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01.
arXiv (CS.LG) 2026-06-19

Effective Dimension Governs Generalization in Quantum Kernel Vision Models

arXiv:2606.20183v1 Announce Type: new Abstract: Recent quantum vision models-quantum vision transformers and quantum convolutional networks-report two striking but unexplained empirical phenomena: (i) ansatze with more, or more uniformly distributed, entanglement generalize better, and (ii) injecting quantum noise can improve test accuracy rather than degrade it. These observations are currently treated as curiosities, discovered by grid search and explained, if at all, by hand. We show that both are manifestations of a single, measurable quantity: the effective dimension $d_eff$ of the (noise-shaped) quantum feature kernel. Working primarily with quantum-kernel vision models-a quantum feature map read out by a kernel classifier-we give a spectral account in which entanglement structure and quantum noise are two knobs that move $d_eff$; in an overfitting regime, contracting $d_eff$ acts as ridge-like regularization. We analyze the mechanism: an exact decomposition of the depolarized kernel $K_p=(1-p)^2K+\tfrac{p(2-p)}{D}\mathbf{1}\mathbf{1}^\top$ with $d_eff(K_p)\to1$, a contraction result (and its boundary) for amplitude damping, a kernel-machine capacity bound, and a capacity/alignment risk decomposition; the monotone contraction operative in our entangled experiments is verified empirically, not proven in general. Along the one-parameter depolarizing family the collapse is instead exact by construction; we use it only to confirm the kernel decomposition to machine precision and at up to $12$ qubits, not as evidence for $d_eff$. Amplitude damping contracts $d_eff$ and lifts test accuracy by up to $+13\%$ along an inverted-U sweet spot; the effect's sign flips between the over- and under-fitting regimes; noise injection matches an explicit spectral-filtering frontier. Our results organize two reported anecdotes into a single measurable principle for designing quantum-vision models.

02.
bioRxiv (Bioinfo) 2026-06-12

ProMiSE: Protein Multi-State Evaluation Benchmark in Biological Contexts

Proteins are inherently dynamic, with biological functions often emerging from transitions between multiple conformational states. While recent breakthroughs have largely addressed the static structure prediction problem, no systematic benchmark exists to demonstrate how well current models capture functionally relevant dynamics. We introduce ProMiSE, the first benchmark that provides both a dataset and an evaluation scheme, based on native biological assemblies and integrating major conformational change mechanisms - intrinsic, ligand-induced, and protein-induced - within a single curated dataset. We conducted a comprehensive evaluation of state-of-the-art structure prediction models, including AlphaFold3 and recent generative approaches. Our findings reveal that current models exhibit a limited ability to sample intrinsic multi-states and are often insensitive to biological context in induced scenarios. Internal representation analysis suggests that training-data exposure can shift predictions toward dominant conformational states over alternative biologically relevant states, primarily at the structure module. In contrast, results from BioEmu indicate that reducing decoding-stage bias can substantially improve multi-state sampling without major changes to upstream pair representations.

03.
arXiv (CS.AI) 2026-06-15

Learning Urban Access Costs from Origin-Destination Flows via Inverse Optimal Transport

arXiv:2606.14157v1 Announce Type: cross Abstract: Cities deliver basic services through mixed public-private facility networks, including schools, clinics, transit providers, and subsidized service points. In these systems, planners often observe where households go, but not the latent cost function through which they trade off factors such as distance, price, and institutional access. We study this urban problem through school choice in the Philippines, where the country's largest national education subsidy is intended to redirect learners from congested public schools to participating private schools. Treating school-to-school enrollment flows as an entropic optimal transport plan, we recover latent choice costs using two complementary inverse optimal transport models: an interpretable distance-banded model with a subsidy term, and a neural cost model trained through a differentiable Sinkhorn forward pass. Applied to 283{,}016 learner trips across 23{,}820 observed flows in the most populated region, the framework estimates a subsidy-equivalent distance, $\lambda^{(k)}$, interpreted as the kilometers of perceived travel cost offset by the subsidy. The case demonstrates how administrative origin-destination data can be transformed into interpretable planning metrics for accessibility-aware subsidy design, facility siting, and urban service allocation.

04.
arXiv (CS.CV) 2026-06-16

Pathway-Structured Privileged Distillation for Deployable Computational Pathology

Integrating transcriptomics and histopathology can improve cancer risk modelling, yet practical use is constrained by the limited availability of RNA profiling in routine settings. Here we introduce Mixture of Pathway Experts (MoPE), a knowledge-distillation framework that reframes multimodal learning as privileged distillation for histology-only inference. MoPE is motivated by the partial observability between RNA profiles and whole-slide images: histology can capture morphology-linked consequences of certain molecular programmes, but cannot be expected to reconstruct the full transcriptomic state. MoPE encodes RNA-derived pathways and transfers the molecular supervision to pathway-indexed pathology experts through memory-usage alignment. Across diverse public benchmarks and two independent breast cancer cohorts, MoPE consistently improved WSI-only inference performance relative to baseline methods. Pathway-usage analyses and human-audited visual inspection provide bounded inspection of model behaviour and candidate morphology-linked readouts. These results support pathway-structured privileged distillation as a promising route to using molecular information during training while preserving RNA-free inference.

05.
arXiv (CS.AI) 2026-06-19

SafeSpec: Fast and Safe LLM via Dynamic Reflective Sampling

arXiv:2606.19755v1 Announce Type: cross Abstract: Speculative inference accelerates large language model (LLM) decoding but provides no inherent safety guarantees. Existing safety defenses are largely incompatible with speculative inference: they either introduce additional computation or disrupt the draft-verify mechanism, negating acceleration benefits. This reveals a fundamental incompatibility between current safety methods and speculative decoding. We propose SafeSpec, a safety-aware speculative inference framework that integrates risk estimation directly into the verification process. SafeSpec attaches a lightweight latent safety head to the target model to jointly evaluate semantic validity and safety in a single forward pass. When unsafe generations are detected, SafeSpec applies rollback and safety-guided reflective multi-sampling to recover safe continuations rather than terminating generation. We model jailbreak attacks as distributional shifts over generative trajectories, where adversarial prompts increase the probability of harmful continuations without eliminating safe ones. Under this model, SafeSpec performs risk-aware trajectory recovery within the speculative decoding process. Across multiple models and adversarial benchmarks, SafeSpec achieves a substantially improved safety-efficiency trade-off. On Qwen3-32B, SafeSpec reduces attack success rates by 15% while preserving a 2.06x inference speedup on benign workloads, demonstrating that speculative acceleration and inference-time safety can be jointly optimized.

06.
arXiv (CS.AI) 2026-06-17

Learning-Infused Formal Reasoning: From Contract Synthesis to Artifact Reuse and Formal Semantics

arXiv:2602.02881v2 Announce Type: replace-cross Abstract: This paper articulates a long-term research vision for formal methods at the intersection with artificial intelligence, outlining multiple conceptual and technical dimensions and reporting on our ongoing work toward realising this vision. It advances a forward-looking perspective on the next generation of formal methods based on the integration of automated contract synthesis, semantic artifact reuse, and refinement-based theory. We argue that future verification systems must builds towards individual correctness proofs toward a cumulative, knowledge-driven paradigm in which specifications, contracts, and proofs are continuously synthesised and transferred across systems. To support this shift, we outline a hybrid framework combining large language models with graph-based representations to enable scalable semantic matching and principled reuse of verification artifacts. Learning-based components provide semantic guidance across heterogeneous notations and abstraction levels, while symbolic matching ensures formal soundness. Grounded in compositional reasoning, this vision points toward verification ecosystems that evolve systematically, leveraging past verification efforts to accelerate future assurance.

07.
arXiv (CS.LG) 2026-06-12

Kareus: Joint Reduction of Dynamic and Static Energy in Large Model Training

arXiv:2601.17654v2 Announce Type: replace Abstract: The computing demand of AI is growing at an unprecedented rate, but energy supply is not keeping pace. As a result, energy has become an expensive and contended resource that requires explicit management and optimization. Although recent works have made significant progress in large model training optimization, they focus on optimizing either dynamic or static energy consumption. We find that fine-grained kernel scheduling and frequency scaling jointly and interdependently impact both dynamic and static energy consumption. Based on this finding, we design Kareus, a training system that pushes the time-energy tradeoff frontier by optimizing both aspects. Kareus decomposes the intractable joint optimization problem into local, partition-based subproblems. It then uses a multi-pass multi-objective optimization algorithm to find execution schedules that push the time-energy tradeoff frontier. Compared to the state of the art, Kareus reduces training energy by up to 28.3% at the same training time, or reduces training time by up to 27.5% at the same energy consumption.

08.
arXiv (CS.CL) 2026-06-12

Reasoning Models Know What's Important, and Encode It in Their Activations

Language models often solve complex tasks by generating long reasoning chains, consisting of many steps with varying importance. While some steps are crucial for generating the final answer, others are removable. Determining which steps matter most, and why, remains an open question central to understanding how models process reasoning. We investigate if this question is best approached through model internals or through tokens of the reasoning chain itself. We find that model activations contain more information than tokens for identifying important reasoning steps. Crucially, by training probes on model activations to predict importance, we show that models encode an internal representation of step importance, even prior to the generation of subsequent steps. The internal representations of importance in different models yield high agreement on which steps are important. The representation is distributed across layers, and does not correlate with surface-level features, such as a step's relative position or its length. Our findings suggest that analyzing activations can reveal aspects of reasoning that surface-level approaches fundamentally miss, indicating that reasoning analyses should look into model internals.

09.
arXiv (CS.CV) 2026-06-12

GeoWorld-VLM: Geometry from World Models for Vision-Language Models

Modern Vision-Language Models (VLMs) achieve strong semantic recognition, yet remain brittle on elementary spatial relations such as left of, on, behind, and between. One cause of this failure arises before language reasoning begins: the visual pathway may compress or discard critical 3D structural cues during feature extraction, so the language model receives image representations that are already insufficient for reliable spatial judgment. We introduce GeoWorld-VLM, a VLM-side distillation framework that transfers geometric structure from frozen camera-conditioned video world models into VLMs. GeoWorld-VLM fine-tunes only the image encoder and multimodal projector, aligning post-projector image features with intermediate world-model representations while leaving the main backbone frozen. Given images, a prompt, and a sampled camera trajectory, the world-model teacher converts static visual input into a synthetic multi-view spatial signal. Training combines spatial answer supervision, teacher-student feature alignment, and a preservation anchor to the original VLM. Since the language model remains frozen, GeoWorld-VLM preserves the original model's linguistic capabilities while attributing spatial improvements to the enhanced visual pathway. To evaluate the effectiveness and generality of the proposed method, we apply GeoWorld-VLM to two distinct VLM architectures and observe consistent improvements across both backbones. GeoWorld-VLM improves performance by approximately 4 percent on both the What'sUp and VSR benchmarks, suggesting that world-model-guided visual alignment generalizes across model structures and spatial reasoning datasets.

10.
arXiv (CS.CL) 2026-06-17

OpenLID-v3: Improving the Precision of Closely Related Language Identification – An Experience Report

Language identification (LID) is an essential step in building high-quality multilingual datasets from web data. Existing LID tools (such as OpenLID or GlotLID) often struggle to identify closely related languages and to distinguish valid natural language from noise, which contaminates language-specific subsets, especially for low-resource languages. In this work we extend the OpenLID classifier by adding more training data, merging problematic language variant clusters, and introducing a special label for marking noise. We call this extended system OpenLID-v3 and evaluate it against GlotLID on multiple benchmarks. During development, we focus on three groups of closely related languages (Bosnian, Croatian, and Serbian; Romance varieties of Northern Italy and Southern France; and Scandinavian languages) and contribute new evaluation datasets where existing ones are inadequate. We find that ensemble approaches improve precision but also substantially reduce coverage for low-resource languages. OpenLID-v3 is available on https://huggingface.co/HPLT/OpenLID-v3.

11.
medRxiv (Medicine) 2026-06-10

Developmental Associations Linking Childhood Trauma and Early Cannabis Use to Adolescent DNA Methylation and Psychotic-Like Experiences

Background. Psychotic-like experiences (PLEs) index early risk for psychotic disorders and are consistently associated with childhood trauma, yet underlying biological mechanisms remain poorly understood. DNA methylation (DNAm) may capture the biological embedding of early adversity, while adolescent exposures such as cannabis use may modify these processes. We examined epigenome-wide associations of childhood trauma and PLEs, tested the moderating role of early cannabis use, and evaluated DNAm as a potential mediator. Methods. We analysed data from the Avon Longitudinal Study of Parents and Children (ALSPAC), a UK population-based birth cohort. Childhood trauma was assessed prospectively and retrospectively. Epigenome-wide DNAm was measured in peripheral blood at ~17 years using the Illumina 450K array, and PLEs were assessed at 18 using a structured interview. Epigenome-wide association studies were conducted for trauma-DNAm and DNAm-PLEs associations in the final sample (n = 1,457), adjusting for demographic, biological, and technical covariates. Differentially methylated regions (DMRs) were identified using DMRff, followed by functional enrichment analyses. Cannabis use at 15.5 was modelled as a moderator with multiple imputation for missing data. Mediation was tested using the Divide-Aggregate Composite-null Test (DACT). Results. Childhood trauma was associated with widespread DNAm differences, primarily at the regional level, with enrichment in pathways related to cellular stress responses. In contrast, DNAm associated with PLEs was more limited and implicated loci involved in epigenetic regulatory processes. These signatures were largely distinct, and there was no evidence supporting mediation after multiple testing correction. Incorporating cannabis use altered the pattern and extent of DNAm associations, with stronger and more significant signals observed at both CpG and regional levels, although these did not translate into evidence of mediation. Conclusion. Childhood trauma and PLEs show distinct DNAm signatures in adolescence, with trauma-related DNAm reflecting broad stress-related processes and PLE-associated DNAm implicating regulatory mechanisms. We found little evidence that DNAm mediates the trauma-PLE association. Instead, adolescent exposures, particularly cannabis use, may distinctly influence trauma-related epigenetic variation with limited detectable downstream effects on PLEs. These findings support a context-dependent model of epigenetic risk and highlight the need for larger longitudinal studies to clarify causal pathways linking early adversity to psychosis.

12.
arXiv (CS.LG) 2026-06-16

Understanding Latent Diffusability via Fisher Geometry

arXiv:2604.02751v2 Announce Type: replace Abstract: Diffusion models often degrade in latent spaces, yet the formal causes remain poorly understood. We quantify latent-space diffusability via the rate of change of the Minimum Mean Squared Error (MMSE) along the diffusion trajectory. Our framework decomposes this MMSE rate into contributions from Fisher Information (FI) and Fisher Information Rate (FIR). We demonstrate that while global isometry ensures FI alignment, FIR is governed by the interplay between encoder and data geometries. Our analysis decouples diffusion degradation into four penalties: dimensional compression, tangential distortion, high-frequency encoder curvature, and intrinsic data curvature. We derive theoretical conditions for FIR preservation to ensure stable diffusability. Experiments across diverse autoencoding architectures demonstrate the implications of our theoretical bounds. We establish FI and FIR as a comprehensive analytical framework for understanding latent diffusability.

13.
medRxiv (Medicine) 2026-06-16

Optimal Clinical Trials Platform for Progressive Multiple Sclerosis (OCTOPUS): protocol for an international, multi-arm, multi-stage, platform, randomized controlled, double-blind, phase 3 clinical trial.

Introduction Current treatments for multiple sclerosis (MS) do not address the pathological processes of neurodegeneration and chronic demyelination. This, coupled with the significant challenges of translating promising phase 2 results to phase 3 trial success, highlights the need for more efficient trial designs, such as platform multi-arm multi-stage (MAMS) trial approaches. MAMS trials have demonstrated success in areas such as oncology and infectious diseases. They are typified by a statistically robust core trial design that allows the addition of further treatment arms and utilisation of interim outcome analyses at pre-defined timepoints, to determine whether to terminate a treatment arm early or proceed to the final outcome analysis. To address the challenges in progressive multiple sclerosis (PMS) treatment discovery, the Optimal Clinical Trials Platform for PMS (OCTOPUS) trial was developed. It currently utilises MRI whole-brain atrophy as its interim outcome measure and the clinically relevant composite Expanded Disability Status Scale Plus (EDSS-Plus) as its final outcome measure. A rigorous and systematic drug selection process that assessed preclinical in vitro and animal model evidence, along with additional human data, led to the prioritisation of R/S-alpha lipoic acid (R/S-ALA) and metformin for testing against placebo, targeting pathobiological mechanisms relevant to PMS. All participants will be eligible to receive the current standard of care, including disease-modifying treatments (DMTs). Method and analysis OCTOPUS will be a multi-centre, randomised, placebo-controlled, double-blind, phase 3, MAMS trial of participants aged 25 to 70 years (inclusive) with PMS and an EDSS score of 4.0 to 8.0 (inclusive). Steady progression must be the major cause of increasing disability rather than relapse in the preceding 2 years. In the trial s first candidate drug cycle, participants will be allocated to R/S-ALA, metformin, or placebo in a 1:1:1 ratio. Cycle 1 active treatments will start as R/S-ALA 600 mg once daily, increased after 4 weeks to 600 mg twice daily, or metformin 1 g once daily, increased after 4 weeks to 1 g twice daily. The trial will be multinational, with participation from 28 hospitals across the UK and 10 hospitals in Australia. Clinician-reported measures will include: the EDSS-Plus and the individual components: EDSS, Timed 25 Foot Walk (T25FW); 9 Hole Peg Test (9HPT); Symbol Digit Modalities Test (SDMT); Sloan Low Contrast Visual Acuity (SLCVA); and Relapse assessment. Patient-reported outcomes include MS specific walking, fatigue, pain, and impact scales. We will include a health economic analysis. Analysis stage 1 will require randomisation of 125 participants per arm and utilise MRI percentage brain volume change (PBVC) with the Structural Image Evaluation using Normalisation of Atrophy (SIENA) technique from baseline to 78 weeks. A positive outcome in analysis stage 1 will detect a 0.15% per year whole brain atrophy difference with a one-sided alpha of 0.35 and power of 95%, ensuring a low probability of erroneously rejecting a treatment arm at this stage. Any arms that show a positive effect will proceed to final analysis stage 2. Analysis stage 2 will require 600 participants per arm. Participants included in stage 1 will also be included in the stage 2. Analysis stage 2 will evaluate time to 6-month confirmed disability progression in the EDSS-Plus, in order to detect a 25% hazard ratio reduction with 90% power and an alpha of 0.05. Assuming one treatment arm proceeds to analysis stage 2, the trial will recruit approximately 1,200 participants and last about 6 years. This is approximately two-thirds the size and half the duration of separately conducted two-arm phase 2 and 3 trials. Ethics and dissemination The protocol was approved by the London Hampstead REC (22/LO/0622). This manuscript is based on protocol version 8.0, 28th August 2025. The findings of this trial will be disseminated through peer-reviewed publications and conference presentations. There will be a close communication strategy developed with the UK MS Society (MSS) and full patient and public involvement and engagement (PPIE). Trial registration ISRCTN: 14048364 EudraCT number: 2021-003034-37 CTA 20363/0445 IRAS number: 1003943 Secondary identifying numbers: ND001, CPMS 54274 Strengths and limitations - The OCTOPUS trial will be the first platform multi-arm multi-stage phase 3 trial in PMS, offering the potential to significantly expedite clinical trial processes with advantages in cost- and time-efficiency, focusing specifically on the poorly treated pathobiological processes of chronic neurodegeneration and demyelination - It will begin by assessing two promising drug candidates, immediate-release metformin and R/S-ALA, and will expand over the duration of the trial to include more drug arms under the same trial master protocol - The flexible and statistically robust trial design means that several components of the design (such as the early analysis stage 1 interim outcome) can be updated in line with evolving scientific knowledge - It will ultimately be the largest ever investigator-initiated phase 3 trial in PMS - It will include a range of national and international trial sites, including neuroscience centres and district general hospitals - It will have a high inclusion limit for age (up to 70 years) and disability (up to EDSS 8.0) - Several components (the telephone EDSS and virtual patient-reported outcome measures) will be amenable to remote collection increasing inclusivity and thus addressing public and participant suggestions, while minimising the risk of missing data - The main challenges in this trial design are the statistical and methodological complexity involved in design and implementation, and interpretation of interim trial results. Conclusion The trial launched cycle 1 in January 2023. Analysis stage 1 recruitment of 375 participants was achieved in November 2024, enabling planned interim analysis stage 1 to be conducted by late 2026 (Figure 1). On the 1st of June 2026, in the UK, 24 sites are active with a further 4 in set-up as part of stage 2, and in the Australian extension, Platform Adaptive Trial for Remyelination and Neuroprotection in Multiple Sclerosis (PLATYPUS), 1 site is active, with 9 additional sites in set-up.

14.
Science (Express) 2026-05-07

TranscriptFormer: A generative cell atlas across 1.5 billion years of evolution | Science

作者: 未知作者

Single-cell transcriptomics is revolutionizing our understanding of cellular diversity, yet comparing transcriptional programs across the tree of life remains challenging. We developed TranscriptFormer, a family of generative foundation models trained on up to 112 million cells spanning 1.53 billion years of evolution across 12 species. We demonstrate state-of-the-art performance on cell type classification, even for species separated over 685 million years of evolution, and zero-shot disease state identification in human cells. Developmental trajectories, phylogenetic relationships and cellular hierarchies emerge naturally in TranscriptFormer’s representations without any explicit training on these annotations. This work establishes a powerful framework for quantitative single-cell analysis and comparative cellular biology, thus demonstrating that universal principles of cellular organization can be learned and predicted across the tree of life.

15.
arXiv (CS.LG) 2026-06-16

Overcoming Rank Collapse in Feedback Alignment

arXiv:2606.11123v2 Announce Type: replace Abstract: Backpropagation (BP) is widely viewed as biologically implausible, in part because it requires feedback weights to be the transpose of forward weights for error propagation. Interestingly, when training a network with fixed random feedback weights to circumvent this issue, learning aligns the forward weights with the feedback weights, leading the backpropagated error signal to become an approximation of the standard gradient used by BP. This process, called Feedback Alignment (FA), occurs in MLPs and very shallow CNNs but does not scale well to deeper architectures. In this work, we first investigated differences between BP and FA models, trained on CIFAR10, specifically focusing on the effective rank of the signal. We found that the FA error has a considerably lower rank and hence is constrained to a lower-dimensional subspace compared to BP, limiting exploration of the parameter space. Motivated by this observation, we evaluated two mechanisms for increasing the effective dimensionality of FA: Muon, an optimiser that orthogonalises weight updates; and hidden activity normalisation, which promotes activation orthogonality. Across larger architectures and benchmarks, we find that these methods consistently improve over FA baselines, for example, on CIFAR100 with a Resnet-18, accuracy increases by 9 percentage points. Our results identify low-dimensional gradient dynamics as a key obstacle to scaling FA and suggest that inducing higher-dimensional update geometry is a promising route toward scaling alternatives to backpropagation.

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

TerraMind: Large-Scale Generative Multimodality for Earth Observation

arXiv:2504.11171v5 Announce Type: replace-cross Abstract: We present TerraMind, the first any-to-any generative, multimodal foundation model for Earth observation (EO). Unlike other multimodal models, TerraMind is pretrained on dual-scale representations combining both token-level and pixel-level data across modalities. On a token level, TerraMind encodes high-level contextual information to learn cross-modal relationships, while on a pixel level, TerraMind leverages fine-grained representations to capture critical spatial nuances. We pretrained TerraMind on nine geospatial modalities of a global, large-scale dataset. In this paper, we demonstrate that (i) TerraMind's dual-scale early fusion approach unlocks a range of zero-shot and few-shot applications for Earth observation, (ii) TerraMind introduces "Thinking-in-Modalities" (TiM) – the capability of generating additional artificial data during finetuning and inference to improve the model output – and (iii) TerraMind achieves beyond state-of-the-art performance in community-standard benchmarks for EO like PANGAEA. The pretraining dataset, the model weights, and our code are open-sourced under a permissive license.

17.
medRxiv (Medicine) 2026-06-22

Agentic Artificial Intelligence for Hospital Readmission Review: A Single-Center Blinded Evaluation and Exploratory Qualitative Analysis

Background: Manual review of 30-day hospital readmissions can identify actionable quality and safety problems, but it is labor-intensive. We developed and evaluated an agentic AI workflow for evidence-grounded readmission review. Materials and methods: We studied adult patients with unplanned 30-day readmission after discharge from a medicine hospitalist service at a single academic health system. An AI agent using a large language model queried a database containing notes, encounters, procedures, laboratory results, and other clinical data, and completed the same structured readmission-review rubric used by physicians. In the primary comparative evaluation, 20 randomly selected readmissions from 2025 were each reviewed by two physicians and the AI system. Blinded physician evaluators rated review quality. After rubric refinement, the AI workflow was applied to 100 recent readmissions in an exploratory expanded-cohort analysis of recurring improvement opportunities. Results: In the primary comparative evaluation, the AI classified 9/20 readmissions (45%) as preventable, compared with 19/40 physician reviews (47.5%). Blinded overall quality ratings were similar for AI and physician reviews (4.35 vs. 4.20 on a 1-5 scale; mean difference 0.15, 95% CI -0.20 to 0.48; p=0.49), as were factuality/support and usefulness/actionability ratings. No AI hallucinations were identified during factuality review. Agreement on preventability and primary readmission category was low for both AI-human and human-human comparisons. The AI system cost $0.23 per chart; physician reviewers took a median of 15 minutes, corresponding to an estimated $42.43 per chart. In the exploratory expanded-cohort analysis, AI-assisted review identified recurring vulnerabilities in post-discharge follow-up plans, incomplete inpatient workups, medication-safety transitions, and indwelling-device transitions. Conclusions: Agentic AI produced readmission reviews with similar blinded quality ratings to physician reviews in this small single-center primary comparative evaluation and supported identification of recurring quality-improvement themes in the exploratory expanded-cohort analysis. Preventability judgments remained variable among both AI and physicians, underscoring the need for human oversight and prospective evaluation before operational use.

18.
PLOS Computational Biology 2026-06-12

A new method for augmenting short time series, with application to pain events in sickle cell disease

by Kumar Utkarsh, Nirmish R. Shah, Tanvi Banerjee, Daniel M. Abrams Researchers across different fields, including but not limited to ecology, biology, and healthcare, often face the challenge of sparse data. Such sparsity can lead to uncertainties, estimation difficulties, and potential biases in modeling. Here we introduce a novel data augmentation method that combines multiple sparse time series datasets when they share similar statistical properties, thereby improving parameter estimation and model selection reliability. We demonstrate the effectiveness of this approach through validation studies comparing Hawkes and Poisson processes, followed by application to subjective pain dynamics in patients with sickle cell disease (SCD), a condition affecting millions worldwide, particularly those of African, Mediterranean, Middle Eastern, and Indian descent.

19.
arXiv (CS.CV) 2026-06-17

DVD: Discrete Voxel Diffusion for 3D Generation and Editing

We introduce Discrete Voxel Diffusion (DVD), a discrete diffusion framework to generate, assess, and edit sparse voxels for SLat (Structured LATent) based 3D generative pipelines. Although discrete diffusion has not generally displaced continuous diffusion in image-like generation, we show that it can be an effective first-stage prior for sparse voxel scaffolds. By treating voxel occupancy as a native discrete variable, DVD avoids continuous-to-discrete thresholding and provides a simple framework for voxel generation, uncertainty estimation, and editing. Beyond quality gains, DVD provides more interpretable generation dynamics through explicit categorical modeling. Furthermore, we leverage the predictive entropy as a robust uncertainty metric to identify ambiguous voxel regions and complicated samples, facilitating tasks such as data filtering and quality assessment. Finally, we propose a lightweight fine-tuning strategy using block-structured perturbation patterns. This approach empowers the model to inpaint and edit voxels within a single sampling round, requiring negligible auxiliary computation and no additional model evaluations. Code is available at https://github.com/TeCai/DVD.

20.
arXiv (CS.LG) 2026-06-19

Towards Graph-Based Deep Learning for Map Generalization: Insights from Building Footprints Simplification and Aggregation

arXiv:2606.19956v1 Announce Type: new Abstract: Map generalization remains one of the fundamental tasks in cartography, especially for the simplification and aggregation of complex building footprints. This study presents the first exploratory application of graph-based deep learning to both tasks, reformulating simplification as node movement prediction and aggregation as link prediction within a unified graph learning framework. We evaluate representative graph neural network architectures (GCN, GAT, and GraphSAGE) on multi-scale building datasets, showing that GraphSAGE demonstrates relative strengths in link prediction accuracy, while also revealing persistent challenges in precise node movement prediction. Beyond quantitative performance, the results highlight that aggregation poses greater complexity and challenges than simplification, underscoring the difficulty of capturing higher-level spatial relationships in map generalization with current deep learning approaches. Although limitations such as data imbalance and the need for post-processing remain, the study provides valuable insights and methodological directions for advancing automated map generalization with deep learning approaches.

21.
arXiv (CS.AI) 2026-06-19

Concept Flow Models: Anchoring Concept-Based Reasoning with Hierarchical Bottlenecks

arXiv:2606.19489v1 Announce Type: cross Abstract: Concept Bottleneck Models (CBMs) enhance interpretability by projecting learned features into a human-understandable concept space. Recent approaches leverage vision-language models to generate concept embeddings, reducing the need for manual concept annotations. However, these models suffer from a critical limitation: as the number of concepts approaches the embedding dimension, information leakage increases, enabling the model to exploit spurious or semantically irrelevant correlations and undermining interpretability. In this work, we propose Concept Flow Models (CFMs), which replace the flat bottleneck with a hierarchical, concept-driven decision tree. Each internal node in the hierarchy focuses on a localized subset of discriminative concepts, progressively narrowing the prediction scope. Our framework constructs decision hierarchies from visual embeddings, distributes semantic concepts at each hierarchy level, and trains differentiable concept weights through probabilistic tree traversal. Extensive experiments on diverse benchmarks demonstrate that CFMs match the predictive performance of flat CBMs, while substantially mitigating information leakage by reducing effective concept usage. Furthermore, CFMs yield stepwise decision flows that enable transparent and auditable model reasoning with hierarchical class structures.

22.
arXiv (quant-ph) 2026-06-16

QALM: Escaping Local Minima via Interleaved Exploration and Exploitation in Quantum Circuit Optimization

arXiv:2606.16221v1 Announce Type: new Abstract: Quantum circuit optimizers face a fundamental limitation in how they tolerate temporary cost increases. At one extreme, greedy rule-based optimizers immediately apply any cost-reducing transformation, achieving high efficiency but quickly becoming trapped in local minima. At the other extreme, search-based optimizers accept cost-increasing moves to explore the circuit space and escape such minima. However, because search-based optimizers cannot determine within a reasonable time budget whether a given point is promising, that is, whether its neighborhood contains a deeper local minimum, they must blindly explore higher-cost regions. As a result, escaping the current basin to reach a promising point takes exponentially many steps. In this work, we show that this limitation can be overcome with a hybrid framework that interleaves the exhaustive exploration capabilities of search algorithms with the efficiency of rule-based optimization. We implement this framework as QALM, a novel optimizer designed to escape local minima without incurring the runtime penalties of pure search. Crucially, our results demonstrate that QALM does not merely strike a balance; it outperforms existing rule-based and search-based optimizers in circuit reduction rates while operating with the computational efficiency of rule-based systems. In a comprehensive evaluation across 248 circuits, QALM matches or exceeds the fidelity of the strongest baseline on 83.9% of these circuits, given the same time budget.

23.
bioRxiv (Bioinfo) 2026-06-18

Benchmarking gene expression reconstruction from single-cell latent representations

Single-cell transcriptomics is typically modeled in low-dimensional latent representations that improve the signal-to-noise ratio of the data. Such representations underpin data integration, cell state discovery, and perturbation prediction, with applications ranging from large-scale organ atlases to latent trajectory modeling. Recent virtual cell approaches further leverage these representations to predict cellular responses as distributional shifts in latent space. Each of these applications ultimately requires faithful gene expression reconstruction from latent spaces for biological interpretation, enabling gene-level analysis of predicted perturbed or batch-corrected cells. Yet representation choice is typically treated as an implementation detail rather than a primary modeling decision, with no systematic evaluation of how well latent representations support gene expression reconstruction. Here, we introduce ReconEval, a benchmark for evaluating gene expression reconstruction from single-cell latent spaces. We benchmark two classes of latent representations: end-to-end trained models such as PCA, autoencoders, and variational autoencoders, and pretrained single-cell foundation model embeddings coupled to newly trained decoders. Reconstruction is evaluated both directly and after latent-space perturbation prediction. Across perturbational and observational datasets totaling over 100 million cells, our metric suite quantifies statistical fidelity; biological signal preservation, including differential expression, coexpression, cell-cycle structure, cytokine response and pathway activity; and perturbation-specific effects. We find that autoencoders achieve the strongest stand-alone reconstruction at low dimensionality, while variational regularization does not improve generalization in reconstruction. Frozen foundation model embeddings retain recoverable gene-level information, with reconstruction quality depending strongly on decoder architecture and pretraining objective. In latent perturbation modeling, high-dimensional PCA matches foundation model embeddings, while low-dimensional AE embeddings are optimal for flow-based generative models. Overall, reconstruction depends critically on the interplay between representation and downstream model, and simpler representations can outperform complex alternatives given appropriate capacity. Our benchmark establishes reconstruction as a critical evaluation axis for single-cell foundation models. We envision it improving the biological interpretability of latent-space modeling, a prerequisite for future virtual cell models to be validated by domain experts and grounded in biology.

24.
arXiv (CS.CV) 2026-06-11

UniReason-Med: A Shared Grounded Reasoning Interface for 2D-to-3D Transfer in Medical VQA

We study whether grounded reasoning supervision from abundant 2D medical images can improve 3D medical VQA when both input types are aligned through a common reasoning interface. We introduce UniReason-Med, a single-checkpoint framework that processes either a 2D image or a slice-serialized 3D volume at inference time, generating interleaved textual reasoning and localized visual evidence through shared box syntax, region-token injection, and a common grounded reasoning policy. To train this interface, we construct UniMed-CoT, a 220K instruction-tuning dataset with interleaved textual reasoning and grounded visual evidence, including 170K 2D and 50K 3D samples. Through supervised fine-tuning followed by outcome-level reinforcement learning, UniReason-Med learns to generate grounded reasoning traces without IoU/Dice-based localization rewards during RL. Data-mixture and component ablations show that joint 2D+3D grounded supervision substantially improves 3D reasoning over 3D-only training, while grounding and region-token injection consistently benefit both 2D and 3D tasks. These results suggest that a shared grounded reasoning interface can transfer reasoning structure from 2D images to slice-serialized volumetric medical understanding. The code and data are publicly available at https://github.com/IQuestLab/unireason-med.

25.
arXiv (CS.CV) 2026-06-18

Confidence is Not Reliability: Rethinking MC Dropout in Brain Tumour Segmentation

Glioma segmentation in multiparametric MRI is a critical component of treatment planning. A segmentation model that fails silently on treatment-critical sub-regions represents a patient safety risk that overlap-based metrics such as Dice scores cannot expose. We ask whether voxel-level uncertainty estimation via Monte Carlo (MC) Dropout can reliably identify segmentation errors in clinically critical sub-regions, and whether calibration failure modes are detectable from standard reporting metrics alone. In an empirical two-model case study on 126 BraTS21 patients, we evaluate a high-performance pretrained SegResNet and a locally trained UNet with residual units (UNet-Res). MC dropout preserved segmentation accuracy ($|\Delta Dice|$ $