to move and coarsening occurs via the mass exchange of clusters. By introducing a new model for this mass exchange, we argue that the PDE exhibits dynamical metastability. We conclude by presenting careful numerical experiments that demonstrate the validity of our model.

10.
arXiv (CS.CL) 2026-06-11

Fine-tuning Multi-modal LLMs with ART: Art-based Reinforcement Training

There are two main Parameter-Efficient Fine-Tuning (PEFT) techniques for Large Language Models (LLMs). While Low-Rank Adaptation (LoRA) introduces additional weights between the LLM layers, Soft Prompting introduces additional fine-tuning-specific raw tokens to an LLM input. However, both require modification to the computational graphs of precompiled, preoptimized LLMs. As a result, neither is fully supported in high-throughput engines like vLLM. We propose fine-tuning with ART (Art-based Reinforcement Training). The method injects information into a frozen Multimodal Large Language Model (MLLM) by optimizing only its raw visual input, thus enabling the soft-token approach on pre-compiled computational graphs. It relies on backpropagation of gradients back into a plain pixel array and thus supports any fine-tuning objective. Moreover, the optimized visual input can be stylized as task-relevant computational artworks. The approach's effectiveness is confirmed for different sizes of a popular open Qwen architecture and for several textual benchmarks. Specifically, ART reaches accuracy competitive with LoRA across mathematics and structured-tool-use benchmarks.

11.
medRxiv (Medicine) 2026-06-19

Reassessing Instrument Strength in Two-Sample Mendelian Randomization Analysis

Mendelian randomization (MR) analysis is widely used to estimate causal relationships between risk factors and outcomes of interest. Two-sample MR approaches have gained increasing attention in genetic epidemiology due to the growing availability of Genome-Wide Association Study (GWAS) summary statistics from public databases. A critical step in two-sample MR is the selection of genetic variants as instrumental variables (IVs). Although genome-wide significant variants are typically preferred, the inclusion of variants with weaker association p-values is considered, as they may potentially improve power through an increased instrument number of instruments, while they may introduce weak instrument bias and attenuate effect estimates towards the null. Our simulation results show that even modest levels of pleiotropy substantially increase the variability of causal effect estimates, while the inclusion of weak IVs does not substantially affect the direction and variability of causal effect estimates in most cases. In real data analyses, we used two released versions of FinnGen GWAS summary statistics with different sample sizes as exposure GWASs to assess the influence of weak IVs. Here, the inclusion of IVs with higher exposure-association p-values resulted in weakened estimated effect sizes, particularly when the exposure GWAS sample size was small. These findings suggest that incorporating weak IVs is reasonable when the exposure GWAS sample size is large, but it poses a risk of falsely concluding null associations when the exposure GWAS sample size is small.

12.
medRxiv (Medicine) 2026-06-16

Enteral docosahexaenoic and arachidonic acid supplementation and retinopathy of prematurity: a re-analysis of randomized controlled trials in preterm infants

Background. A recent meta-analysis by Dang et al. [1] concluded that enteral supplementation with docosahexaenoic acid (DHA), with or without arachidonic acid (ARA) did not significantly affect retinopathy of prematurity (ROP) outcomes in preterm infants. Of four eligible trials that supplemented both DHA and ARA, only two contributed to each ROP outcome analyzed, and severe ROP was not assessed. Methods. We replicated the eligibility criteria and search strategy of Dang et al., restricted to trials that supplemented both DHA and ARA, and reanalyzed three ROP endpoints (any ROP, ROP requiring treatment, and severe ROP [stage 3 and/or treated]) using complete outcome records from all eligible trials. Crude risk ratios (RR) were pooled by Mantel-Haenszel fixed-effect meta-analysis. Gestational age-adjusted odds ratios (adjOR) were pooled on the log scale by inverse-variance random-effects meta-analysis with restricted maximum likelihood (REML) estimation of between-study variance and Hartung-Knapp confidence intervals. Results. Five trials were included; one trial was identified in our replicated search but was excluded by Dang et al. without a stated rationale. The pooled estimate for any ROP was consistent with Dang et al. (RR 0.87 [95% CI 0.71-1.08]; adjOR 0.70 [0.46-1.08]). For ROP requiring treatment, the crude RR suggested a lower risk but did not reach statistical significance (RR 0.60 [0.35-1.04]), whereas the gestational age-adjusted estimate indicated lower odds (adjOR 0.47 [0.23-0.94]). For severe ROP, DHA+ARA supplementation produced a significant protective effect in both unadjusted and adjusted models (RR 0.56 [0.36-0.86]; adjOR 0.42 [0.19-0.96]). Conclusions. When all eligible trials contribute to each endpoint and severe ROP is included as an outcome, enteral DHA+ARA supplementation reduces severe ROP and is associated with lower odds of ROP requiring treatment after adjustment for gestational age. These findings differ from the conclusions of Dang et al. and support reconsideration of DHA+ARA supplementation as a strategy to reduce sight-threatening ROP in preterm infants.

13.
arXiv (CS.AI) 2026-06-11

FACTR 2: Learning External Force Sensing for Commodity Robot Arms Improves Policy Learning

arXiv:2606.12406v1 Announce Type: cross Abstract: Contact-rich manipulation requires force sensitivity, but many robot arms lack dedicated force sensors due to their high cost. We present Neural External Torque Estimation (NEXT), a data-driven method that estimates external joint torques without needing any dedicated force sensors. NEXT trains in 1 minute from only 10 minutes of free-motion data, yet achieves estimates comparable to dedicated joint-torque sensors. NEXT enables force-feedback teleoperation on low-cost arms and improves policy learning through Force-Informed Re-Sampling Training (FIRST), which up-samples pre-contact and contact segments during behavior cloning. Across five long-horizon tasks, FIRST outperforms prior force-aware policies by over 17% in task progress. Together, NEXT and FIRST bring force-aware teleoperation and policy learning to off-the-shelf robots without additional sensing hardware. Video results and code are available at https://jasonjzliu.com/factr2

14.
arXiv (CS.AI) 2026-06-19

Learner-based Concept Drift Detection: Analysis and Evaluation

arXiv:2606.20216v1 Announce Type: cross Abstract: Machine learning algorithms deployed for evolving streaming environments must handle the non-stationary data distributions, commonly referred to as concept drift. The presence of concept drift poses a major challenge for many real-world applications because it can severely degrade their predictive performance, hindering their ability to support robust decision-making. Consequently, the timely and efficient detection of drift events is critical for sustaining high accuracy over time. This study examines theoretically the concept drift characteristics and numerous drift detection algorithms across several categories. Furthermore, we evaluate their performance on both synthetic and real-world datasets exhibiting diverse streaming scenarios and drift characteristics, such as abrupt and gradual changes. This study aims to enhance understanding of the complex notion of concept drift characteristics and behavior of drift detectors, along with their applicability to diverse contexts.

15.
arXiv (CS.AI) 2026-06-19

BrainG3N: A Dual-Purpose Tokenizer for Controllable 3D Brain MRI Generation

arXiv:2606.19651v1 Announce Type: new Abstract: Three-dimensional (3D) brain MRI is central to clinical neurology and neuro-oncology, where generative models could augment under-represented cohorts, simulate disease trajectories, and support privacy-preserving data sharing. Latent diffusion has been the go-to solution for modeling imaging data, but it places two competing demands on the tokenizer: encoder embeddings must retain the clinical information that downstream tasks act on, and the decoder must reconstruct anatomically faithful volumes. Existing reconstruction-driven tokenizers achieve the second at the expense of the first. To address this, we introduce a fully volumetric masked-autoencoder (MAE) based tokenizer for 3D brain MRI latent diffusion, decoupling encoder and decoder: a frozen 3D MAE encoder produces clinically informative embeddings, while a dedicated CNN decoder reconstructs voxels from a linear projection of those embeddings. We pretrain the encoder on 35,309 volumes from 18 public cohorts spanning four modalities, ten disease categories, and 200+ acquisition sites, and demonstrate its dual utility in two settings. First, on a 23-task linear-probing benchmark, the encoder outperforms or matches SOTA models (i.e., BrainIAC, BrainSegFounder, and MedicalNet) on 21 of 23 tasks. Second, a conditional diffusion transformer (DiT) trained on these clinically informative embeddings supports both conditional generation across six variables and patient-specific longitudinal forecasting. Together these results establish a single 3D brain-MRI embedding space capable of both downstream clinical tasks and controllable generation.

16.
medRxiv (Medicine) 2026-06-22

Leishmaniasis on YouTube: a critical appraisal of the quality, reliability, and transparency of educational content

Background: Leishmaniasis is a neglected tropical disease of significant global public health importance, for which accurate information is essential to support prevention and early care-seeking, particularly in endemic, resource-limited settings. YouTube is a widely used source of health information, but the quality and reliability of leishmaniasis-related content have not been evaluated. We aimed to assess the quality, reliability, and transparency of English-language YouTube videos on leishmaniasis. Methods: We conducted a cross-sectional analysis of YouTube videos retrieved via the YouTube Data API on 15 June 2026 using the terms "leishmaniasis," "cutaneous leishmaniasis," and "visceral leishmaniasis." After applying eligibility criteria and screening the 150 most-viewed eligible videos, 48 videos were included. Two reviewers independently assessed each video using the modified DISCERN (mDISCERN) tool, the Global Quality Score (GQS), and the JAMA benchmark criteria, with disagreements resolved by consensus. Inter-rater agreement was assessed using the intraclass correlation coefficient (ICC), and associations were examined using Spearman's rank correlation. Results: Of 402 videos retrieved, 48 met the inclusion criteria. The median GQS was 3.00 (IQR 2.00-4.00) and median mDISCERN was 3.00 (IQR 2.38-4.50), indicating moderate quality and reliability, while the median JAMA score was 2.00 (IQR 1.00-2.00), reflecting limited transparency; no video met all four JAMA criteria. The overwhelming majority of videos (47/48, 97.9%) were of professional or institutional origin. Inter-rater agreement was good to excellent (ICC 0.883 for GQS, 0.896 for mDISCERN, 1.000 for JAMA). The instruments were strongly inter-correlated (mDISCERN-GQS rho = 0.841, p < 0.001). Quality scores did not correlate positively with views, likes, or video duration; comments correlated weakly and negatively with mDISCERN (rho = -0.337, p = 0.031) and JAMA (rho = -0.381, p = 0.014). Conclusions: YouTube videos on leishmaniasis are of moderate quality and reliability but limited transparency, and are produced almost exclusively by professional sources. Video popularity, length, and age were not indicators of quality. There is a need for experts and institutions to produce clearly authored, well-sourced, and transparent educational content on this neglected tropical disease.

17.
arXiv (CS.CL) 2026-06-12

When Does Mixing Help? Analyzing Query Embedding Interpolation in Multilingual Dense Retrieval

While mixed-language querying is ubiquitous in multilingual communities, the sensitivity of dense retrievers to such queries remains poorly understood. We present a ratio-controlled study on mMARCO that systematically evaluates retrieval performance by varying the mixing proportion of parallel query translations via embedding-level mixing – constructing mixed queries as an interpolation of monolingual embeddings. Experiments with BGE-M3 demonstrate that an optimal mixing ratio outperforms the best monolingual endpoint in 88/105 cases. We uncover a distinct asymmetry driven by English dominance: mixing is uniformly beneficial when retrieving from non-English document indices, whereas indices containing English are best served by pure English queries. Furthermore, English acts as the strongest mixing partner for every non-English document language. Finally, when controlling for English dominance, mixing gains correlate negatively with typological distance. We conclude that language-mix sensitivity is structured and predictable, and we validate the robustness of these patterns across model families and scales.

18.
medRxiv (Medicine) 2026-06-11

Electrical signatures of divergent connectivity in the human subgenual cingulate cortex

Background: Major depressive disorder remains a leading cause of disability. While subgenual cingulate cortex (sgCC) deep brain stimulation (DBS) shows promise for medically refractory depression, clinical outcomes have been heterogeneous, suggesting that individual differences in neural circuitry engagement may critically influence therapeutic efficacy. We aimed to define the electrophysiological signatures of sgCC efferent connectivity using single-pulse electrical stimulation (SPES) with intracranial stereo-EEG (sEEG) to inform rational targeting and physiological biomarkers for sgCC-DBS. Methods: In four patients undergoing clinically indicated sEEG for seizure mapping, SPES was delivered through sgCC pairs, while distributed brain stimulation-evoked potentials (BSEPs) were recorded across cortical and subcortical sites. Responses were characterized using Canonical Response Parameterization to extract reproducible waveforms and per-trial reliability. Results: sgCC stimulation elicited reproducible, spatially organized BSEPs across frontal, limbic, and paralimbic networks, aligning with known anatomical pathways. Frontal recruitment featured robust, lateralized orbitofrontal activation favoring the ipsilateral central, medial OFC and bilateral ventromedial prefrontal responses. Limbic effects demonstrated bilateral cingulate activation with stronger ipsilateral recruitment and lateralized amygdala and hippocampal responses. Paralimbic engagement included insular responses with subject-specific anterior predominance and bi-hemispheric temporal-polar slow-wave deflections. Conclusion: These findings provide direct electrophysiological evidence of distributed, lateralized sgCC divergent network connectivity in the human brain, offering physiologic confirmation of its role in affective circuitry. The observed topography and laterality have direct applications for sgCC-DBS targeting and implicate BSEP signatures as candidate biomarkers to guide patient-specific therapy.

19.
arXiv (CS.AI) 2026-06-16

An Empirical Investigation of Pre-Trained Deep Learning Model Reuse in the Scientific Process

arXiv:2603.13584v2 Announce Type: replace-cross Abstract: Deep learning has achieved recognition for its impact within natural sciences, yet the prohibitive financial and technical cost of training models from scratch inhibit adoption. Following software engineering community guidance, natural scientists are reusing pre-trained deep learning models (PTMs) to amortize these costs. While prior works recommend PTM reuse patterns, we present the first empirical study of PTM reuse patterns in the natural sciences, quantifying the utilization and impact of PTM reuse within the scientific process across 17,718 peer reviewed, open access papers. Our results show that "Biochemistry, Genetics and Molecular Biology" has outpaced other natural scientific fields in PTM reuse, "adaptation" reuse is the most prevalent PTM reuse pattern identified across all natural science fields, and the "testing" stage of the scientific process has been most impacted by PTM integration.

20.
arXiv (CS.CV) 2026-06-18

Toward Training-Free Zero-Shot Anomaly Detection in 3D Medical Images: A Batch-Based Approach Using 2D Foundation Models

作者:

Zero-shot anomaly detection (ZSAD) is attractive for medical imaging because clinical systems must handle heterogeneous acquisition protocols, changing patient populations, and pathologies for which annotated training data may be unavailable. Most existing zero-shot anomaly detection methods are designed for 2D images, and their direct extension to 3D medical volumes is limited by the scarcity of large-scale volumetric foundation models or by the difficulty of utilizing volumetric context. We propose CS3F, a training-free batch-based framework for ZSAD in 3D medical images using 2D foundation models. Each volume is decomposed along multiple anatomical axes and encoded slice-wise by a 2D vision transformer. These are then converted into localized volumetric tokens by pooling neighboring slice features. Anomaly scores are obtained from cross-subject mutual similarity: tokens that lack close analogues in other subjects are assigned higher anomaly scores. To reduce the attenuation of focal lesion signals caused by depth pooling, we introduce a coarse-to-fine tokenization strategy that enables fine-resolution volumetric scoring without exhaustive matching. CS3F is evaluated on brain MRI across metastases, glioma, and stroke, as well as validated on lung CT to test generalizability beyond atlas-aligned brain MRI. The results show that frozen 2D foundation models can support anomaly localization in 3D medical images, and that the benefit of fine tokenization depends strongly on lesion contrast and imaging modality.

21.
arXiv (CS.CL) 2026-06-16

Data-Driven Decoding of Russell's Circumplex Model of Affect

Affective computing increasingly relies on deep learning to represent emotions, yet latent spaces often remain opaque, high-dimensional black boxes. This paper investigates whether Transformers' embeddings recover the geometric regularities of Russell's circumplex model. We unify two complementary experiments testing the hypothesis that, after training models on text and speech, their resulting latent spaces encode a topology consistent with valence-arousal and reproduce human-like neighborhood relations. Specifically, we evaluate deep representations extracted from Transformer-based text (RoBERTa) and speech (wav2vec 2.0) encoders, along with a multimodal Transformer fusion architecture, across naturalistic datasets like MSP-Podcast and controlled LLM-generated stimuli. Our analysis reveals that multimodal fusion of text and audio yields perfect topological alignment with Russell's primary emotion ordering. Furthermore, in a zero-shot setting using generic text embeddings, projected fine-grained emotion terms fall close to their established human-mapped coordinates. Our contribution is a novel, data-driven framework for validating emotion models, demonstrating that Russell's circumplex structure is intrinsically encoded in the embeddings of these modalities rather than being solely an artifact of human labeling, thereby bridging the gap between psychological theory and representation learning.

22.
arXiv (CS.AI) 2026-06-12

Deterministic Integrity Gates for LLM-Assisted Clinical Manuscript Preparation: An Auditable Biomedical Informatics Architecture

arXiv:2606.09500v3 Announce Type: replace Abstract: As autonomous research agents and AI co-scientist systems push large language models (LLMs) from drafting toward end-to-end manuscript production, the bottleneck shifts from generation to verification. Fluent LLM output can hide fabricated citations, numbers that drift from source tables, and unmet reporting-guideline items; existing tools generate without verifying, and self-critique inherits the blind spots that produce confident fabrication. We describe an architecture pairing generation with verification, resting on three principles: decompose the workflow into self-contained skills, gate every stage transition with halt-on-failure, and resolve each integrity question with the cheapest sufficient mechanism, a deterministic, re-executable check where one suffices and a prose-level probe only where interpretation is unavoidable. This determinism-where-possible split, organized as an integrity-gate taxonomy, is the core contribution. It is realized as MedSci Skills, an open-source toolkit of 43 skills with a 21-detector deterministic tier, evaluated on three public-dataset pipelines (STARD, PRISMA, STROBE) and a seeded-defect ablation. Across the three pipelines every content-hash manifest verified clean and the gates surfaced real defects; on 27 identical injected defects the deterministic gates detected all 27 with no false positives on the matched clean fixtures, whereas a single-prompt LLM reviewer detected 11, its misses in code, bibliography, and style defects the prose hides. Determinism-where-possible verification yields an auditable, re-executable trail that exposes the evidence a human needs to check an LLM-assisted manuscript: feasibility and reproducibility evidence, not a claim of human-competitive quality, which a separate blinded study addresses. MedSci Skills is MIT-licensed and archived (v3.8.0).

23.
bioRxiv (Bioinfo) 2026-06-19

Simulation-based Bayesian deep learning enables uncertainty-aware tumor fraction estimation in cell-free DNA

Background: Estimating tumor fraction from whole-genome cell-free DNA sequencing is critical for liquid biopsy, but is hampered by weak signals and baseline noise at low tumor fractions. Existing computational methods often require matched controls or large labeled datasets for training and lack uncertainty quantification. To address these gaps, we developed purNPE, a Bayesian deep-learning framework trained without labeled cancer cell-free DNA samples. Specifically, purNPE leverages a two-part generative model: one component simulates diverse tumor copy-number profiles based on evolutionary genealogies, while a second, data-driven component learns and replicates realistic sequencing background patterns from cancer-free cell-free DNA. By training a Neural Posterior Estimator on synthetic tumor profiles augmented with learned noise, purNPE performs amortized inference in milliseconds without needing a reference sample set at inference. Results: In a real-world pan-cancer cohort, purNPE achieved comparable performance with existing methods against orthogonal mutant-allele-fraction validation (MAE = 0.066). In silico and semi-synthetic experiments suggested analytical sensitivity around 1% tumor fraction under the evaluated conditions and showed strong classification accuracy in low tumor fractions (AUC = 0.98 for TF [&le;] 3% versus controls). Conclusions: This work provides a framework for using simulation-based inference to derive calibrated, uncertainty-aware TF estimates, offering a potential alternative to traditional data-dependent methods.

24.
arXiv (CS.AI) 2026-06-19

FlowMaps: Modeling Long-Term Multimodal Object Dynamics with Flow Matching

arXiv:2606.20209v1 Announce Type: cross Abstract: Joint spatial and temporal understanding of 3D scenes is a crucial requirement for robots deployed in everyday household environments. Such agents must not only comprehend and navigate spatial layouts, but also reason about how these spaces evolve over time. In particular, humans interact with objects daily, causing them to change position throughout the environment and making it difficult for robots to reliably associate current observations with previously seen objects. However, these interactions are not random: human habits and routines induce spatio-temporally consistent patterns in object locations, which robotic agents can potentially learn and then exploit for downstream tasks such as navigation. To this end, we introduce FlowMaps, a latent flow matching model for estimating multimodal distributions over the future locations of dynamic objects in a continuous 3D space. By learning the implicit dependencies among objects and their temporal evolution, FlowMaps predicts likely changes in object locations conditioned on past human interactions, while supporting generalization across previously unseen environments that share similar object routines. To demonstrate the utility of this method, we deploy FlowMaps in a downstream dynamic Object Navigation task in both simulated and real-world environments. Across more than 600 episodes, FlowMaps outperforms state-of-the-art approaches, showing that modeling object dynamics through continuous, multimodal spatio-temporal distributions improves robotic search and navigation in changing household environments. Code and additional material is available at https://fra-tsuna.github.io/flowmaps/.

25.
arXiv (CS.LG) 2026-06-15

Deep Doubly Debiased Longitudinal Effect Estimation with ICE G-Computation

arXiv:2602.12379v2 Announce Type: replace Abstract: Estimating longitudinal treatment effects is essential for sequential decision-making but is challenging due to treatment-confounder feedback. While Iterative Conditional Expectation (ICE) G-computation offers a principled approach, its recursive structure suffers from error propagation, corrupting the learned outcome regression models. We propose D3-Net, a framework that mitigates error propagation in ICE training and then applies a robust final correction. First, to interrupt error propagation during learning, we train the ICE sequence using Sequential Doubly Robust (SDR) pseudo-outcomes, which provide bias-corrected targets for each regression. Second, we employ a multi-task transformer with a covariate simulator head for auxiliary supervision, regularizing representation learning, and a target network to stabilize training dynamics. For the final estimate, we discard the SDR correction and instead use the uncorrected nuisance models to perform Longitudinal Targeted Minimum Loss-Based Estimation (LTMLE) on the original outcomes. This second-stage, targeted debiasing ensures robustness and optimal finite-sample properties. Comprehensive experiments demonstrate that our model, D3-Net, robustly reduces bias and variance across different horizons, counterfactuals, and time-varying confoundings, compared to existing state-of-the-art ICE-based estimators.