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01.
arXiv (CS.LG) 2026-06-24

A Theory of Saddle Escape in Deep Nonlinear Networks

arXiv:2605.01288v3 Announce Type: replace Abstract: In deep networks with small initialization, training exhibits long plateaus separated by sharp feature-acquisition transitions. Whereas shallow nonlinear networks and deep linear networks are well studied, extending these analyses to deep nonlinear networks remains challenging. We derive an exact identity for the imbalance of Frobenius norms of layer weight matrices that holds for any smooth activation and any differentiable loss and use this to classify activation functions into four universality classes. On the permutation-symmetric submanifold, the identity combines with an approximate balance law to reduce the full matrix flow to a scalar ODE, giving a critical-depth escape time law $\tau_\star = \Theta(\varepsilon^{-(r-2)})$ governed by the number $r$ of layers at the bottleneck scale rather than the total depth $L$. We find that this same $r-2$ exponent is recovered under He-normal initialization with $r$ bottleneck layers rescaled by $\varepsilon$, where the symmetry manifold is preserved by the flow but not attracting. We find close agreement between our theory and numerical simulations.

02.
arXiv (math.PR) 2026-06-15

Lehner's operator norm formulas, semidefinite programming, and spiked matrix models

arXiv:2606.14687v1 Announce Type: new Abstract: Lehner (1999) derived elegant formulas for the operator norm $\|\mathfrak{X}\|$ of operators of the form $\mathfrak{X} = \mathbf{A}_0 \otimes \mathfrak{1} + \sum_{i = 1}^n \mathbf{A}_i \otimes \mathfrak{m}_i$, also easily generalized to the spectral edge $\lambda_{\max}(\mathfrak{X})$, in terms of nonlinear optimization problems over positive definite matrices. Here the $\mathbf{A}_i$ are finite-dimensional Hermitian matrices, the $\mathfrak{m}_i$ are either free semicircular or free Rademacher families of operators, and $\mathfrak{1}$ is the identity operator. We first show that both of Lehner's nonlinear optimizations can be rewritten as linear semidefinite programs (SDPs), even in the Rademacher case where Lehner's optimization is not itself convex. We give the primal and dual forms of these SDPs, derive the complementary slackness relations and consequences thereof, and propose that the SDPs are more stable and accurate than the iterative numerical scheme proposed in Lehner's original work. We then apply the SDPs from the semicircular case to spiked matrix models, studied recently via Lehner's formula by Bandeira, Cipolloni, Schröder, and van Handel (2024). We give a new proof of the Baik–Ben Arous–Péché (BBP) transition they establish in models with isotropic (but possibly correlated) Gaussian noise by constructing feasible variables for the associated primal and dual SDPs. Combining our construction with a sensitivity interpretation of optimal dual variables, we study the fluctuations of leading eigenvectors of such models. We conjecture and give numerical evidence that these fluctuations are Gaussian but anisotropic and non-universal, and that their covariance may be computed in terms of the optimizer of the dual of Lehner's formula, which in turn is approximately the leading eigenmatrix of a completely positive operator associated to the covariance of the noise model.

03.
bioRxiv (Bioinfo) 2026-06-19

Morpho-FM: spatial molecular reconstruction from routine H&E histology using transcriptomic foundation-model priors

Routine haematoxylin and eosin (H&E) histology captures tissue architecture at clinical scale, but lacks a direct molecular readout of the transcriptional programmes that organise tumour epithelium, stroma, vasculature and immune compartments. Spatial transcriptomics provides this context, yet cost, workflow complexity and sparse sampling limit routine use. Most existing histology-to-expression models are trained de novo on small paired cohorts and therefore remain weakly constrained when extrapolating from sparse measurements to dense, tissue-wide molecular maps. Here we introduce Morpho-FM, a weakly supervised framework that predicts spatial gene expression from routine H&E whole-slide images by conditioning a pretrained single-cell transcriptomic foundation-model prior on local histological neighbourhoods. A lightweight morphology-to-transcriptome adapter maps cached whole-slide histology features into a transcriptomic decoder, enabling prediction at measured locations, dense full-section reconstruction, and re-aggregation to the original measurement support. Across harmonized prostate cancer benchmarks, Morpho-FM achieved the strongest overall performance among five representative methods, reaching mean per-gene Pearson correlations of 0.286 in rotating single-slide evaluation and 0.298 in multi-slide held-out validation. The framework reproduced this advantage across kidney cancer sections, achieved a mean correlation of 0.210 across 56 directed single-slide evaluations and retained measurable predictive signal after external transfer to clear-cell renal cell carcinoma sections. Controlled ablation analyses identified pretrained transcriptomic initialization as a reproducible source of performance gain exceeding that attributable to changes in the histology feature backbone. Beyond predictive accuracy benchmarks, Morpho-FM recovered ERBB2-enriched tumour compartments, boundary-associated molecular gradients, and annotation-aligned tissue domains across Xenium and HER2ST breast cancer datasets. Together, these results support transcriptomic foundation-model priors as an effective constraint for morphology-conditioned molecular decoding and demonstrate the potential of Morpho-FM to extend spatial transcriptomic insight across routine pathology sections.

04.
arXiv (CS.LG) 2026-06-24

Flow-Corrected Thompson Sampling for Non-Stationary Contextual Bandits

arXiv:2606.23933v1 Announce Type: cross Abstract: We study non-stationary linear contextual bandits where the reward model drifts over time, rendering classical contextual bandit algorithms brittle because historical data becomes systematically biased. We propose Flow-Corrected Thompson Sampling (fcTS), a Bayesian method that reuses experience by transporting past rewards to the present using an explicit drift model and incorporating each transported observation with a confidence weight that reflects transport reliability. This yields a unified template that specializes in (i) linear parameter drift via online slope estimation and reward correction, (ii) periodic variation via phase-aware reuse across cycles, and (iii) recurring regime switches via changepoint detection and regime-specific posterior memory. The resulting posterior updates remain closed-form under a linear Gaussian model and can be implemented efficiently with truncated, incrementally updated sufficient statistics. Across five controlled case studies and a semi-synthetic portfolio-selection benchmark with multiple overlapping non-stationarities, fcTS outperforms standard forgetting-based baselines (discounting, sliding windows, and periodic restarts), with the largest gains in settings exhibiting recurring temporal structure. These results demonstrate that when non-stationarity is structured, correcting and reweighting historical observations can be substantially more sample-efficient than uniformly discarding them.

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

Uncertainty Decomposition for Clarification Seeking in LLM Agents

Recent position papers argue that the classical aleatoric/epistemic uncertainty framework is insufficient for interactive large language model (LLM) agents and call for underspecification-aware, decomposed, and communicable uncertainty representations that can unlock new agent capabilities such as proactive clarification seeking and shared mental-model building. Practical deployment constraints – black-box APIs, interactive latency budgets, and the absence of labeled trajectories – rule out logprob-based, multi-sampling, and training-based methods, leaving prompt-based estimation as the most viable family for surfacing such signals at deployment time. We answer this call with a simple prompt-based decomposition that separates action confidence from request uncertainty (u), enabling the agent to ask for clarification when the task specification is ambiguous. To evaluate it, we introduce two clarification-augmented benchmarks (WebShop-Clarification and ALFWorld-Clarification) in which 50% of tasks are deliberately underspecified, and systematically compare the proposed decomposition against ReAct+UE and Uncertainty-Aware Memory (UAM) across five LLM backbones (GPT-5.1, DeepSeek-v3.2-exp, GLM-4.7, Qwen3.5-35B, GPT-OSS-120B) on these variants together with the standard WebShop, ALFWorld, and REAL benchmarks for fault detection. Averaged across the five backbones, the proposed decomposition improves clarification F1 on ALFWorld-Clarification by 73% over ReAct+UE and by 36% over UAM, and leads clarification F1 on every backbone on WebShop-Clarification and on four of five backbones on ALFWorld-Clarification, indicating that the gains generalize beyond a single LLM.

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

UST-GNN: A Unified Spatial–Topological Graph Neural Network Framework for Urban Analytics–Demonstrated through a Case Study on Urban Health Prediction

arXiv:2504.04739v3 Announce Type: replace Abstract: Understanding how social, demographic, environmental, and spatial factors jointly shape urban outcomes is essential for sustainable urban development and evidence-based policy. Traditional statistical approaches often struggle to capture complex non-linear relationships, while many machine learning methods overlook the joint roles of spatial autocorrelation and network topology in urban systems. Recent advances in GeoAI have addressed these challenges only partially, often treating spatial effects, graph structure, evaluation, and interpretability separately. We present UST-GNN, a unified spatial–topological graph neural network framework that integrates neighbourhood connectivity, heterogeneous urban features, and positional/locational embeddings into a single representation. Using the MedSAT dataset, which contains over 150 environmental and socio-demographic variables and six prescription outcomes across 4,835 neighbourhoods in Greater London, UST-GNN outperforms strong statistical, geographically enhanced, and graph Machine Learning baselines, improving out-of-sample $R^2$ by 8.4–13.2\% under strict spatial cross-validation. We further introduce a lightweight principal-component module to interpret learned node embeddings geographically and relate them to policy-relevant covariates. The resulting analyses recover established patterns, offer new perspectives on debated associations, and reveal novel predictors warranting further causal investigation. Together, these findings demonstrate the value of graph-based spatial machine learning for urban health analytics, environmental inequality assessment, and evidence-based urban policy. Beyond predictive gains, UST-GNN provides a unified GeoAI analytical pipeline that can be embedded into urban digital twin workflows for scenario testing, monitoring, and data-informed decision-making for healthier, more sustainable cities.

07.
arXiv (quant-ph) 2026-06-17

Creating squeezed and non-classical collective motional many-body states through stroboscopic Rydberg dressing

arXiv:2606.17849v1 Announce Type: cross Abstract: Realizing conditional quantum operations, e.g., quantum gates, for quantum computing and simulation requires controlled interactions between particles. Often, these interactions depend on the interparticle distance, and accordingly, an uncertainty of the relative particle position may translate into gate infidelities. We consider here a quantum computing platform based on an array of neutral atoms and present a method that allows to reduce the uncertainty of all interatomic distances. Our approach exploits the coupling between atomic motion and stroboscopically excited atomic Rydberg states. It allows to collectively squeeze the modes corresponding to interatomic displacements, thereby reducing distance fluctuations down to a fraction of the motional vacuum state. Furthermore, the method permits the creation of non-classical states with substantial Wigner negativity. These correlated states may allow reducing motional decoherence, increasing gate fidelity, and potentially yield a resource for quantum-enhanced metrology.

08.
arXiv (CS.CL) 2026-06-16

DoubtProbe: Black-Box Jailbreak Defense via Structural Verification and Semantic Auditing

As large language models (LLMs) are increasingly deployed in user-facing systems, black-box jailbreak defense has become an important practical problem. Existing defenses often rely on known-attack coverage, prompt-level semantic judgment, or local runtime control, yet these paths can become unstable under evolving prompt packaging, expression rewriting, and structure manipulation. We observe that many black-box jailbreaks do not remove the harmful goal, but reorganize the information needed to express and execute it, thereby evading safety alignment while remaining recoverable during generation. Motivated by this observation, we propose DoubtProbe, a dual-branch inference-time defense framework that combines structural verification with semantic auditing and formulates black-box jailbreak defense as consistency checking under controlled transformation. The structural branch extracts a structured representation from the original request, reconstructs the request under representation constraints, and detects information-preservation failures between the original and reconstructed requests; the semantic branch audits the original prompt directly. We evaluate DoubtProbe against representative black-box defenses on jailbreak and benign-request benchmarks, and further test backbone transfer from Qwen2.5-72B to Llama-3.1-70B. Results show that DoubtProbe achieves a stronger and more stable defense-utility trade-off: on Qwen2.5-72B, it reduces the JBB attack success rate from 0.293 to 0.100 and the CodeAttack attack success rate from 0.152 to 0.001, while maintaining false positive rates of 0.022 and 0.016 on AlpacaEval and OR-Bench; the same pattern remains stable on Llama-3.1-70B. These findings show that structural inconsistency signals provide a practical and generalizable basis for black-box jailbreak defense, especially when combined with semantic auditing.

09.
arXiv (CS.AI) 2026-06-16

EMS: Multi-Agent Voting via Efficient Majority-then-Stopping

arXiv:2604.02863v2 Announce Type: replace Abstract: Majority voting is the standard for aggregating multi-agent responses into a final decision. However, traditional methods typically require all agents to complete their reasoning before aggregation begins, leading to significant computational overhead, as many responses become redundant once a majority consensus is achieved. In this work, we formulate efficient multi-agent voting as a reliability-aware agent scheduling problem and propose Efficient Majority-then-Stopping (EMS) to improve reasoning efficiency. EMS first estimates a Task-Conditioned Reliability Ordering (TCRO) for each agent by retrieving its historical consensus evidence on semantically similar queries, and then invoking agents in descending reliability order. Next, Adaptive Incremental Voting (AIV) terminates the process once the current leading answer cannot be overturned by any possible votes from the remaining agents, and returns this answer. Finally, Reliability History Updating (RHU) updates only the invoked agents according to their consensus with the final decision. Extensive evaluations across five benchmarks show that EMS preserves the accuracy of Majority Voting while reducing the average number of invoked agents by 35% and token consumption by 44%, respectively. The code is available at https://github.com/fuyu66/EMS.

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

Searching Neural Architectures for Sensor Nodes on IoT Gateways

arXiv:2505.23939v2 Announce Type: replace Abstract: This paper presents an automatic method for the design of Neural Networks (NNs) at the edge, enabling Machine Learning (ML) access even in privacy-sensitive Internet of Things (IoT) applications. The proposed method runs on IoT gateways and designs NNs for connected sensor nodes without sharing the collected data outside the local network, keeping the data in the site of collection. This approach has the potential to enable ML for Healthcare Internet of Things (HIoT) and Industrial Internet of Things (IIoT), designing hardware-friendly and custom NNs at the edge for personalized healthcare and advanced industrial services such as quality control, predictive maintenance, or fault diagnosis. By preventing data from being disclosed to cloud services, this method safeguards sensitive information, including industrial secrets and personal data. The outcomes of a thorough experimental session confirm that – on the Visual Wake Words dataset – the proposed approach can achieve state-of-the-art results by exploiting a search procedure that runs in less than 10 hours on the Raspberry Pi Zero 2.

11.
Nature (Science) 2026-06-17

Molecular basis of polyadenylated RNA fate determination in the nucleus

作者:

Eukaryotic genomes generate a plethora of polyadenylated (pA+) RNAs1,2, which are packaged into ribonucleoprotein particles (RNPs). To ensure faithful gene expression, functional pA+ RNPs, including protein-coding RNPs, are exported to the cytoplasm, whereas transcripts within non-functional pA+ RNPs are degraded in the nucleus1–4. How cells distinguish these opposing fates remains unknown. The DExD-box ATPase UAP56 (also known as DDX39B) is a central component of functional pA+ RNPs, and promotes their docking to the nuclear pore complex-anchored TREX-25,6, which triggers transcript release from UAP56 to facilitate export7. Here we reveal that the poly(A) tail exosome targeting (PAXT) connection8 binds a TREX-2-like module, which releases pA+ RNAs from UAP56 for decay by the nuclear exosome. The core of this module consists of a LENG8–PCID2–SEM1 trimer, which we show is structurally and biochemically equivalent to the central GANP–PCID2–SEM1 trimer of TREX-2. Mutagenesis and transcriptomic data demonstrate that the nuclear fate of pA+ RNPs is governed by the contending actions of nucleoplasmic PAXT and nuclear pore complex-associated TREX-2, which interpret RNA-bound UAP56 as a signal for RNA decay or export, respectively. As RNA targets of PAXT are generally short and intron-poor, we propose an overall model for pA+ RNP fate determination whereby the distinct sub-nuclear localizations of PAXT and TREX-2 govern the degradation of short non-functional pA+ RNAs while allowing export of their longer and functional counterparts. Biochemical, structural and cell biological analyses reveal that UAP56 (DDX39B) assembles with a TREX-2–like module that redirects non-functional polyadenylated RNAs from export to degradation.

12.
Nature Medicine 2026-06-24

Automated reanalysis of genomic data for rare disease diagnostics at scale

Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necessary to ensure scalability, adoption and sustainability of iterative reanalysis. We developed Talos, an open-source tool that automates variant prioritization by integrating dynamically updated gene−disease and variant-level evidence with inheritance-aware filtering and validated its performance using data from 1,089 individuals with rare disease. Trio-based analysis identified 90% of known diagnoses, returning 1.3 variants per case on average. Variant burden reduced to one variant per 200 cases on iterative monthly reanalysis. Application to an unselected cohort of 4,735 undiagnosed individuals identified 241 diagnoses (5.1% yield): 78 (32%) due to new gene−disease relationships, 54 (22%) due to new variant-level evidence and 109 (45%) due to improved analysis strategies. Our automated, iterative reanalysis model demonstrates the feasibility of delivering frequent, systematic reanalysis at scale. Talos, a new tool for the automated analysis of genomic data, demonstrates the feasibility and diagnostic utility of systematic reanalyses of data in rare diseases.

13.
arXiv (math.PR) 2026-06-16

Risk or Replace: Efficient Asymptotics for Data-Driven Maintenance

arXiv:2606.14706v1 Announce Type: cross Abstract: Condition-based maintenance (CBM) is an approach that plans interventions for deteriorating systems according to their observed operational state. CBM reduces unplanned downtime and extends usable lifetime. We study a heterogeneous population of components that degrade over time according to a stochastic processes with non-negative and i.i.d. increments that are characterized by component-specific parameters that remain unobservable to the decision maker. We rely on degradation data to estimate these parameters and determine replacement actions at equidistant epochs. The goal is to minimize the long-run average cost, which incorporates fixed replacement costs, failure costs, and operating costs. This problem can be formulated as a high-dimensional partially observable Markov decision process (POMDP), which is generally intractable. We develop a tractable, data-driven CBM policy that estimates the optimal policy of a hypothetical Oracle that has full information of the underlying degradation parameters and call this policy the Estimated Oracle's Optimal Policy (EOP). We introduce a scaling regime where both the failure thresholds and cost parameters increase proportionally, reflecting practical settings in which component lifetimes and maintenance costs are large relative to the time between two consecutive CBM decision moments. We show that the regret of the EOP, defined as the difference between its long-run average cost and that of the Oracle, converges to zero in the scaling regime when the parameter estimator is consistent. Across extensive experiments using both real and simulated data, the EOP achieves very low regret and, whenever the optimal POMDP policy can be computed exactly, a negligible optimality gap.

14.
arXiv (quant-ph) 2026-06-24

When does dissipation help neural surrogates learn open quantum dynamics?

arXiv:2606.23894v1 Announce Type: new Abstract: Dissipation is usually viewed as an obstacle to predicting quantum dynamics, yet it can also contract trajectories toward steady states and thereby suppress accumulated prediction errors, leaving it unclear whether dissipation ultimately helps or hinders the learnability of open quantum dynamics. We investigate this question using Neural Ordinary Differential Equation (NODE) surrogates for open Heisenberg XYZ spin chains. Closed-system learnability deteriorates rapidly with system size, culminating in a static-prediction collapse at four qubits; dissipation reverses this trend, creating a broad high-fidelity regime at intermediate system sizes, while at four qubits a fidelity-aware objective recovers learnable rollout structure that is absent under closed-system training. Comparison against static and steady-state baselines reveals that dissipation improves performance through two fundamentally different mechanisms: at weak-to-moderate dissipation the surrogate captures nontrivial transient dynamics and substantially outperforms trivial predictors, whereas at stronger damping high fidelity increasingly reflects trajectory simplification toward the steady state rather than improved learned dynamics. These results show that dissipation can enhance the learnability of open quantum dynamics, but that fidelity alone is insufficient to distinguish genuine dynamical learning from steady-state trivialization: dissipative contraction and trajectory simplification are distinct effects that peak in different regimes and should be disentangled when evaluating learned quantum-dynamical surrogates.

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

Metis: A Generalizable and Efficient World-Action Model for Autonomous Driving and Urban Navigation

World action models~(WAMs) have shown great promise for autonomous driving and urban navigation. Built upon Vision-Language-Action models or video generation models, existing approaches suffer key limitations: (1) High inference latency due to future observation prediction at test time, and (2) tightly coupled video and action modeling leading to representational mismatch and degraded generalization. To address both issues, we propose Metis, an end-to-end WAM framework that decouples video generation and action prediction. Specifically, Metis employs a Mixture-of-Transformers architecture with dedicated experts for video generation and action prediction, preserving the intrinsic distributional properties of each task. To enhance efficiency, we introduce an asymmetric attention mask that enables joint training of both experts while allowing the action model to bypass explicit video generation during inference. This design ensures training-inference consistency and significantly reduces computational costs without compromising planning performance. Extensive experiments demonstrate state-of-the-art performance on the NAVSIM navhard and navtest benchmarks and the CityWalker navigation benchmark, validating both the generalizability and efficiency across diverse tasks. Real-robot deployments further confirm the practical feasibility of our approach.

16.
arXiv (CS.CV) 2026-06-11

OpenMedReason: Scientific Reasoning Supervision for Medical Vision-Language Models

High-stakes clinical use of large vision-language models (LVLMs) requires reasoning that is grounded in visual evidence and clinical knowledge, not just correct final answers. We introduce OpenMedReason, a large-scale, open multimodal medical reasoning corpus comprising approximately 450K image-question-answer instances whose reasoning traces are primarily derived from curated biomedical, human-authored scientific articles. OpenMedReason provides high-fidelity supervision beyond synthetic chains of thought, covering diverse medical domain vision modalities such as radiological scans, microscopic images, visible light photographs, charts, and others. We complement it with OpenMedReason-Bench, a held-out benchmark that allows fine-grained evaluation of LVLMs along three complementary axes of capability, including perception, medical knowledge, and rationale, enabling diagnostic evaluation beyond final-answer accuracy. OpenMedReason is a rich training resource that exhibits its effectiveness in both supervised fine-tuning (SFT) and reinforcement-based alignment. Training with OpenMedReason yields a 20% average improvement in VQA accuracy over the base model and achieves performance within 4.2% of the strongest comparable-scale medical LVLMs. Fine-grained performance analysis confirms that the gains are not concentrated in any single axis: OpenMedReason improves perception, medical knowledge, and rationale jointly, and its reasoning traces are preferred over those of the base model in 86.1% of pairwise comparisons. We release the code and dataset at huggingface.co/datasets/neginb/OpenMedReason.

17.
Nature (Science) 2026-06-17

A mosaic of whole-body representations on the human precentral gyrus

Understanding how the body is represented in the motor cortex is key to understanding how the brain controls movement. Although the motor cortex has been mapped in animal models at a fine scale1–10, characterization in humans remains primarily limited to low-resolution recording11–16 and stimulation techniques17–20. Here we created a comprehensive map of the human motor cortex at single-neuron resolution, spanning microelectrode array recordings from 20 arrays across 8 individuals with paralysis from spinal cord injury, amyotrophic lateral sclerosis or brainstem stroke, all enrolled in brain–computer interface clinical trials. These arrays broadly sample the crown of the precentral gyrus (PCG; thought to be composed largely of the premotor cortex (Brodmann area 6)). We found that body parts were highly intermixed, such that the entire body was represented in all sampled locations of the PCG, although the relative strength of body parts was roughly consistent with the motor homunculus17,18. We also found two speech-preferential areas with a broadly tuned, orofacial-dominant area in between them. Throughout the PCG, movement representations of the four limbs were interlinked, with homologous movements of different limbs (for example, toe curl and hand close) having correlated representations. These data provide evidence consistent with an intermixed, interrelated and behaviour-centred organization of the motor cortex3,21. The resulting map also provides important targeting information for brain–computer interfaces that seek to restore motor function. A comprehensive map of the human motor cortex at single-neuron resolution is described.

18.
medRxiv (Medicine) 2026-06-22

Symptom-based phenotype discovery in motor neuron disease using natural language processing of electronic health records

Background: Motor neuron disease (MND) is a fatal neurodegenerative condition with significant clinical heterogeneity that is incompletely captured by existing phenotype classifications based on onset site. Electronic health records (EHRs) contain detailed symptom documentation in clinical narratives that may enable data-driven discovery of clinically meaningful patient subgroups. Methods: We developed a natural language processing (NLP) pipeline using MedCAT to extract symptoms from clinical notes of 2,361 people with a confirmed diagnosis of MND at a tertiary neurology center. MND cohort confirmation used three complementary methods: clinic attendance records, text-based diagnosis detection, and NLP extraction with negation detection. Extracted symptoms were filtered to Unified Medical Language System semantic type T184 (Sign or Symptom) with removal of negated concepts. Patients were clustered using latent class analysis on binary symptom profiles. Survival differences were assessed using Kaplan-Meier analysis, log-rank tests, and Cox proportional hazards regression. Results: From the first clinical notes, we identified four clusters of symptoms among 872 patients and 76 symptoms: Motor-Bulbar (n=373), Motor-Tremor (n=154), Sensory-Pain (n=222), and Motor-Respiratory (n=123). When extended to all clinical notes (n=2,065; 184 symptoms), these reorganized into three clusters: Autonomic-Respiratory (n=472), Nocturnal-Respiratory (n=338), and Classic Motor (n=1,255). Survival differences were significant across all clusters in both the first notes and all notes analyses (log-rank p < 0.001). Conclusions: NLP-based symptom extraction from EHRs identifies clinically meaningful MND subgroups that extend beyond traditional onset-site classifications. Autonomic-respiratory symptom burden is associated with poorer survival while a newly identified Sensory-Pain subtype with a better prognosis. These data-driven phenotypes may improve prognostication and inform targeted supportive care.

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

Robust and Fast Training via Per-Sample Clipping

arXiv:2605.02701v2 Announce Type: replace-cross Abstract: We propose a robust gradient estimator based on per-sample gradient clipping and analyze its properties both theoretically and empirically. We show that the resulting method, per-sample clipped SGD (PS-Clip-SGD), achieves optimal in-expectation convergence rates for non-convex optimization problems under heavy-tailed gradient noise. Moreover, we establish high-probability convergence guarantees that match the in-expectation rates up to polylogarithmic factors in the failure probability. We complement our theoretical results with multiple numerical experiments. In particular, we demonstrate that PS-Clip-SGD outperforms both vanilla SGD with momentum and standard gradient clipping when training AlexNet on the CIFAR-100 dataset, even after accounting for the additional computational time caused by per-sample clipping. We also empirically show that, in the presence of gradient accumulation, applying clipping at the mini-batch level can improve training performance while incurring virtually no additional computational cost. This finding is particularly interesting, as it contradicts the common practice of applying clipping only after all accumulation steps have been completed.

20.
arXiv (CS.LG) 2026-06-15

Testing For Distribution Shifts with Conditional Conformal Test Martingales

arXiv:2602.13848v2 Announce Type: replace Abstract: We propose a sequential test for detecting arbitrary distribution shifts that allows conformal test martingales (CTMs) to work under a fixed, reference-conditional setting. Existing CTM detectors construct test martingales by continually growing a reference set with each incoming sample, using it to assess how atypical the new sample is relative to past observations. While this design yields anytime-valid type-I error control, it suffers from test-time contamination: after a change, post-shift observations enter the reference set and dilute the evidence for distribution shift, increasing detection delay and reducing power. In contrast, our method avoids contamination by design by comparing each new sample to a fixed null reference dataset. Our main technical contribution is a robust martingale construction that remains valid conditional on the null reference data, achieved by explicitly accounting for the estimation error in the reference distribution induced by the finite reference set. This yields anytime-valid type-I error control together with guarantees of asymptotic power one and bounded expected detection delay. Empirically, our method detects shifts faster than standard CTMs, providing a powerful and reliable distribution-shift detector.

21.
arXiv (CS.CL) 2026-06-15

CoRe: A Continuously Reward-Finetuned LLM Query Rewriter for Multi-Stage Context-Aware Relevance in Web-Scale Video Search

LLM-based query rewriters in production face a tension: the training reward must reflect how the rewrite is consumed by the production ranker, yet the training procedure must be cheap enough to support continuous redeployment as data drifts. We present CoRe (Context Relevance), such a system, redeployed weekly for over five months in a major short-video search engine. Our reward uses the deployed multimodal relevance model as its source and a multiplicative ratio form mirroring the production fusion algebra, closing the simulation-production gap that offline reward proxies leave open. A semi-online Mixed Preference Optimization loop makes this reward affordable at multi-million-instance weekly scale: a DPO-style pairwise objective restricts the gradient pass to a small top-k/bottom-k subset of sampled trajectories, and a phase structure reduces trainer/inference-server parameter syncs from per-step to per-phase. An automated promotion gate over reward-like and stability metrics detected and recovered from a real reward-hacking incident in production. Rewriter output is consumed as parallel relevance signals at recall, rawrank, and finerank without displacing the original signals, bounding rewriter-failure blast radius. Online A/B from two sequential production launches, first deploying the rewriter at finerank, then extending consumption to recall and rawrank, delivers statistically significant reductions in change-query rate on rewrite-impacted queries, with all headline relevance and engagement metrics moving in the expected direction.

22.
bioRxiv (Bioinfo) 2026-06-11

DivQuant: Estimation of Species Richness and Entropy from Small Samples

Estimating diversity properties of discrete distributions from a small observed sample is a fundamental problem in algorithmic statistics that has applications in many fields, in particular bioinformatics, but also in ecology or linguistics. The two most common diversity measures are the number of distinct elements in a multiset, also referred to as species richness in ecology or alpha diversity in microbial analysis, and the Shannon entropy, also referred to as evenness. Estimating these properties from a small sample is particularly challenging for distributions with many rare elements. Thus, many estimators have been proposed in the past that, in practice, work well for different types of distributions. We present DivQuant, an optimization-based, extrapolating richness and entropy estimator with three contributions. First, we formulate the upsampling problem as a convex quadratic program with a Neyman {chi}2 objective. Unlike the linear program of its predecessor RichnEst, DivQuant admits confidence intervals via {chi}2 test inversion that are empirically well-calibrated. Second, we replace RichnEst's fixed-threshold fingerprint truncation with the rare/abundant fingerprint split of Valiant and Valiant, which strongly reduces problem size and preserves enough degrees of freedom for the confidence-interval program to remain valid and feasible. Third, we plug the optimal population fingerprint returned by the program into Shannon's entropy formula to obtain an entropy estimate. DivQuant attains close-to-nominal 95% confidence intervals in essentially all tested regimes, including six simulated distribution families, Tara Oceans microbiome data, and 10X Genomics scRNA-seq data, while competing state-of-the-art methods (RichnEst, iNext, PreSeq) miss the true richness in up to 80% of instances, well above the nominal 5%. In addition, DivQuant outperforms classical asymptotic entropy estimators (Miller-Madow, CAE) and the extrapolating iNext estimator. Running times remain competitive, with DivQuant typically completing in seconds. DivQuant is available as a command-line tool at https://gitlab.com/rahmannlab/divquant.

23.
arXiv (CS.CL) 2026-06-11

Substrate Asymmetry in User-Side Memory: A Diagnostic Framework

作者:

User-side memory in LLMs is typically scored as a single "personalization" capability: given a user's history, is the output more user-aware? We show this aggregate metric hides opposite-direction failures. Memory factorises into at least three orthogonal axes – behavioral consistency (style, voice), factual presence (recall facts in history), and factual absence (abstain when a fact is absent) – and no single substrate wins all three. Comparing per-user gamma-LoRA (a small LoRA adapter trained on each user's history; gamma denotes per-user, not per-task) against BGE-large dense top-K retrieval on a controlled 50-user synthetic corpus and a real-data probe (LaMP-3), we find gamma-LoRA decisively wins behavioral style while RAG decisively wins factual absence – and the same query-projection cells in attention layers 21-35 causally load-bear both effects in opposite directions (zeroing those LoRA weights raises absence-probe TPR by +33 pp and drops presence-probe TPR by 20 pp). On the more heavily RLHF-tuned Llama-3.1-8B-Instruct the asymmetry strengthens, not heals: parametric memory's behavioral advantage collapses while its absence-calibration deficit against retrieval widens – an alignment tax on parametric user-memory. On real-data LaMP-3, gamma-LoRA underperforms a majority baseline; a 9-condition mitigation sweep diagnoses this as instruction-following collapse, not substrate failure (a 9x2 cross-product shows the eval-time {1..5} logit mask drives main_acc to >=0.995 on every recipe), and the best training-time fix replicates bit-identically on Llama. Finally, substrate-selection routing is question-classification, not calibration: a 110M DistilBERT on the question text alone beats every logit-based router. We contribute the diagnostic framework, the diagnosed real-data negative, the alignment-tax replication, and the routing-as-classification finding.

24.
arXiv (quant-ph) 2026-06-16

Complete entanglement detection using polynomial invariants

arXiv:2606.16712v1 Announce Type: new Abstract: Existing methods for deciding whether a bipartite quantum state is separable or entangled typically fall into one of two categories: they are either complete but require access to an explicit density matrix followed by numerical optimization, or they can be evaluated directly by measuring the quantum system but are incomplete, in the sense that they cannot detect all forms of entanglement. In this work, we overcome both limitations in a unified framework. First, we bypass numerical optimization by deriving separability criteria in the form of universal bounds on tensor powers of separable states. We prove that these bounds are complete: every entangled state violates them for sufficiently large tensor powers. Second, we explicitly construct a corresponding complete family of nonlinear entanglement witnesses, which can detect all forms of entanglement without requiring an explicit density matrix. The witnesses we construct are moreover basis-independent, in the sense that they are invariant under conjugation by local unitaries. Altogether, our results expand the toolbox for entanglement detection in arbitrary local dimensions in a manifestly invariant way.

25.
arXiv (CS.CL) 2026-06-16

All-Mem: Agentic Lifelong Memory via Dynamic Topology Evolution

Lifelong interactive agents are expected to assist users over months or years, which requires continually writing long term memories while retrieving the right evidence for each new query under fixed context and latency budgets. Existing memory systems often degrade as histories grow, yielding redundant, outdated, or noisy retrieved contexts. We present All-Mem, an online/offline lifelong memory framework that maintains a topology structured memory bank via explicit, non destructive consolidation, avoiding the irreversible information loss typical of summarization based compression. In online operation, it anchors retrieval on a bounded visible surface to keep coarse search cost bounded. Periodically offline, an LLM diagnoser proposes confidence scored topology edits executed with gating using three operators: Split, Merge, and Update, while preserving immutable evidence for traceability. At query time, typed links enable hop bounded, budgeted expansion from active anchors to archived evidence when needed. Experiments on LoCoMo and LongMemEval-s show improved retrieval and QA over representative baselines. The code is available at https://github.com/LvCan926/All-Mem.