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01.
arXiv (CS.AI) 2026-06-12

CausalMoE: A Billion-Scale Multimodal Foundation Model for Granger Causal Discovery with Pattern-Routed Heterogeneous Experts

arXiv:2606.13024v1 Announce Type: cross Abstract: Granger Causal Discovery (GCD) is fundamental for analyzing temporal dependencies in complex systems. However, existing neural GCD methods predominantly rely on a "one-size-fits-all" paradigm, struggling to capture distribution shifts and dynamic regime changes inherent in real-world time series. This often leads to entangled representations and spurious causal graphs. In this paper, we propose CausalMoE, a billion-scale multimodal Granger causal foundation model that explicitly models patch-level heterogeneity. CausalMoE introduces a Pattern-Routed Mixture of Heterogeneous Experts, which dynamically identifies latent temporal patterns and routes patches to specialized domain experts, effectively decoupling regime-specific mechanisms from shared dynamics. To ensure interpretable graph recovery, we design a Causality-Aware Self-Attention mechanism operating across variables, yielding sparse Granger causal graphs via proximal optimization. Furthermore, CausalMoE is the first to integrate LLMs and VLMs to align numerical signals with textual and visual priors, regularizing causal estimation in complex scenarios. Extensive experiments demonstrate that CausalMoE establishes a new state-of-the-art on fully supervised benchmarks, while effectively generalizing to few-shot settings where traditional methods fail.

03.
arXiv (math.PR) 2026-06-11

Exact Fourier dimensions of dyadic Mandelbrot cascades on curves of nonvanishing curvature under minimal integrability

arXiv:2606.11758v1 Announce Type: new Abstract: We prove an exact Fourier-dimension formula for scalar dyadic Mandelbrot cascades pushed forward to fixed C^2 Jordan curves with nonvanishing curvature. Let W be in the minimal Kahane-Peyriere regime, let the scalar dyadic cascade live on T = R/Z, and let gamma map T to R^2 be a fixed C^2 Jordan curve with nonvanishing curvature, parametrized at constant speed. For the push-forward measure mu_gamma, we prove that, almost surely on non-extinction, its Fourier dimension is A_loc(W), the usual local exponent obtained by optimizing over q>1 from the moment expression involving E[W^q]. The upper bound follows from the scalar circle local-dimension theorem, bi-Lipschitz transfer to the fixed curve, and a deterministic curved-support obstruction for Fourier dimension. The lower bound follows from a fixed-curve finite-r annular theorem, which gives summable annular Fourier decay under a single finite moment witness. The main analytic input is a deterministic phase-geometry package for fixed nondegenerate C^2 curves: stationary tubes, derivative bands, and phase-bin coefficient estimates replacing the explicit trigonometric structure available on the unit circle.

04.
arXiv (CS.AI) 2026-06-15

Hidden in Plain Sight: Benchmarking Agent Safety Against Decomposition Attacks with DECOMPBENCH

arXiv:2606.13994v1 Announce Type: cross Abstract: LLM-based Agents are becoming increasingly capable and widely deployed, creating growing incentives for adversarial misuse in the real-world. A key emerging threat is Decomposition Attacks [glukhov2024breach, jones2024adversaries] in which a harmful task is broken into simpler, benign subtasks that evade safety mechanisms when executed separately but cumulatively fulfill the malicious intent. Although recent benchmarks assess agent safety in multi-turn and multi-tool-use settings, they do not explicitly capture this form of decompositional misuse and may not represent realistic adversarial execution flows. To this end, we introduce DeCompBench, a benchmark designed specifically to evaluate agentic safety under decomposition attacks. DeCompBench is created with a decomposition-by-design principle using a graphical framework and enables harmful task decomposition into individually benign and executable subtasks with realistic workflows. Our experiments using a custom decomposer show that state-of-the-art agents exhibit high refusal rates on monolithic harmful tasks, but significantly lower refusal rates on their decomposed variants, while often inadvertently fulfilling the adversarial objectives. These findings underscore the need for safety evaluations against decomposition attacks and corresponding defenses. Our dataset is publicly available and can be found at https://huggingface.co/datasets/decompositionbench/DeCompBench.

05.
arXiv (CS.CV) 2026-06-11

AerialClaw: An Open-Source Framework for LLM-Driven Autonomous Aerial Agents

Unmanned aerial vehicles (UAVs) are increasingly used in inspection, search and rescue, environmental monitoring, and emergency response. However, most UAV applications still rely on pre-defined command sequences or task-specific pipelines, where developers manually connect perception, planning, flight control, simulation, logging, and safety modules. This limits the flexibility, reproducibility, and extensibility of autonomous aerial systems. This paper presents AerialClaw, an open-source software framework that enables UAVs to operate as decision-making aerial agents rather than merely command-following platforms. Given a natural-language mission, AerialClaw allows an LLM-based agent to understand the task, maintain context, invoke executable aerial skills, observe perception and runtime feedback, and iteratively update its decisions in a closed loop. The framework adopts a modular brain-skill-runtime architecture, combining hard skills for atomic UAV operations, Markdown-based soft skills for reusable task strategies, document-driven agent state and capability boundaries, memory-driven reflection, safety-oriented runtime validation, and platform-agnostic execution adapters. AerialClaw supports lightweight mock execution, PX4 SITL with Gazebo, and AirSim-based simulation, together with a web console, pluggable model backends, example missions, simulation assets, and staged deployment scripts. By combining standardized aerial skills, document-driven agent state, memory, and closed-loop LLM decision-making, AerialClaw provides a reproducible and extensible open-source framework for building UAV systems that can interpret missions, make decisions, execute skills, and adapt their behavior from feedback.

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

Very large cliques in a scale-free random graph

arXiv:2606.18722v1 Announce Type: new Abstract: In this short article we consider a preferential attachment random graph model with edge steps, studied by Alves, Ribeiro and Sanchis. Starting with an initial graph $\mathbb{G}_1$ formed by a vertex with a self-loop attached to it, the model evolves as follows. At every subsequent (discrete) time step, either with probability $p$ we add a vertex to the graph and connect it to exactly one of the older vertices selected with probability proportional to its degree, or with probability $1-p$ we add one edge between two existing vertices, both selected (independently) with probability proportional to their degrees. Let $\omega(\mathbb{G})$ be the clique number of a graph $\mathbb{G}$, i.e.\ the number of vertices in a largest complete subgraph of $\mathbb{G}_{}$. Alves, Ribeiro and Sanchis showed that, for any given $\varepsilon>0$, we have $\omega(\mathbb{G}_{2t})\geq t^{\frac{1-p}{2-p}(1-\varepsilon)}$ with high probability (i.e.\ with probability tending to $1$ as $t\rightarrow \infty$). Here we strengthen this bound by showing that, for any function $f:\mathbb{N}\mapsto \mathbb{N}$ that satisfies $f(t)\rightarrow \infty$ as $t\rightarrow \infty$, with high probability \[\omega(\mathbb{G}_{2t}) = \Omega\left(t^{\frac{1-p}{2-p}}\Big(\log^{\frac{1}{2-p}}(t)f(t)\Big)^{-1}\right).\]

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

TENSO: Software Package for Numerically Exact Open Quantum Dynamics Based on Efficient Tree Tensor Network Decomposition of the Hierarchical Equations of Motion

arXiv:2603.17711v2 Announce Type: replace-cross Abstract: TENSO is a versatile and powerful open-source software package for numerically exact simulations of the dynamics of quantum systems immersed in structured thermal environments. It is based on a tree tensor network decomposition of the hierarchical equations of motion (HEOM) that efficiently curbs its curse of dimensionality with bath complexity. As such, TENSO enables exact non-Markovian open quantum dynamics simulations even with complex environments typical of chemistry and quantum information science. TENSO allows for time-dependent drive in the system, and for non-commuting fluctuations. More generally, TENSO efficiently propagates the dynamics for any method with a generator of the dynamics that can be expressed in a sum-of-products form, including the HEOM and multi-layer multiconfigurational time-dependent Hartree methods. TENSO enables simulations using tensor trees and trains of arbitrary order, and implements three propagation strategies for the coupled master equations; two fixed-rank methods that require a constant memory footprint during the dynamics and one adaptive rank method with a variable memory footprint controlled by the target level of computational error. In contrast to the accompanying theory and algorithmic paper [J. Chem. Phys. 163, 104109 (2025)] the focus here is on the practical usage and applications of TENSO with underlying theoretical concepts introduced only as needed.

09.
arXiv (CS.LG) 2026-06-15

Beyond task performance: Decoding bioacoustic embeddings with speech features

arXiv:2606.14662v1 Announce Type: new Abstract: Pretrained audio embeddings are standard in bioacoustics, yet little is known about which acoustic features these models encode, nor which are useful for a given task. This hinders transparency and limits extension to rare species or data-scarce domains. Here we reveal which speech-like features are encoded in bioacoustic representations. Using the 88~eGeMAPS features across six taxonomic groups, we apply linear and nonlinear regression probes to quantify which acoustic properties each model captures. Results confirm a ``no free lunch'' pattern: no single model captures the full feature space. A concatenated embedding achieves the highest performance, suggesting complementary acoustic space coverage across models. Loudness features are best encoded ($R^2 = 0.76$) while F0 is hardest to recover ($R^2 = 0.33$). By cross-referencing recoverability with per-species feature salience (NMI), we derive data-driven model selection guidance for bioacoustics.

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

Multi-Adapter PPO: A Cross-Attention Enhanced Wavelength Selection Framework for LIBS Quantitative Analysis

arXiv:2606.17476v1 Announce Type: new Abstract: Laser-induced breakdown spectroscopy (LIBS) quantitative analysis faces critical challenges in wavelength selection due to high-dimensional spectral data and the fundamental trade-off between prediction accuracy and feature efficiency. This paper presents a novel Multi-Adapter PPO framework that transforms wavelength selection into a reinforcement learning problem, leveraging cross-attention mechanisms and multiple specialized adapters to capture complex spectral relationships. Our approach outperforms traditional Particle Swarm Optimization (PSO) by an average of 28.4\% in comprehensive score and 45.2\% in prediction accuracy across steel and coal datasets. The proposed method demonstrates superior performance in balancing prediction accuracy with feature efficiency, achieving state-of-the-art results in LIBS quantitative analysis while maintaining interpretability and computational efficiency. We released our code and dataset here: https://github.com/Hflying/MAPPO

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

MB-Loc: Multi-planar Bird's-eye-view Localization in outdoor LiDAR scenes

Global LiDAR localization is a fundamental task for autonomous navigation systems. Recent methods perform Scene Coordinate Regression (SCR) and achieve superior accuracy over Absolute Pose Regression (APR) solutions by predicting dense 3D world coordinates. However, SCR approaches introduce two major bottlenecks: severe computational inefficiency from processing raw 3D geometries and significant performance degradation under varying sensor viewpoints. To address these limitations, we present MB-Loc, a lightweight and viewpoint-robust SCR framework. Instead of relying on heavy 3D convolutions, we project the input LiDAR scan into a 2.5D Multi-planar Bird's-Eye View (BEV) representation. By slicing the point-cloud along the Z-axis and mapping signed depths into discrete 2D planes, MB-Loc retains essential 3D geometric structures while exploiting the computational tractability of standard 2D CNNs. To handle the inherent sparsity of outdoor LiDAR, we introduce a KL-regularized latent bottleneck that explicitly models spatial uncertainty without injecting stochastic noise. Finally, to ensure rotation robustness, we apply 3D spatial augmentations prior to planar projection, forcing the network to implicitly learn viewpoint-invariant features. We perform extensive experiments on the publicly available NCLT dataset and demonstrate that our proposed method outperforms the current state-of-the-art. Operating at real-time inference speeds, MB-Loc significantly outperforms traditional 3D-SCR architectures in computational efficiency.

12.
arXiv (quant-ph) 2026-06-16

Boson Sampling as a Probe of Chaotic and Integrable Quantum Dynamics in a Photonic Chip

arXiv:2605.25398v2 Announce Type: replace Abstract: Quantum chaos plays a key role in understanding complex quantum dynamics, while integrated photonics offers unique advantages for quantum applications, including high-speed operation, scalability, and programmable unitary transformations. However, integrated photonic approaches to probing quantum chaos remain largely unexplored, owing to the absence of a clear connection between programmable photonic dynamics and established chaos diagnostics. In this work, we establish Fock-state boson sampling as a practical probe of quantum chaos by exploiting the sensitivity of multiphoton interference to the random-matrix properties of underlying single-particle unitary dynamics. More importantly, we design and fabricate a programmable quantum photonic chip to experimentally implement this framework, achieving the first integrated-photonic demonstration of quantum-chaos probes based on boson sampling. Experimental results show that the three complementary probes proposed in this work, namely the distance to Porter–Thomas statistics, Shannon entropy, and Out-of-Time-Ordered-Correlator-equivalent observables, exhibit close agreement with theoretical predictions and consistently distinguish chaotic and integrable dynamics. Our work provides a scalable route for investigating complex quantum dynamics on programmable photonic platforms while leveraging the intrinsic advantages of boson sampling through multiphoton interference and complex output statistics.

13.
arXiv (CS.AI) 2026-06-16

FlowState: Sampling-Rate-Equivariant Time-Series Forecasting

arXiv:2508.05287v3 Announce Type: replace-cross Abstract: Existing time series foundation models (TSFMs), often based on transformer variants, lack adaptability to different sampling rates, struggle with generalization across varying context and target lengths, and are computationally inefficient. We introduce FlowState, a novel TSFM architecture that achieves sampling-rate-equivariant forecasting through a unified design that pairs a state space model (SSM) encoder with a functional basis decoder (FBD). This design enables continuous-time modeling and dynamic time-scale adjustment, allowing FlowState to inherently generalize across all possible temporal resolutions, and dynamically adjust the forecasting horizons without retraining. We further propose an efficient pretraining strategy that improves robustness and accelerates training. Despite being one of the smallest TSFMs, FlowState achieves state-of-the-art results on the widely used GIFT-Eval benchmark, while demonstrating superior adaptability to unseen sampling rates. Our detailed analyses confirm the effectiveness of its components, and we demonstrate its unique ability to adapt to varying input sampling rates.

14.
medRxiv (Medicine) 2026-06-22

A Parent-Generated Framework of Early Connection: Findings from a CBPR Qualitative Study

Background: Early relational health (ERH) constructs are derived fromresearch observations rather than lived experiences. This study foregrounds diverse parent voices to examine how they describeconnectionwith their young children. Methods: Usingcommunity-based participatory research (CBPR),this study was co-designed withparent leadersfromReach Out and Read. A semi-structured interview guidewas co-designed,and parent leaderssubsequentlyconducted and transcribed 18 interviews with parents from their networks.Researchersanalyzed transcripts using Reflexive Thematic Analysis.Member checking sessions with parent leadersinformedthe analytic framework. Results:Sixorganizing principleswereidentified.(1) Parent-child connection begins with an instinctual sense of responsibility.(2)Connectionebbs and flows as parent and child adapt to one another through dailyactivities.(3) Family circumstances, including family structure, cultural expectations, and intergenerational values, directly shape this connection. (4) Parents' own upbringings and past relationships indirectly shape how they connect with their child. (5) Forconnectionto grow, parents must show up physically and emotionally for their children despite competing demands. (6) Parentsgrow through engaged parenting, and that growth feeds back into the connection, creating a self-sustaining cycle of relational health.Conclusions:Our analysis generated twoconstructs underspecified in ERH frameworks.Parents described their sense of responsibility as immediate and instinctual, preceding an emotional bond.Parentsdemonstratedtheir agency in deciding what to carry forward from their relational histories, a pattern this study termsrelational legacy. Integrating parent-generated language into ERH measurementresearchmay shape a more comprehensive picture of ERHreflectinghow families experience connection.

15.
arXiv (CS.AI) 2026-06-17

Models Take Notes at Prefill: KV Cache Can Be Editable and Composable

Authors:

arXiv:2606.17107v1 Announce Type: cross Abstract: Prefix caching reuses prefill only across an exactly shared prefix, so one changed field invalidates the entire downstream cache. Yet overwriting the field's own key/value vectors and reusing the rest leaves the model acting on the old value. The reason, established causally across four model families: at prefill the model has already written the field-conditioned conclusion onto downstream notes; the field's own key/value drives under 1% of the decision. Read as a notebook of memoized conclusions, two capabilities follow. (1) It is editable. A salient erratum amends the notes; and with chain-of-thought, editing the field alone recovers the decision (1.00 at 8B, ~1% compute), while without CoT it is ignored. (2) It is composable. The notes are position-portable, so a precompiled skill can be RoPE-repositioned and spliced into any context, indistinguishable from full recompute (logit cosine 0.90-0.999, twelve models) at O(L) rather than O(L^2) time-to-first-token. A unified edit+compose agent stays decision-identical to recompute at up to 14.9x lower latency. The approach applies to any per-token attention KV cache, validated across scale, quantization, Mixture-of-Experts, and multimodal caches, and extends to several attention variants through small adapters. Because the erratum is append-only, it composes with production prefix caching: in an online vLLM benchmark it keeps the prefix cache-aligned (98.5% hit-rate), cutting p90 time-to-first-token by 53-398x.

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

Learning from Your Own Mistakes: Constructing Learnable Micro-Reflective Trajectories for Self-Distillation

arXiv:2606.18844v1 Announce Type: new Abstract: Self-distillation improves reasoning in large language models by using the model's own rollouts as training signal, typically through implicit logit-level alignment that minimizes KL divergence toward a privileged target distribution. However, because this supervision is generated via uncontrolled sampling, it provides no diagnostic insight into the model's specific errors or corrective guidance for its individual failure patterns. Consequently, the model learns to imitate a privileged distribution rather than receiving fine-grained corrections that pinpoint where and why its reasoning fails. In this paper, we propose Trajectory-Augmented Policy Optimization (TAPO), which advances self-distillation from implicit distributional alignment to explicit trajectory construction. During RL training, the model produces both correct and incorrect rollouts to the same query, and TAPO leverages this contrastive structure to construct micro-reflective corrections, new training trajectories that retain the model's erroneous reasoning up to the point of failure, then insert a natural-language diagnosis and corrected reasoning guided by a correct reference from the same sampling group. Since each trajectory is anchored in the learner's own prefix and solutions, the corrective signal preserves the model's on-policy distribution to a greater extent than the position-wise alignment imposed by KL-based methods. To integrate these trajectories, TAPO introduces difficulty-aware candidate selection at the model's capability boundary and decoupled advantage estimation to prevent gradient contamination. Experiments on AIME 2024, AIME 2025, and HMMT 2025 show that TAPO achieves consistent improvements over GRPO under the same number of training steps. Further analysis demonstrates that TAPO strengthens both first-pass reasoning and error-correction effectiveness.

17.
arXiv (math.PR) 2026-06-18

Stable size-biasing and the positive scale-mixture order of generalized Gaussian laws

arXiv:2606.18458v1 Announce Type: new Abstract: Let $X_r\sim N_r(0,1)$ be the centered unit-scale generalized Gaussian random variable with density proportional to $\exp(-|x|^r/2)$. We prove that, for $p,q>0$, there exists a strictly positive random variable $V$, independent of $X_q$, such that $X_p\stackrel{d}{=}VX_q$ if and only if $p\le q$. Moreover, the law of $V$ is unique. For $pq$, the required Mellin quotient, viewed as the candidate characteristic function of $\log V$, is unbounded by Stirling's formula, and hence cannot be a characteristic function. The factor laws form a multiplicative cocycle, $V_{p,r}\stackrel{d}{=}V_{p,q}V_{q,r}$, for $p\le q\le r$, where the factors on the right-hand side are independent copies. Thus the Mellin quotient isolated by Dytso, Bustin, Poor and Shamai is realized constructively throughout the $p

18.
medRxiv (Medicine) 2026-06-16

AI-assisted continuous-time modelling of metastatic breast cancer reveals subtype-specific spatiotemporal organ interactions

Metastatic breast cancer is one of the leading causes of premature mortality among women worldwide. A major barrier to optimal care is the marked heterogeneity in both the temporal dynamics of metastatic spread and the organ-specific spatial distribution of metastases. Existing analyses do not adequately capture this complexity, as they either neglect temporal dependencies or assume independence between metastasic sites. As a result, it remains unclear how established metastases influence subsequent organ-specific dissemination. We address this question using patient-level longitudinal trajectories from a large multicentre real-world metastatic breast cancer registry, combined with an AI-assisted disease-progression modelling framework based on continuous-time Markov chains that represent combinations of metastatic sites and the non-uniform and practice-driven timing of radiologic response assessments, as encountered in routine clinical care. We present a stochastic model determined by progression rates, which are parameterised to capture baseline organ-specific transition risks, patient-level covariates, and pairwise inter-organ interaction effects. High-dimensional treatment information is incorporated using an large language model based encoding. We find that metastatic spread follows non-independent, subtype-specific spatiotemporal patterns, with subtype-specific inter-organ interaction patterns that shape progression. Visceral metastases, particularly lung and liver metastasis, are associated with an increased hazard of subsequent brain metastasis, with effects varying across hormone receptor-positive, HER2-positive, and triple-negative subtypes. Together, these findings define a clinically relevant spatiotemporal architecture of metastatic progression in breast cancer. This framework enables refined mechanism-informed risk stratification and provides a data-driven rationale for targeted and risk-adapted – rather than symptom-triggered – surveillance strategies.

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

Goal-Autopilot: A Verifiable Anti-Fabrication Firewall for Unattended Long-Horizon Agents

Authors:

Long-horizon LLM agents are not trusted to run unattended: with no human watching, they confidently report success they never verified. We treat honesty – bounding what an agent may claim at termination – as a first-class metric for unattended autonomy, distinct from capability. We present Autopilot, an execution model that makes silent fabricated success structurally impossible rather than merely rarer. Autopilot externalizes all working state into a durable, gated finite-state machine that a scheduler advances one stateless tick at a time; a hard floor forbids any terminal "done" claim whose falsifiable gate did not actually execute and pass. We prove a No-False-Success theorem – under gate soundness, floor enforcement, and plan coverage, termination implies the goal holds – whose only trust points are empirically measurable, and show the worst case degrades to an honest stall, never a fabricated success. Because each tick rehydrates only the state machine, per-step context cost is constant in the horizon. Across a 3,150-cell paired corpus (70 tasks $\times$ 3 systems $\times$ 3 models $\times$ 5 seeds, including 50 SWE-bench Lite tasks across 11 OSS repos), Autopilot fabricates on 0.95% of cells [95% CI 0.38–1.62] while Reflexion and StateFlow baselines fabricate on 8.10% [6.48–9.81] and 25.05% [22.48–27.62] respectively. The headline contrast lives in the hard regime: on SWE-bench Lite, the firewall reduces fabrication from 33.7% (StateFlow) to 0.67%, a paired difference of $-33.07$ pp [95% CI $-36.53, -29.73$]. The mechanism is the gate, not the model: all ten Autopilot fabrications come from the strongest model, while two weaker mid-tier models never fabricate across 700 paired cells. The firewall trades coverage for honesty by design – an honest stall is recoverable; a confident wrong output shipped downstream is not.

20.
arXiv (CS.CL) 2026-06-11

Automated Scoring of Arabic Text Using Large Language Models: A Literature Review

In modern educational systems, Automatic Text Scoring (ATS) plays a central role by enabling scalable and consistent evaluation of learner responses without human intervention. Recently, the increased accessibility of LLMs and Arabic-specific datasets has sparked renewed interest in this area. In this work, we investigate LLM-Based approaches for the automated evaluation of Arabic texts, focusing on both short answer grading (ASAG) and essay scoring (AES). We further introduce a structured taxonomy comprising five dimensions: application domain, feedback generation capability, LLM architecture deployed, alignment with competency referential frameworks, and prompt engineering strategy. By applying this taxonomy, we conduct a comparative analysis of existing studies, examining their methodological approaches, datasets, evaluation metrics, and reported performance. The findings highlight the need for sustained and pedagogically grounded research efforts in Arabic ATS, given its significance for improving educational quality across Arabic-speaking communities.

21.
PLOS Computational Biology 2026-06-23

CARGO: A cytometry analysis framework via Regularized graph optimal-transport

by Abida Sanjana Shemonti, Grzegorz B. Gmyrek, Katrien L. A. Quintelier, Sofie Van Gassen, Yvan Saeys, Marcella Willemsen, Joachim G. J. V. Aerts, Eva V. E. Madsen, J. Paul Robinson, Alex Pothen, Bartek Rajwa Conventional data visualization techniques in single-cell analysis (such as two-dimensional dot plots, SPADE, PCA, t-SNE, or UMAP) often fall short in enabling an intuitive understanding of high-parameter flow cytometry data. These methods tend to oversimplify complex biological relationships, lack biologically meaningful interpretations, and offer no principled framework for downstream quantitative analysis. To address these limitations, we present a graph-based (network-based) visualization framework grounded in optimal transport theory. In this framework, cell populations are defined by their marker-expression profiles, and inter-population similarity is quantified using an efficiently computable optimal transport formulation known as the Sinkhorn distance. Our approach produces biologically consistent two-dimensional graph layouts using a phenotype-aware Hamming distance. Structural differences between sample graphs are characterized through a customized graph-edit distance that captures changes in population size, marker expression, and relationships between populations. We demonstrate our methods on two flow cytometry datasets: one from a clinical trial of dendritic cell-based immunotherapy in malignant peritoneal mesothelioma, involving 14 patients sampled at three time points with 14-color panels, and another from FlowCAP-II, which involved 43 acute myeloid leukemia patient samples analyzed with 7-color panels. Our framework produces robust, quantitative visual summaries of cell populations and supports statistical analysis based on graph edit distances, thereby offering new insights into disease progression and treatment response. Ultimately, our method bridges the gap between flow cytometry data visualization and biological interpretation.

22.
arXiv (quant-ph) 2026-06-12

Beyond-Third-Order Quantum Coherence in Two-Dimensional Spectroscopy via Order-Selective Isolation

arXiv:2606.12794v1 Announce Type: new Abstract: A central challenge in nonlinear spectroscopy is the order-selective readout of weak higher-order responses that spectrally overlap with dominant lower-order signals. This bottleneck is particularly severe in two-dimensional (2D) spectroscopy, where extending conventional phase-cycling schemes to higher orders rapidly increases measurement and analysis complexity. Here we introduce a computation-assisted strategy that combines rotating-frame acquisition with a frame-shift tracking algorithm to separate signals by their frame-dependent spectral shifts. In a rubidium vapor experiment, we use this approach to isolate a 7th-order nonlinear contribution from coexisting 3rd-order components, enabling direct access to higher-order quantum-coherence dynamics without sacrificing operation at comparatively high pulse intensities. The method is broadly compatible with multidimensional spectroscopy platforms and provides a practical route to probing many-body and collective ultrafast dynamics beyond third order.

23.
arXiv (CS.AI) 2026-06-18

AdsMind: A Physics-Grounded Multi-Agent System for Self-Correcting Discovery of Adsorption Configurations on Heterogeneous Catalyst Surfaces

arXiv:2606.19152v1 Announce Type: cross Abstract: Identifying the lowest-energy surface-adsorbate configuration is critical for modeling heterogeneous catalysis, yet exhaustive exploration with ab initio calculations is computationally prohibitive. Machine-learning force fields (MLFFs) accelerate structural relaxation but leave the search over the vast configurational space a major bottleneck, and open-loop large language model (LLM) agents lack a physics-grounded feedback mechanism to correct erroneous initial guesses. We propose AdsMind (Adsorption configuration discovery with Machine intelligence and relaxation feedback), a closed-loop multi-agent framework that enables autonomous error correction through MLFF relaxation feedback. Across four LLM backends, AdsMind achieves consistently high search reliability, with success rates of 100% and 98.8% on the benchmarks AA20 and OCD-GMAE62. Relative to its single-pass (1-Shot) ablation it reduces cross-backend energy dispersion, and it uses only 4.11 and 4.67 MLFF relaxations per case, respectively – an approximately 14-fold reduction over heuristic enumeration baselines. Density functional theory (DFT) validation using VASP/PBE on six representative AA20 systems shows that the reported open-loop Adsorb-Agent outputs exhibit qualitative adsorption-energy sign errors for molecular adsorbates, whereas AdsMind preserves the correct sign in all tested cases with closer quantitative agreement. AdsMind thus delivers reliability, self-reflection, and interpretability simultaneously, supporting more DFT-informed autonomous chemistry workflows.

24.
bioRxiv (Bioinfo) 2026-06-14

Systematic AI-Driven Drug Repurposing via Clinical Trial Data Mining: A Framework and Six Cross-Therapeutic Case Studies.

Authors:

Drug repurposing, the application of approved or shelved compounds to new therapeutic indications, offers a cost- and time-efficient alternative to de novo drug discovery. However, the systematic identification of repurposing candidates from the rapidly expanding body of clinical trial data remains a significant challenge. Here we present a publicly accessible AI-powered tool that mines the ClinicalTrials.gov registry to identify approved drugs with under-explored therapeutic potential in high-value disease areas. The tool integrates natural language processing, mechanism-of-action pathway analysis, and trial density scoring to surface candidates where biological plausibility is high and clinical trial coverage is sparse. We demonstrate the tool's utility across six cross-therapeutic case studies spanning oncology, cardiology, neurology, rare diseases, immunology, and infectious disease. Key findings include: the identification of Zonisamide as an under-explored combination candidate for obesity alongside GLP-1 receptor agonists; mechanistic validation of SGLT2 inhibitors in heart failure with preserved ejection fraction (HFpEF); and a novel cross-domain mapping of anti-TNF biologics to early-stage neurodegeneration via shared neuroinflammatory pathways. The tool is freely accessible and designed to lower the barrier for academic and industry researchers to systematically pursue repurposing opportunities.

25.
medRxiv (Medicine) 2026-06-11

Malaria Risk among Internally Mobile Individuals and Heterogeneous Mobility Patterns in Two Hypoendemic Communities: Implications for Malaria Elimination in the Peruvian Amazon.

Background: Human mobility is increasingly recognized as a key factor influencing malaria transmission dynamics, particularly in low-transmission settings approaching elimination. This study aimed to assess mobility patterns and their association with malaria risk in two hypoendemic communities in the Peruvian Amazon. Method: A longitudinal study was conducted in the communities of Libertad and Urcomirano (Mazan River basin). Monthly population screenings were combined with weekly active and passive case detection. A total of 678 individuals were enrolled. Mobility patterns were assessed through structured questionnaires, and social network analysis was used to characterize travel connections. Log-binomial regression analysis was applied to identify risk factors associated with malaria infection. Result: Internally, mobile individuals in Libertad showed a higher malaria incidence (>32.47 cases per 1,000 person-months) than those in Urcomirano (