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

FlowRAG: Synergizing Explicit Reasoning via Frequency-Aware Multi-Granularity Graph Flow

arXiv:2606.17856v1 Announce Type: new Abstract: Graph-based retrieval-augmented generation (GraphRAG) is effective for knowledge-intensive and multi-hop query tasks; however, many existing methods primarily seed entity-based graphs and rely on implicit semantic relevance propagation. This often (i) under-retrieves when user queries are abstract and semantically sparse at the entity level, and (ii) suffers from brittle multi-hop reasoning, where noisy activations can derail entity-to-entity transitions and corrupt the inferred relation chain, yielding unreliable conclusions. To this end, we propose \texttt{FlowRAG}, a semantic-aware retrieval framework that improves both semantic recall and explicit reasoning. Specifically, \texttt{FlowRAG} constructs a quad-level heterogeneous graph over passages, summaries, sentences, and entities, where summary nodes serve as a coarse semantic hub. At retrieval time, a dual-granularity activation module combines summary–query alignment with sentence-level matching to activate relevant entities under paraphrase and abstraction robustly. We then introduce a frequency-aware weighted flow module that routes relevance through entity–passage links weighted by within-passage term frequency, pruning noisy connections and extracting high-confidence reasoning paths as an explicit logic skeleton for generation. Extensive experiments show that \texttt{FlowRAG} obtains state-of-the-art performance on complex reasoning benchmarks.

02.
arXiv (CS.CL) 2026-06-11

GraphInfer-Bench: Benchmarking LLM's Inference Capability on Graphs

Graph analysis underlies many applications whose answers cannot be looked up in a single record or retrieved along a path: laundering rings, drug repurposing, user preference, and scientific theme are all inferred from a node together with its neighbourhood. We introduce GraphInfer-Bench, a benchmark for whether LLMs can perform this graph inference: producing an open-ended answer that no single node supports and no path retrieves. Existing graph-QA protocols cannot test this capability: algorithm simulation, node classification, single-node description, KG-QA, and GraphRAG all admit answers retrievable from one node or along a path. GraphInfer-Bench defines five tasks along Description (what a region is) and Comparison (how regions differ), each constructed so the ground truth lives in no single node. The release contains 42,000 samples across six real-world graphs, produced automatically and screened by a four-layer quality-control protocol. We evaluate four method families against the same tasks: graph-token alignment models, zero-shot frontier closed-source LLMs, Graph2Text supervised fine-tuning, and plain GNNs as a structural reference. No method family closes the gap. Graph-token alignment partially handles description tasks (relational, theme) but collapses on comparison tasks. Frontier LLMs lead on outlier detection and community partition among LLM-based methods but lag on masked-node prediction. Graph2Text SFT is the strongest LLM-based method on the description side yet falls behind frontier LLMs on comparison. Across every task, plain GNNs match or beat the strongest LLM-based row, with the largest margin on community detection. GraphInfer-Bench surfaces graph inference as an open capability gap rather than a property of any one architecture.

03.
bioRxiv (Bioinfo) 2026-06-10

Promera: a unified model for biomolecular structure prediction, filtering, and design

Generative models have become staple tools for modeling and designing biomolecular structures. However, although these tools have improved in structural prediction accuracy, their ability to filter designed binders—an essential use case—remains insufficient; whereas design methods have focused more on unconstrained binder generation rather than capabilities enabled by controllable design. We introduce Promera, a unified generative model that combines all-atom structure prediction with improved filtering and controllable design. We find that Promera's confidence metrics are more accurate for filtering binders from non-binders for both miniproteins and nanobodies, while its co-folding performance surpasses popular open-source models (OpenFold3-p2, Boltz-2) on therapeutically relevant categories. As a design model, Promera generates binders by predicting masked protein sequences with optional epitope, paratope, and template constraints. Remarkably, our nanobody designs match the in silico success rates from backprop-based techniques (mBER) when evaluated under co-folding confidence filters. We further provide two in silico demonstrations of the the versatile capabilities of our design method: epitope targeting of the Andes hantavirus glycoprotein with VHHs and active state stabilization of the beta-2 andrenergic GPCR. We conclude by proposing a scaling law for co-folding models, suggesting a path for further performance improvement.

04.
medRxiv (Medicine) 2026-06-22

Clinical-grade Cuffless Blood Pressure Monitoring via Deep-tissue Diffuse Speckle Pulsatile Flowmetry

Blood pressure (BP) is a vital sign which is measured to diagnose and manage hypertension. However, current methods to measure BP use inflatable cuffs which cause discomfort and limit the frequency at which measurements can be made, or intra-arterial catheters which are invasive and pose infection risks. Here, we propose and evaluate the use of Diffuse Speckle Pulsatile Flowmetry (DSPF) as a cuffless BP measurement method to address these limitations. DSPF is a laser speckle-based technique which simultaneously records blood flow rate and blood volume (i.e. photoplethysmography or PPG) signals from relatively deep vascular tissue. Using information from these signals, we studied DSPFs effectiveness in measuring systolic BP (SBP) and diastolic BP (DBP) through an outpatient study in which 133 patients were recruited, and in measuring beat-to-beat BP waveforms through an inpatient study in which two patients were recruited. In the outpatient study, the DSPF method was able to achieve mean absolute errors (MAEs) of 4.17 mmHg and 2.42 mmHg for SBP and DBP respectively compared to conventional cuff-based methods. It was also able to fulfil the requirements of the AAMI/ESH/ISO 81060-2:2018 standard for BP measurement devices and attain an "A" grade according to the British Hypertension Society grading scheme. For the inpatient study, it produced BP waveforms which had MAEs of 2.35 mmHg and 3.06 mmHg compared to arterial-line measurements for the two patients, respectively. Compared to PPG which has been studied more extensively as a cuffless BP measurement method, we found through ablation studies that DSPF was able to reach significantly lower MAEs and hence better accuracies. DSPF augments the performance of PPG-only methods by leveraging additional information from the blood flow rate signal, and we therefore find it to be a superior cuffless BP measurement method which can potentially be used in outpatient, inpatient, and remote settings.

05.
bioRxiv (Bioinfo) 2026-06-12

DNA Compression with Genomic Language Models: Tokenization, Benchmarking, and an Information-Content Map

Lossless compression and probabilistic sequence modeling are two faces of the same coin: a model that assigns high probability to a sequence can encode it in few bits via arithmetic coding. We exploit this duality to evaluate genomic language models as compressors of DNA, using compression primarily as an objective probe of generative sequence modeling rather than as a deployable storage system. We release DNAGPT2, a family of ten GPT-2-small models pretrained for one epoch on a single A40 using the DNABERT2 multi-species corpus that differ only in byte-pair encoding vocabulary size. Coupled with arithmetic coding, the best model reaches 1.47 bits per base (bpb) on the T2T human genome, fourth in the Cobilab compression benchmark and ahead of every general-purpose compressor. Our results suggest that NLP-style tokenization choices may be suboptimal for DNA: a 32-token BPE vocabulary compresses better than larger vocabularies. We also find that, in this benchmark, published long-context genomic LMs underperform a much shorter-context BPE GPT-2; we discuss in Section 5 that this is not a controlled context-length ablation, since the compared models also differ in architecture, training data, parameter count, and tokenization. Finally, we compute a per-nucleotide information-content map of the human genome and show that exons, introns, intergenic regions, and Alu repeats have statistically distinct information profiles.

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

AAPA: Adversarially Anchored Preference Alignment for Post-Training of Large Language Models

arXiv:2509.25148v2 Announce Type: replace Abstract: Post-training alignment of large language models often combines supervised fine-tuning (SFT) on expert demonstrations with reinforcement learning (RL) from preference or verifiable feedback. SFT provides a useful behavioral anchor but can overfit to static demonstrations, whereas RL encourages exploration but may drift from expert behavior or exploit imperfect rewards. We propose AAPA (Adversarially Anchored Preference Alignment), a plug-in framework that augments existing post-training objectives with a sentence-level adversarial anchoring signal. AAPA compares policy rollouts with offline, pre-collected expert responses using a fixed lightweight discriminator, and therefore requires neither online teacher inference nor discriminator co-training during policy optimization. The same anchoring term can be added to SFT, GRPO, and CHORD while preserving their original training pipelines. Experiments on instruction-following benchmarks show that AAPA consistently improves the corresponding base objectives across model scales. In particular, the staged AAPA configuration improves over a strong GRPO baseline by 5.77\% on \texttt{Qwen3-0.6B} and 3.75\% on \texttt{Qwen3-4B}. Further analyses on response length, log-probability distributions, and discriminator variants suggest that adversarial anchoring provides a stable semantic grounding signal for preference optimization. Code is available at \url{https://github.com/IsFaqq/AAPA}.

07.
arXiv (quant-ph) 2026-06-16

Quantum learning with a single-atom sensor

arXiv:2606.15071v1 Announce Type: new Abstract: The ability to gather information and to act upon it is at the core of every learning agent. But what is the impact of quantum mechanics on an agent's ability to sense external inputs and to translate them into actions? Here we address the question for a prototype task of learning agency at the quantum scale: rotating a single spin based on information gathered by a single atom. We determine the ultimate performance limit for this task, revealing a fundamental tradeoff between entanglement at the sensing stage and coherence at the action stage: if the single-atom sensor is not entangled with the quantum system serving as the agent's internal memory, then the best learning strategy requires a coherent transfer of quantum information from the sensor to the system that controls the agent's actions. In contrast, if the sensor is initially entangled with the agent's memory, then the transfer of quantum information is no longer necessary. Our results indicate that the quantum properties of the sensor radically affect the optimal way to convert external stimuli into actions, revealing a link between quantum sensing and the behavior of quantum agents.

08.
arXiv (quant-ph) 2026-06-17

Universal features of high-energy scattering of Laguerre-Gaussian states

arXiv:2604.00575v2 Announce Type: replace-cross Abstract: Vortex states of photons, electrons, and other particles are wave packets that carry intrinsic orbital angular momentum (OAM) and exhibit other features unavailable for plane waves. Collisions of high-energy vortex states can become a promising tool for nuclear and particle physics, once experimental challenges are overcome. An extensive literature exists on scattering processes involving vortex states; however, most works rely on assumptions that will be challenging to achieve in experiment. In this work, we initiate a systematic re-analysis of vortex-state scattering processes using paraxial Laguerre-Gaussian (LG) wave packets colliding at a non-zero impact parameter $b$. Since the total final transverse momentum $P_\perp$ is no longer fixed, we focus on how the differential cross section depends on $P_\perp$. We emphasize that non-trivial $P_\perp$-dependent features can originate either from the shape of the LG wave packets or from the dynamics of the scattering process under interest. Here, we focus on the former source and explore in detail these universal kinematic features, while the study of process-specific modifications, along with the novel insights they may bring, is delegated to a future work. Interestingly, the non-zero impact parameter $b$ plays a key role in many $P_\perp$-dependent effects, making it a useful probe of vortex states, not a nuisance factor as often assumed.

09.
arXiv (CS.AI) 2026-06-11

Reliability-Calibrated Edge-IoT Early Fault Warning for Rotating Machinery with a Physics-Guided Tiny-Mamba Transformer

arXiv:2601.21293v3 Announce Type: replace-cross Abstract: Industrial Internet of Things (IIoT) systems increasingly rely on distributed vibration sensing to support predictive maintenance of rotating machinery. In practical deployments, however, raw signal upload is costly and alarm decisions must be made locally under limited computation, changing operating conditions, and strict nuisance-alarm budgets. This paper presents a reliability-calibrated edge-IoT early-warning framework, in which a compact Physics-Guided Tiny-Mamba Transformer (PG-TMT) acts as the representation module and an extreme value theory (EVT) layer converts streaming anomaly scores into event-level alarm episodes. PG-TMT combines a depthwise-separable convolutional stem, a Tiny-Mamba state-space branch, and a lightweight local Transformer to capture transient, long-horizon, and multichannel degradation cues under batch-size-one inference. To improve auditability, temporal attention is projected to the frequency domain and softly aligned with analytical bearing fault-order bands. EVT calibration, dual-threshold hysteresis, and trimmed-tail fitting provide controllable false-alarm intensity even when healthy calibration data are imperfect. Experiments on CWRU, Paderborn, XJTU-SY, and an industrial pilot demonstrate that the proposed framework improves PR-AUC, reduces detection delay under a controlled nuisance-alarm budget, and remains robust to structured interference, metadata uncertainty, compound fault mixtures, and domain transfer. With a sub-1 MB footprint and Jetson p99 latency below 7 ms, the framework supports calibrated and interpretable early warnings for IIoT predictive maintenance.

10.
arXiv (math.PR) 2026-06-18

On two overlooked stick-breaking constructions of the normalized inverse Gaussian process

arXiv:2606.19306v1 Announce Type: new Abstract: We shed light on two alternative stick-breaking constructions of the normalized inverse Gaussian (NIG) random discrete distribution which appear to have been overlooked so far in the Bayesian nonparametric setting. The first is derived from a result in Aldous and Pitman (1998) for the conditional Brownian excursion partition, mixing over the local time at zero up to time one. The second arises as a particular case of a result in James (2013) for priors obtained by a random spatial and temporal change of the normalized generalized Gamma subordinator. Both constructions are in terms of straightforward transformations of standard random variables and can be easily generalized to provide the stick-breaking construction of any element, respectively, in a) the family of mixed Poisson-Kingman models driven by the $1/2$ stable Lévy measure and b) the family of Poisson-Gamma processes driven by the Inverse Gaussian subordinator.

11.
arXiv (quant-ph) 2026-06-12

Roto-Reflection Geometry of Pure Two-Qubit Entanglement

arXiv:2606.12637v1 Announce Type: new Abstract: Pure two-qubit entanglement is usually characterized by scalar quantities such as concurrence. Here we show that it also has a natural geometric form. In the Pauli correlation tensor, maximally entangled states appear as improper orthogonal maps between two local Bloch spheres. These maps are roto-reflections. For partially entangled pure states, the same roto-reflection geometry is recovered after separating the contraction associated with concurrence. We call the corresponding geometric object the Entanglement Roto-Reflection Plane (ERRP). It organizes the maximally correlated directions of the two-qubit state and provides a covariant geometric complement to the scalar magnitude of entanglement.

12.
arXiv (CS.AI) 2026-06-18

LivePI: More Realistic Benchmarking of Agents Against Indirect Prompt Injection

arXiv:2605.17986v3 Announce Type: replace-cross Abstract: AI agents such as OpenClaw are increasingly deployed in local workflows with access to external tools. This creates indirect prompt-injection (IPI) risk: an agent may execute harmful instructions embedded in untrusted inputs such as email, downloaded files, webpages, repositories, or group-chat messages. Existing evaluations are often small, purely simulated, or focused on a narrow set of channels. We introduce LivePI (Live Prompt Injection), a structured benchmark for IPI risk in a production-like but test-controlled environment. LivePI covers seven input surfaces, twelve attack/rendering families, and five malicious goals, including protected-information exfiltration, unauthorized security-control changes, unsafe code retrieval or execution, inbox-summary exfiltration, and cryptocurrency transfer. We run LivePI on a real virtual machine with live but test-controlled email, chat, web, local-file, repository, and wallet interfaces. Across GPT-5.3-Codex, Claude Opus 4.6, Gemini 3.1 Pro, Kimi K2.5, and GLM-5, total attack success rates range from 10.7% to 29.6%. Group-chat injection is uniformly successful across the evaluated backbones in our deployment, and repository-link attacks produce high-severity failures despite a small denominator. We also evaluate a two-layer defense consisting of prompt-level filtering and pre-execution tool-call authorization. In the GPT-5.3-Codex setting, the defense intercepts all tested malicious-goal completions in LivePI before execution while preserving benign utility on PinchBench-derived workloads.

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

Scenario-based Probing and Steering Cultural Values in Large Language Models–Extended Version

Large Language Models (LLMs) are deployed across cultural contexts but often reflect homogenized values inherited from training data. Evaluations of cultural alignment typically rely on direct prompting with survey-style questions, which frequently elicit neutral or safety-aligned responses and fail to capture underlying model preferences. We propose a framework for probing and steering latent cultural representations in LLMs along the two Inglehart–Welzel axes of the World Values Survey (WVS). By translating social value questions into scenario-based behavioral dilemmas, we extract token-level probabilities to measure implicit values and apply activation steering, optionally combined with country-conditioned prompting, to shift model behavior without retraining. Across three open-source LLMs and four target cultures, we find substantial variation in steerability and identify latent entanglement, where interventions along one cultural dimension induce shifts along another. This coupling mirrors correlations in human WVS data and persists across activation, prompt, and hybrid steering. It constrains axis-independent alignment, though general task performance is largely preserved.

14.
arXiv (math.PR) 2026-06-16

A Concavity Theorem for the Parisi PDE

作者:

arXiv:2606.15432v1 Announce Type: new Abstract: We prove that the map sending the diffusion profile to the solution of a time-changed Parisi PDE evaluated at time-space $(0,0)$ is concave. This result strengthens the raywise concavity result proven by Auffinger and Chen (2016). As an application, for the balanced multispecies Ising spin glasses, the lower bound of Bates and Sohn (2025) matches the Hopf-type upper bound given by the Hamilton–Jacobi framework developed by Mourrat, Chen and Xia.

15.
arXiv (CS.AI) 2026-06-12

SAIGuard: Communication-State Simulation for Proactive Defense of LLM Multi-Agent Systems

arXiv:2606.12474v1 Announce Type: cross Abstract: LLM-based multi-agent systems (MAS) solve complex tasks through inter-agent collaboration, but their communication-driven nature also allows security risks to spread across agents and trigger system-wide failures. Existing MAS defenses mainly follow a reactive paradigm after execution by detecting and isolating harmful agents, which may cause irreversible damage and degrade collaborative utility. To address this, we propose a proactive defense framework for MAS security, namely a Simulation-aware Interception Guard (SAIGuard). SAIGuard performs communication-state simulation over the MAS interaction graph, estimates the impact of incoming messages on local agent states and the global MAS state, and detects risky messages via reconstruction deviations from benign communication patterns. Instead of isolating agents, SAIGuard sanitizes or regenerates suspicious messages before it propagation into system. Experiments across diverse topologies and attack scenarios show that SAIGuard reduces attack success rates while maintaining MAS utility, outperforming reactive defenses.

16.
arXiv (CS.CV) 2026-06-18

Technical Report for ICRA 2026 GOOSE 2D Fine-Grained Semantic Segmentation Challenge: Leveraging DINOv3 for Robust Outdoor Scene Understanding in Field Robotics

The GOOSE 2D Fine-Grained Semantic Segmentation Challenge at the ICRA 2026 Workshop on Field Robotics evaluates dense semantic segmentation of off-road imagery over a fine-grained taxonomy of 64 classes and 11 evaluated non-void coarse categories. We present the first-place solution to this challenge. Our solution comprises two complementary improvements: (a) a network-level design that combines a self-supervised DINOv3 ViT-L/16 backbone, a ViT-Adapter, and a Mask2Former mask-classification decoder, together with a coarse-category auxiliary loss on the global [CLS] token; and (b) an inference-time aggregation strategy based on multi-scale and horizontal-flip test-time augmentation and an ensemble of the top three checkpoints selected using Codabench scores. Our method achieves an official composite score of 76.57%, consisting of 69.32% fine-class mIoU and 83.81% category-level mIoU, and ranks first on the final phase leaderboard: www.codabench.org/competitions/14257/#/results-tab.

17.
bioRxiv (Bioinfo) 2026-06-16

Accelerating String Comparison in RLZ Compressed Sequences via LCE Jumps

Relative Lempel-Ziv (RLZ) is an effective compression method for large, repetitive collections; however, the fundamental primitives required to elevate it from a passive archival format to a tractable representation for compressed construction have yet to be fully established. In this paper, we introduce an algorithmic framework for structurally comparing and lexicographically sorting sequences of RLZ factors. We characterize when direct factor comparisons are necessary and when they can be bypassed using RLZ specific shortcuts. We further introduce a method for extending truncated factors into right-maximal matches, enabling the recovery of matching statistics from the RLZ parse. Experimentally, RLZ sorting achieved speedups of up to 3.93x over character-based sorting. Together, these results advance the use of the RLZ format as a foundation for compressed construction.

18.
bioRxiv (Bioinfo) 2026-06-15

Biological meaning in protein embedding space is resolution-dependent

Protein language model embeddings are increasingly used to organise biological sequences, yet how biological meaning is encoded within embedding neighbourhoods remains poorly understood. Using two independent hierarchical enzyme systems, carbohydrate-active enzymes and peptidases, we investigated how biological interpretation changes across embedding organisations aligned to different levels of biological hierarchy. Different embedding organisations give rise to distinct neighbourhood semantics. When aligned to membership-boundary resolution, embeddings robustly separated artefacts and unrelated proteins from members of the target category. However, embeddings aligned to functional-grouping resolution maintained compositional neighbourhood structure for multi-domain proteins spanning more than one functional or catalytic group. Finally, embeddings aligned to local-family resolution recovered compact family-like neighbourhoods, including families withheld from training, while weakening broader membership-boundary and functional-grouping relationships. Moreover, embeddings optimised toward the same level of biological organisation retain different biological relationships depending on optimisation trajectory employed. Together, our results show that proximity in protein embedding space has no fixed biological interpretation. Instead, biological meaning emerges across embedding resolutions through selective preservation of different forms of biological organisation.

19.
arXiv (CS.LG) 2026-06-11

SPADE: Split-and-Delay Embeddings for Autoregressive High-Granularity Calorimeter Simulation

arXiv:2606.11304v1 Announce Type: cross Abstract: We introduce SPADE (SPlit And Delay Embeddings), an autoregressive transformer for sequences whose tokens carry multiple features. Rather than embedding these features jointly, SPADE embeds them independently. Delaying each feature stream relative to the previous one allows intra-token correlations to be learned by the standard self-attention mechanism. Applied to point-cloud calorimeter shower generation in the highly granular ILD detector, SPADE is competitive with the state of the art AllShowers model on photon showers, and substantially outperforms its VQ-VAE-based predecessor OmniJet-$\alpha_C$. The mechanism is applicable to any generative task with multi-feature tokens, enabling LLM-style pretraining workflows for higher-dimensional data.

20.
arXiv (CS.AI) 2026-06-12

Parthenon Law: A Self-Evolving Legal-Agent Framework

arXiv:2606.04602v3 Announce Type: replace Abstract: As agents grow more capable, legal-domain LLM agents promise to turn document-heavy matters into reviewable work products – yet reliable deployment faces three obstacles: no large-scale evidence on how today's strongest model-and-harness combinations behave on end-to-end legal matters; no agent architecture adapted to the legal vertical, only general-purpose harnesses; and, in a setting that keeps shifting with new facts, authorities, and deadlines, no mechanism for systems to learn from their own outcomes. We address each. A large-scale empirical study on Harvey LAB – $12{,}510$ agent trajectories – shows that even frontier agents remain far from completing matters in a single pass: per-criterion accuracy climbs with stronger models while strict matter completion stalls. We then introduce \textsc{Parthenon}, a self-evolving legal-agent framework that factors Model, Harness, Agent roles, legal Knowledge, deterministic Tools, and procedural Skills into auditable surfaces for source traceability, date and number grounding, deliverable compliance, and issue closure. Finally, an anti-leakage learning loop converts scored failures into task-agnostic edits to skills, tools, and knowledge, letting the system improve with experience – as a firm refines its checklists and playbooks after each matter – without touching model weights. Across our large-scale empirical analysis, \textsc{Parthenon} substantially improves the performance of state-of-the-art models and harnesses on legal-matter tasks.

21.
medRxiv (Medicine) 2026-06-10

A risk-of-contagion index using a Bayesian based model for the COVID-19 epidemic in Mexico

During the COVID-19 pandemic, limited testing capacity and reporting delays complicated epidemic surveillance and decision-making in Mexico. We calibrated textit{covidestim}, a Bayesian nowcasting model, to estimate the total SARS-CoV-2 infections from reported cases and deaths using Mexican surveillance data. Disease-progression distribution priors were calibrated using Mexico City records and validated through comparisons with national seroprevalence surveys, hospitalization data, and annual reported severe-case rates across all states. Using the reconstructed estimates of active infections, we implemented an event-based risk framework that quantifies the probability of encountering at least one infectious individual in gatherings of different sizes. This probability was subsequently translated into a four-level epidemiological traffic-light indicator and computed at both state and municipality levels. The resulting estimates revealed substantial spatial heterogeneity that is obscured by state-level aggregation, particularly in states with marked differences between urban and rural municipalities. To evaluate consistency with public-health indicators, we compared the proposed risk classification with the official Mexican epidemiological traffic-light system, considering interpretable gathering sizes relevant to public-health decision making. Weekly reports derived from this framework were delivered to policymakers in the State of Queretaro in Mexico, as an anticipation tool for school reopening and public-space management. This demonstrates that this Bayesian reconstruction of infections combined with event-based risk metrics can provide an interpretable and generalizable municipality-level complement to routine surveillance systems, particularly in regions with limited testing capacity and heterogeneous local transmission dynamics.

22.
arXiv (CS.LG) 2026-06-11

On Regret Bounds of Thompson Sampling for Bayesian Optimization

arXiv:2603.09276v2 Announce Type: replace-cross Abstract: We study a widely used Bayesian optimization method, Gaussian process Thompson sampling (GP-TS), under the assumption that the objective function is a sample path from a GP. Compared with the GP upper confidence bound (GP-UCB) with established high-probability and expected regret bounds, most analyses of GP-TS have been limited to expected regret. Moreover, whether the recent analyses of GP-UCB for the lenient regret and the improved cumulative regret upper bound can be applied to GP-TS remains unclear. To fill these gaps, this paper shows several regret bounds: (i) a regret lower bound for GP-TS, which implies that GP-TS suffers from a polynomial dependence on $1/\delta$ with probability $\delta$, (ii) an upper bound of the second moment of cumulative regret, which directly suggests an improved regret upper bound on $\delta$, (iii) expected lenient regret upper bounds, and (iv) an improved cumulative regret upper bound on the time horizon $T$. Along the way, we provide several useful lemmas, including a relaxation of the necessary condition from recent analysis to obtain improved regret upper bounds on $T$.

23.
medRxiv (Medicine) 2026-06-15

Validating Field-Feasible Measures of Recent Khat Use: A Diagnostic Accuracy Study Comparing Amphetamine Immunoassay and Assisted Self-Report Against HPLC in an Ethiopian Male Cohort

Background: Khat (Catha edulis) is a widely consumed natural amphetamine-analog used across East Africa and the Arabian Peninsula. Accurate field-feasible measurement of recent khat use is a prerequisite for large-scale epidemiological research; yet no validated alternatives to laboratory reference methods have been identified in the scientific literature. This nested validation study evaluated the diagnostic accuracy of two point-of-care measures, a commercial amphetamine immunoassay and a Timeline Followback (TLFB) Assisted Self-Report (ASR), against high-performance liquid chromatography (HPLC) quantification of urinary norephedrine (NE), while additionally assessing agreement between the two field measures. Methods: A prospective, random sub-sample of 119 male participants aged 18-40 years from the Gilgel Gibe Field Research Center (GGFRC) longitudinal cohort, Ethiopia (validation timepoint T2, 2015), was used. Three index-reference comparisons were conducted: (1) amphetamine immunoassay (nal von minden, Drug-Screen AMP test, 300 ng/mL cutoff) vs. HPLC; (2) binary ASR (past-week use) vs. HPLC; and (3) binary ASR vs. immunoassay. Sensitivity (positive percent agreement, PPA), specificity (negative percent agreement, NPA), positive predictive value (PPV), negative predictive value (NPV), overall accuracy (overall percent agreement, OPA), and Cohen's kappa were calculated with 95% confidence intervals. Pre-specified secondary analyses applied three pharmacokinetically-informed recall windows (0-2, 3-5, and 6-7 days prior to interview) to ASR. Results: Against HPLC (77 positive, 42 negative), the immunoassay showed perfect specificity (1.0 [0.916-1.0]) and PPV (1.0 [0.91-1.0]) but low sensitivity (0.52 [0.40-0.64]), NPV (0.53 [0.42-0.65]), overall accuracy (0.69 [0.60-0.77]), and weak kappa (0.43 [0.34-0.52]). Binary ASR showed high sensitivity (0.96 [0.89-0.99]), specificity of 0.60 [0.433-0.74], PPV (0.81 [0.72-0.89]), NPV (0.89 [0.72-0.98]), with overall accuracy 0.83 [0.75-0.89] and moderate kappa (0.60 [0.51,0.69]). Restricting ASR to use within 0-2 days improved specificity to 0.69 [0.52-0.84], PPV to 0.86 [0.77-0.93], overall accuracy to 0.87 [0.79-0.93], and kappa to 0.69 [0.61-0.78] (moderate), while sensitivity (0.96 [0.89-0.99]) and NPV (0.89 [0.72-0.98]) remained stable. Against the immunoassay, ASR achieved high PPA of (1.0 [0.91-1.0]), NPA of 0.35 [0.25-0.47], OPA of 0.57 [0.48-0.66], and minimal kappa (0.27 [0.19-0.35]). Conclusions: Time-stratified ASR (0-2 days) is a valid, scalable alternative to biological testing for recent khat use in resource-limited settings. The immunoassay's 300 ng/mL cutoff functions as a marker of heavy or recent high-dose khat use rather than any-use detection. Its perfect specificity and PPV make it valuable as a confirmatory test for substantial exposure, while its lower sensitivity reflects calibration to amphetamine rather than to khat-derived cathinone metabolite. Keywords: khat; Catha edulis; diagnostic accuracy; STARD; self-report; immunoassay; HPLC; Ethiopia; substance use measurement

24.
bioRxiv (Bioinfo) 2026-06-11

Viability of engineered AAVs via protein language models

Capsid engineering has greatly improved the performance of recombinant AAV vectors used for gene therapy. One commonly used strategy is the insertion of a short, 7-mer, peptide into surface-exposed loops to modify receptor interactions and enhance cell entry. While effective in receptor retargeting and improved transduction, these insertions might destabilize the capsid protein, hinder assembly, and thus limit production. While previous attempts have used deep mutational scanning and AI to predict which insertions are viable, there is lack in understanding the structural consequences of these peptide insertions at the amino-acid level. Here we combined experiments, deep sequencing and large protein language models to gain insight on the impact of 7-mer insertions on the VR-VIII region. We first characterize the biochemical properties of viable insertions, thus identifying which residues are well tolerated, and which should instead be avoided. We then focus on the nearby context of those insertions, by studying the effect of the linkers, either for highly diverse libraries or for individual variants known for their efficiency. Next, we study the broader context, by extending our analysis to the whole capsid sequence, and identifying regions that can tolerate insertions without long-ranged structural deformations that could affect capsid functionality. We conclude with a cross-serotype comparison and a viability analysis of tens of previously engineered variants. Our work showcases how AI can uncover structure-function rules governing the success of engineered AAV capsids.

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

LEPO: Latent Reasoning Policy Optimization for Large Language Models

arXiv:2604.17892v4 Announce Type: replace-cross Abstract: Recently, latent reasoning has been introduced into large language models (LLMs) to leverage rich information within a continuous space. However, without stochastic sampling, these methods inevitably collapse to deterministic inference, failing to discover diverse reasoning paths. To bridge the gap, we inject controllable stochasticity into latent reasoning via Gumbel-Softmax, restoring LLMs' exploratory capacity and enhancing their compatibility with Reinforcement Learning (RL). Building on this, we propose \underline{L}atent R\underline{e}asoning \underline{P}olicy \underline{O}ptimization~(LEPO), a novel framework that applies RL directly to continuous latent representations. Specifically, in rollout stage, LEPO maintains stochasticity to enable diverse trajectory sampling, while in optimization stage, LEPO constructs a unified gradient estimation for both latent representations and discrete tokens. Extensive experiments show that LEPO significantly outperforms existing RL methods for discrete and latent reasoning.