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01.
arXiv (CS.CL) 2026-06-11

An Ontology-Guided Multi-Anchor Graph Retrieval Framework for Traffic Legal Liability Determination

Traffic law liability determination is critical for assigning legal penalties, requiring the simultaneous identification of interdependent statutory provisions across multiple legal dimensions. However, existing retrieval-augmented generation methods suffer from a multi-dimensional retrieval bottleneck: single axis architectures compress complex legal queries into a single pathway, causing interdependent statutory dimensions to be overlooked. To address this, we propose OMAGR, an ontology-guided framework that decomposes queries into ontology-aligned anchors and executes parallel graph retrieval across each dimension, ensuring independent retrieval across dimensions before fusion. To evaluate the proposed method, we created the TrafficLaw-QA dataset, an expert-validated benchmark dataset containing 200 questions and 527 legal provisions. Results show that TrafficOmni-RAG outperforms baselines on Context Precision and Faithfulness metrics. The findings demonstrate that parallel multi-anchor retrieval effectively resolves the multi-dimensional retrieval bottleneck, offering a promising direction for traffic law liability determination research.

02.
arXiv (quant-ph) 2026-06-12

Non-invertible symmetries out of equilibrium: Eigenstate order and Floquet physics

arXiv:2508.14213v2 Announce Type: replace-cross Abstract: Through the study of the Rep($D_8$) non-invertible symmetry, we show how non-invertible symmetries manifest in dynamics. Results are presented for dynamics generated by Hamiltonians as well as Floquet unitaries. For both examples, the role of the non-invertible symmetry is studied through the appearance of non-invertible symmetry protected edge modes. In addition, the role of the non-invertible symmetry for the Hamiltonian is studied through eigenstate order. In particular, by considering the effect of symmetry preserving disorder, the non-invertible symmetry is shown to give rise to degeneracies in the spectra of the Hamiltonian that can only be completely lifted at orders of perturbation that scale with system size. The eigenstates of disordered Hamiltonians, whose ground state correspond to non-trivial symmetry protected topological (SPT) states, are shown to have either trivial or non-trivial SPT order that are detected as non-zero expectation value of string order-parameters. In contrast, non-trivial SPT order is absent in the eigenstates of trivial SPT Hamiltonians with disorder. The interface between two different SPT phases host edge modes whose dynamics is studied numerically and analytically. The edge mode is shown to oscillate at frequencies related to different effective chain lengths that are weighted by the temperature, becoming an exact zero mode in the limit of zero temperature. A Floquet model with the non-invertible symmetry is constructed whose edge mode is shown to exhibit period-doubled dynamics at low effective-temperatures. The zero and period-doubled edge modes differ from those in conventional SPTs by being symmetric under the invertible symmetry, while being charged under the non-invertible symmetry.

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

Structured Representation Learning with Locally Linear Embeddings and Adaptive Feature Fusion

arXiv:2606.18469v1 Announce Type: cross Abstract: Neuroscientific research has revealed that the brain encodes complex behaviors by leveraging structured, low-dimensional manifolds and dynamically fusing multiple sources of information through adaptive gating mechanisms. Inspired by these principles, we propose a novel reinforcement learning (RL) framework that encourages the disentanglement of dynamics-specific and reward-specific features, drawing direct parallels to how neural circuits separate and integrate information for efficient decision-making. Our approach leverages locally linear embeddings (LLEs) to capture the intrinsic, locally linear structure inherent in many environments, mirroring the local smoothness observed in neural population activity, while concurrently deriving reward-specific features through the standard RL objective. An attention mechanism, analogous to cortical gating, adaptively fuses these complementary representations on a per-state basis. Experimental results on benchmark tasks demonstrate that our method, grounded in neuroscientific principles, improves learning efficiency and overall performance compared to conventional RL approaches, highlighting the benefits of explicitly modeling local state structures and adaptive feature selection as observed in biological systems.

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

QPILOTS: Efficient Test-Time Q-Steering for Flow Policies

arXiv:2606.14801v1 Announce Type: cross Abstract: Flow-matching and diffusion policies are expressive action generators, but optimizing them with temporal-difference reinforcement learning (RL) remains difficult. Effective policy extraction requires exploiting the critic's action gradient, yet directly backpropagating this signal through a multi-step denoising process can be numerically unstable. Existing methods work around this either by discarding gradient information, distilling the policy into a simpler one-step actor, or repeatedly fine-tuning the denoising policy as the critic improves. We propose QPILOTS, a method that leaves the original policy unmodified and steers the denoising process at inference time. At each denoising step, instead of evaluating the critic on the noisy intermediate action where critic predictions are unreliable, we first project that intermediate state to an estimate of the final clean action and compute the critic gradient there. We introduce two variants: QPILOTS-U uses a fast single-point approximation, while QPILOTS-M draws differentiable posterior samples via a learned auxiliary network. On a standard offline-to-online RL benchmark, QPILOTS achieves the best aggregate performance, reaching an average success rate of 90% across 50 tasks. We also apply QPILOTS to steer a large, frozen, pretrained Vision-Language Action (VLA) foundation model, outperforming or matching prior inference-time approaches across six manipulation tasks in simulation.

05.
arXiv (quant-ph) 2026-06-12

Experiment-compatible measurement–feedback quantum state preparation with reinforcement learning

arXiv:2606.13005v1 Announce Type: new Abstract: Ground-state preparation is a critical task in quantum simulation and quantum computing, as it enables the study of correlated phases and the generation of entangled resource states. While measurement–feedback control has emerged as a promising route to state preparation, existing schemes either rely on handcrafted, task-specific policies or are designed using full quantum-state information that is unavailable in real experiments and becomes impractical for large many-body systems. Here we develop an adaptive measurement–feedback protocol based on reinforcement learning under partial observability. The controller uses only the history of experimentally accessible measurement outcomes to choose both the measurement operator and the feedback action in real time. To make training compatible with experiments, we introduce a stochastic terminal reward built from one-shot measurements of randomly sampled Hamiltonian components, avoiding unphysical full-state reconstruction while remaining an unbiased estimator of the target energy. We demonstrate the method by preparing ground states of the Bose–Hubbard model and by generating GHZ states, establishing a scalable and hardware-compatible route to quantum state preparation.

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

Plan, Don't Pose: Long Composite Motion Generation with Text-Aligned BFM

arXiv:2605.29906v2 Announce Type: replace Abstract: Text-to-motion (T2M) generation has broad applications in character animation, virtual avatars, and human-robot interaction. Existing methods typically generate pose trajectories or motion tokens directly from language, forcing a single model to handle semantic interpretation, long-horizon structure, and low-level physical realization. This coupling makes them costly and often unreliable for long, compositional, or semantically dense prompts. We propose Text2BFM, the first framework that aligns natural language with pretrained Behavioral Foundation Models (BFMs) for T2M generation without relying on heavy end-to-end motion generators. Text2BFM operates in the latent policy space of a frozen BFM, using it as an executable motion prior. A text-aligned variational behavioral bottleneck compresses BFM policy-latent sequences into compact motion representations that are compatible with language and preserve long-horizon behavioral structure. Generation is performed in this compact behavioral manifold with a lightweight conditional generator, and the resulting latent encoded behaviors are decoded into policy latents that drive the pretrained frozen BFM. By decoupling semantic planning from motion execution, Text2BFM achieves efficient, robust T2M generation and strong performance on long, compositional textual descriptions.

07.
arXiv (math.PR) 2026-06-16

Asymptotic behavior of some strongly critical decomposable 3-type Galton–Watson processes with immigration

arXiv:2406.09852v2 Announce Type: replace Abstract: We study the asymptotic behavior of a critical decomposable 3-type Galton-Watson process with immigration when its offspring mean matrix is triangular with diagonal entries 1. It is proved that, under second or fourth order moment assumptions on the offspring and immigration distributions, a sequence of appropriately scaled random step processes formed from such a Galton-Watson process converges weakly. The limit process can be described using independent squared Bessel processes $({\mathcal X}_{t,1})_{t\geq0}$, $({\mathcal X}_{t,2})_{t\geq0}$, and $({\mathcal X}_{t,3})_{t\geq0}$, the linear combinations of the integral processes of $({\mathcal X}_{t,1})_{t\geq0}$ and $({\mathcal X}_{t,2})_{t\geq0}$, and possibly the 2-fold iterated integral process of $({\mathcal X}_{t,1})_{t\geq0}$. The presence of the 2-fold iterated integral process in the limit distribution is a new phenomenon in the description of asymptotic behavior of critical multi-type Galton-Watson processes with immigration. Our results complete and extend some results of Foster and Ney (1978) for some strongly critical decomposable 3-type Galton-Watson processes with immigration.

08.
medRxiv (Medicine) 2026-06-15

Population-scale genomics reveals divergent pathogenicity of variant classes across paralogous collagen IV genes

Monoallelic pathogenic or likely pathogenic variants in COL4A3 and COL4A4 occur in approximately 1 in 106 individuals, yet whether these paralogous genes confer equivalent pathogenicity for the same variant classes has not been tested at population scale. Using whole-genome sequencing data from the UK Biobank (UKB; n = 500,000), with replication in the All of Us Research Program (n = 414,000), we performed per-variant association testing, gene-based collapsing analyses and phenome-wide association studies (PheWAS) across haematuria, proteinuria and chronic kidney disease. We identified 64 COL4A3 and 92 COL4A4 rare variants significantly associated with haematuria or proteinuria, generating a quantitative allelic series for clinical variant interpretation. Glycine substitutions within collagenous domains conferred similar risks in both genes. In contrast, truncating and non-collagenous domain (NC1) missense variants were strongly associated with haematuria and proteinuria in COL4A4 carriers but showed substantially attenuated or absent associations in COL4A3 carriers despite comparable carrier frequencies and predicted pathogenicity scores. These findings were independently replicated in All of Us. Genome-wide association analysis identified the COL4A3/COL4A4 locus as the dominant genetic determinant of haematuria, with the signal attributable to the aggregate effects of rare coding variants and no evidence of independent common variant or trans-acting modifier effects. These findings demonstrate substantial gene-specific differences in tolerance to truncating and NC1 variants between COL4A3 and COL4A4, challenging assumptions of equivalent pathogenicity across paralogous collagen IV genes. Gene identity and not variant class alone, should inform risk stratification, variant interpretation and genetic counselling in individuals carrying collagen IV risk genotypes.

09.
bioRxiv (Bioinfo) 2026-06-12

Generalisable tissue-wide molecular reconstruction from histology

Spatial transcriptomics technologies measure gene expression within intact tissues but remain difficult to scale across large tissue sections and patient cohorts. Consequently, many studies rely on tissue microarrays (TMAs) or sparse spatial profiling designs, where molecular measurements are available for only limited tissue regions and are often generated using heterogeneous gene panels. Existing H&E to spatial gene expression prediction methods remain challenged by sparse molecular measurements, partially overlapping gene panels and tissue-wide reconstruction across heterogeneous spatial datasets. Here, we present GHIST+, a framework for tissue-wide reconstruction of single-cell molecular states from H&E histology. GHIST+ integrates cellular morphology, local tissue context and shared tissue representations to extend sparse molecular measurements into tissue-wide molecular maps across heterogeneous spatial datasets. Across multiple cancer types and GTEx breast tissues, GHIST+ reconstructs biologically meaningful tissue-wide molecular organisation from sparse TMA-derived measurements while preserving spatial tissue structure, cell-type organisation and age-associated tissue states across cancer and non-cancer settings. GHIST+ establishes a scalable framework for transforming sparse spatial profiling experiments into tissue-wide molecular maps, enabling cohort-scale molecular reconstruction from routine histology under heterogeneous spatial transcriptomic settings.

10.
bioRxiv (Bioinfo) 2026-06-13

Virus-human protein-protein interactions predict viral phenotypes

Viral phenotypes such as host and tissue tropism are critical determinants of viral infection and transmission. Inferring viral phenotypes presents unique challenges compared to cellular organisms, as viruses rely entirely on host machinery for replication and survival. Current methods for predicting viral phenotypes mainly rely on viral genomic data, often overlooking host-related information. Here, we evaluated the utility of predicted virus-human protein-protein interactions (PPIs) in inferring diverse viral phenotypes using machine-learning algorithms. For predicting human infectivity, a PPI-based machine learning model outperformed both virus genomic and protein sequence-based models that used large language model embeddings. It also surpassed previous methods that incorporated both viral and host genomic data. The human proteins identified by the model were significantly enriched in functions related to viral infection and immune response. In predicting various phenotypes of human RNA viruses, PPI-based models performed better than virus sequence-based models in forecasting virulence, human transmissibility and transmission routes, while showing comparable performance to genomic sequence-based models in predicting tissue tropism. Finally, we demonstrated that a PPI-based model could distinguish high-risk HPV genotypes from low-risk ones. Proteins associated with high-risk HPV were involved in apoptosis and immune regulation, whereas those linked to low-risk HPV were enriched in telomere maintenance and DNA repair. Collectively, this study is the first to demonstrate the value of predicted virus-human PPIs in inferring viral phenotypes, thereby enhancing our understanding of the molecular mechanisms underlying these phenotypes. It also provides effective tools for risk assessment of emerging viruses, contributing to improved pandemic preparedness.

11.
arXiv (CS.LG) 2026-06-18

MetaboNet-Bench: A Multi-modal Benchmark for Glucose Forecasting in Type 1 Diabetes

arXiv:2606.18640v1 Announce Type: new Abstract: Glucose forecasting algorithms are an important aspect of glycemic control management in type 1 diabetes. So far, the research community has developed numerous algorithms and models for forecasting. However, it is well-recognized that the lack of standardized model performance evaluation benchmarks makes fair comparison difficult and hinders further innovation, and thus benchmark standardization is in urgent need. Furthermore, many published glucose forecasting algorithms are limited to CGM data alone, ignoring other multimodal signals such as insulin dosing and carbohydrate intake. Here, we introduce MetaboNet-Bench, a benchmark for multimodal glucose forecasting for patients with type 1 diabetes that provides an extensible open-source evaluation framework for comparison of glucose forecasting algorithms that leverage glucose, insulin, and carbohydrate data. We then demonstrate its utility by benchmarking several recently published glucose forecasting models and a custom multimodal time-series model, representing different model architectures. The results show that the benefit of adding data modalities is conditioned on the complexity of the model and that incorporating more clinical metrics helps identify meaningful gaps to fill for future research.

12.
arXiv (CS.AI) 2026-06-19

Automating SKILL.md Generation for Computer-Using Agents via Interaction Trajectory Mining

arXiv:2606.20363v1 Announce Type: new Abstract: Explicit skill libraries make computer-using agents easier to inspect, but it remains unclear whether such libraries can be mined from interaction data in a way that improves downstream policies. We study this question through a three-stage pipeline that segments GUI trajectories, clusters segments into candidate skills, and trains a skill-aware policy from the resulting annotations. The mined clusters are readable on the source benchmark: five of eight clusters have at least 0.95 purity against InteraSkill Workflows labels. However, readability does not imply transfer. GRPO improves IW skill-step accuracy only from 18.5\% to 20.5\%, leaves BrowseComp+ essentially unchanged, and underperforms trivial frequency priors on key source-domain metrics. We therefore present the method as a diagnostic study: trajectory mining can expose inspectable skill structure, but the current boundary detector, orderless segment representation, and offline reward model are insufficient for reliable cross-domain policy improvement.

13.
arXiv (CS.CV) 2026-06-18

Characterizing Brazilian Atlantic Forest Restoration Outcomes with Geospatial AlphaEarth Embeddings

作者:

The Atlantic Forest in Brazil is a critical biodiversity hotspot, yet less than 12-15% of its original cover remains. Although monitoring forest restoration on a large scale is essential, traditional methods are limited by the impracticality of on-the-ground reporting on such a scale and by the saturation of remote-sensing indices such as NDVI. Furthermore, reforestation is a gradual process as opposed to the rapid spectral changes caused by deforestation. In this study, we examine 1,729 restoration sites in S\~ao Paulo, using satellite embeddings from the AlphaEarth Foundation's model to evaluate their effectiveness in characterising early restoration success. We introduce the concept of a 'Reference Trajectory Embedding', defining a metric of restoration success based on cosine similarity to reference sites of mature secondary forest. We observe distinct clusters in embedding space according to different land use and land cover (LULC) types, and we can identify sites with clear change vectors. However, the signal can be noisy, and embeddings may require further fine-tuning to capture and predict site metadata beyond LULC.

14.
arXiv (quant-ph) 2026-06-16

Quantifying Coherence-to-Entanglement Conversion Efficiency under Noisy Operations

arXiv:2606.16916v1 Announce Type: new Abstract: We investigate the noise-limited conversion of local quantum coherence into bipartite entanglement in a minimal two-qubit protocol comprising a coherent single-qubit input, an incoherent ancilla, an ideal CNOT operation, and subsequent environmental noise. Employing the $l_1$-norm of coherence and the entanglement negativity as resource quantifiers, we establish an exact closed-form correspondence between local single-qubit input coherence and the two-qubit entanglement generated in the noiseless limit, showing that the output negativity is precisely one half of the initial $l_1$-coherence. We then derive analytic expressions for the surviving entanglement and the associated coherence-to-entanglement conversion efficiency under two representative noise mechanisms: independent phase damping and global two-qubit depolarizing noise. The two channels exhibit qualitatively distinct degradation behavior. Phase damping induces a universal multiplicative suppression of the generated entanglement, yielding a coherence-independent conversion efficiency and no finite-noise entanglement sudden death. In contrast, global depolarization introduces an isotropic mixing contribution that shifts the partial-transpose spectrum, producing coherence-dependent degradation and a finite sudden-death threshold. We show that maximally coherent inputs not only maximize the entanglement generated by the CNOT protocol but also optimize its robustness against depolarizing noise. Direct density-matrix simulations validate the analytic results to numerical precision. These findings provide a compact analytic benchmark for assessing how different noise mechanisms constrain coherence-to-entanglement conversion in elementary quantum-information protocols and near-term quantum devices.

15.
medRxiv (Medicine) 2026-06-10

"We don't complain; it's just part of being a woman": frequency, knowledge, and sociocultural beliefs about dysmenorrhoea in a South African university cohort

Introduction Dysmenorrhoea is highly prevalent globally and interferes with engagement in education, work, social participation, and quality of life. Although evidence suggests that sociocultural beliefs influence how menstrual pain is understood and managed, relatively little research has explored dysmenorrhoea-related knowledge and beliefs within South Africa. This study aimed to (1) determine the frequency of dysmenorrhoea, (2) assess dysmenorrhoea-related knowledge and compare knowledge between menstruating and non-menstruating individuals, and (3) explore commonly held generational, cultural, and religious beliefs related to dysmenorrhoea in a South African university cohort. Methods We analysed data collected as part of a cross-sectional survey conducted among staff and students at a South African university. Participants completed demographic questions, items assessing dysmenorrhoea-related knowledge, and an adapted Working Ability, Location, Intensity, Days of Pain, Dysmenorrhoea (WaLIDD) questionnaire. Participants were also invited to provide free-text responses describing generational, cultural, and religious beliefs about dysmenorrhoea. Quantitative data were analysed descriptively and compared between menstruating and non-menstruating participants. Free-text responses were analysed using reflexive thematic analysis. Results A total of 863 participants completed the survey, including 578 current or past menstruators. The frequency (95%CI) of dysmenorrhoea was 75.4% (71.7-78.9). Most participants were classified as having moderate (53%) or severe (31%) dysmenorrhoea on the WaLIDD scale. Awareness of dysmenorrhoea was higher among participants who had menstruated than among those who had never menstruated (80.4% vs 55.3%, p

16.
arXiv (math.PR) 2026-06-19

A Cycle Walk for Sampling Measures on Spanning Forests for Redistricting

arXiv:2509.08629v2 Announce Type: replace-cross Abstract: We introduce the Cycle Walk, a new Markov chain Monte Carlo method for sampling distributions on balanced graph partitions, motivated by applications in political redistricting. The method operates on spanning forests and combines two types of updates: local "cycle" moves within districts and global moves that exchange population between adjacent districts while preserving balance constraints. This construction enables efficient Metropolis–Hastings correction while allowing proposals at multiple spatial scales. We show that the Cycle Walk naturally interpolates between existing approaches based on local updates and a class of global update methods derived from recombination (RECOM). Through a range of numerical experiments on synthetic graphs and real-world precinct data, we demonstrate that the Cycle Walk exhibits improved empirical convergence diagnostics for distributions that place weaker weight on spanning-tree counts, a regime that is challenging for existing methods. In particular, the algorithm remains effective when incorporating alternative compactness measures that more closely reflect policy-relevant criteria. These results suggest that the Cycle Walk provides a flexible and computationally efficient framework for sampling from a broader class of redistricting distributions than previously accessible with MCMC techniques.

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

Vorticity Induced by Non-frontal Collisions of Quantum Droplets

arXiv:2606.17498v1 Announce Type: cross Abstract: The rotational dynamics induced by the non-frontal binary collisions of quantum droplets composed of ultracold alkali atoms are analyzed. A theoretical study is presented within the extended Gross-Pitaevskii equation framework, using experimentally feasible conditions. Numerical experiments elucidate a rich landscape of possible topological excitations in the system that are robust towards measurements. The collision of heteronuclear quantum droplets composed of $^{41}$K and $^{87}$Rb atoms in the incompressible regime, gives rise to dynamical instabilities that spontaneously generate topological defects: vortex rings, dislocation lines, and vortices in one species. Their presence depends on the Weber number and the impact parameter. An experimental proposal for vortex detection in both real and Fourier space using interaction ramps is described.

18.
arXiv (CS.CL) 2026-06-19

When Does Streaming Tool Use Help? Characterizing Tool-Intent Stabilization in Streaming Retrieval-Augmented Generation

Streaming Retrieval-Augmented Generation (Streaming RAG) reduces user-perceived latency by issuing tool queries in parallel with ongoing user input, before the utterance is complete. Reported gains are aggregate, yet the mechanism's benefit is fundamentally query-intrinsic: speculation can only help when the correct tool query becomes determinable before the user stops speaking or typing. We isolate and measure this property – tool-intent stabilization, the point in the input stream at which a speculative query's retrieval converges to the answer-bearing result. On the CRAG benchmark (1371 validation questions) we (i) measure the distribution of stabilization, (ii) derive a model-agnostic bound H on the portion of tool latency that can be hidden behind the user's remaining input, as a function of tool latency L and input cadence {\delta}, (iii) validate against a working streaming pipeline that realized savings meet or exceed this bound, and (iv) identify which query properties predict early versus late stabilization. The study requires no model training and runs on commodity CPU hardware. We find that at a realistic operating point (L=600ms, {\delta}=3w/s, {\theta}=0.8), 73.9% of queries across the full benchmark admit substantial latency hiding – a blended figure that mixes sufficiency stabilization on the 21.3% of questions where gold evidence is verbatim-present and BM25-retrievable (95.2% streamable on this favorable slice) with a grounding-free top-1-settling fallback on the remainder. On the favorable slice, {\phi}_suf is bracketed to [0.26, 0.281] by exact and relaxed grounding – both early. Question type produces a significant but coarse early/late split (Kruskal-Wallis p=0.017, epsilon^2=0.04), directly informing when a learned speculative trigger is worth its cost.

19.
arXiv (quant-ph) 2026-06-11

Towards the implementation of a quantum classifier

arXiv:2606.10150v2 Announce Type: replace Abstract: In this work, we investigate the use of a quantum circuit as a binary classification model in the context of quantum machine learning. We call this model, binary quantum classifier. First, we describe fundamental concepts of quantum computing and introduce the computational tool used: Qibo, an open-source framework for efficient quantum simulations and quantum hardware control. Then, we describe how to design a binary quantum classifier for the classification of images and small arrays of variables by showing how to input data in the circuit, defining a quantum circuit model Ansatz with trainable parameters and a loss function, and implementing multiple minimizers. We test our quantum classifier with two data sets. The first one is the MNIST data set which is composed of handwritten digits (reduced to only handwritten zeros and handwritten ones for binary classification). We study the behavior of different minimizers by increasing the number of layers of the Ansatz. The second data set represents two different high energy collisions that can occur at colliders such as LHC (CERN). Due to in-time proton-proton interactions known as pile-up, we distinguish two different data sets: "without pile-up" and "with pile-up". These collisions can be represented by images of size 32x32 or by six high-level variables that we call features. By increasing the size of the training data set and the number of layers of the Ansatz, we search for the best minimizer. Splitting the data set in training set and test set, we compute: ROC curve, AUC score, confusion matrices and test set accuracy. For "with pile-up" images, we compare the results obtained with the quantum classifier with a small convolutional neural network. We conclude that is possible to build a binary quantum classifier with a quantum circuit and we highlight its performances and limitations in comparison with classical technologies.

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

PEFT-MedSAM: Efficient Fine-Tuning of Medical Foundation Models for Explainable Skin Lesion Segmentation

Automated segmentation of skin lesions using deep learning models for dermoscopic images can be very helpful in finding melanomas earlier than they would normally be detected. However, most deep learning methods available do not perform well. The aim of this paper is to present a parameter-efficient fine-tuning method called PEFT-MedSAM for adapting the Medical Segment Anything Model (MedSAM) to automatically segment dermoscopic skin lesions. The PEFT-MedSAM method uses only the lightweight mask decoder for training the model while keeping the pre-trained image encoder and prompt encoder frozen. The experiments performed on the ISIC 2018 benchmark dataset shows that PEFT-MedSAM obtains a dice coefficient of .9411 and an intersection over union value of .8918 when compared to both a fully trained U-Net baseline (.8715 dice coefficient) and zero-shot MedSAM inference (.8997 dice coefficient). The external validation of the model using PH2 dataset shows .9467 dice coefficient with +/- .0310 standard deviation. Supportive evidence for these claims include a p-value less than .0001 for Wilcoxon signed rank tests comparing the two datasets and bootstrap-estimated 95% confidence intervals of [.9364,.9447] that represent the estimated range of possible values for the average dice coefficient obtained by repeating the test. To increase clinical trustworthiness, we used Grad-CAM explainability along with a pointing game based evaluation methodology to evaluate the CNN baseline model on the validation set. The results showed that we had an accuracy rate of 98.27% on the validation set of 519 images and confirmed that the model classified regions containing skin lesions.

21.
PLOS Computational Biology 2026-06-22

GrassSV – hybrid method to detect structural variants in high throughput DNA-seq data

by Dominik Witczak, Krzysztof Sychla, Julia Wysocka, Artur Laskowski, Wojciech Frohmberg, Marta Glowacka, Alicja Dzik, Piotr Lukasiak, Jacek Blazewicz, Aleksandra Swiercz Genetic diversity is crucial for populations to adapt and survive in dynamic environments. This diversity arises from genetic mutations, which manifest in the genome as structural variants (SVs). Several types of SVs exist, but not all are equally easy to detect. Current SV detection tools tend to specialize in certain SV types or require the use of multiple tools to obtain a comprehensive variant profile, which increases computational cost and complexity. While some methods excel at identifying breakpoints, they often struggle with accurately classifying variant types, and their precision depends strongly on data quality and sequencing technology. At present, the majority of available genomic data originates from high-quality short reads, which remain the most affordable sequencing technology. In this manuscript, we introduce GrassSV, a novel and computationally efficient method that employs a hybrid pattern-matching approach to detect all major classes of structural variants using short-read sequencing data. GrassSV integrates depth-of-coverage analysis with contig-based pattern recognition to ensure both sensitivity and precision while minimizing false positives and runtime. Its robustness was demonstrated on the human Genome in a Bottle dataset, as well as on synthetic data derived from the yeast genome, where it achieved high accuracy across all SV types at a lower computational cost compared to existing methods. This makes GrassSV a practical alternative to multi-tool pipelines typically required for comprehensive SV detection. GrassSV is available at https://github.com/Domomod/GrassSV under GPL-3.0 license and the benchmark at: https://github.com/Domomod/GrassBenchmark.

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

Free-Placement Optimization of Ground Station Locations for Low-Earth Orbit Satellites

arXiv:2606.12667v1 Announce Type: cross Abstract: Rapidly expanding low Earth orbit satellite constellations are placing increasing demands on terrestrial ground networks, motivating the development of more efficient ground station network designs. Current approaches select sites from predefined locations, limiting optimization to existing infrastructure and constraining performance. In contrast, free-placement optimization operates over a continuous spatial domain on Earth, broadening the search space and allowing higher-throughput configurations at the cost of potentially requiring new infrastructure deployment. In this work, we introduce SCORE (Sequential Cyclic Optimization via Refinement & Evaluation), a two-stage free-placement method for ground station design. SCORE combines sequential coordinate selection with cyclic refinement to manage high-dimensionality, non-convexity, and local minima that challenge global optimizers. We benchmark SCORE against one-shot methods such as differential evolution (DE) and integer programming approaches using locations from Kongsberg Satellite Services and the World Teleport Association. Tests across two commercial Earth observation constellations (Capella Space and ICEYE) and one synthetic Walker-Star constellation show that SCORE requires up to 5x fewer function evaluations to converge relative to DE while improving downlink throughput by up to 13%. Compared to fixed-site methods, unconstrained SCORE achieves up to 15% greater total downlink, establishing a strong empirical performance benchmark for flexible placement; infrastructure-constrained SCORE retains over 92% of this gain while restricting placement to within proximity of existing fiber and power infrastructure. We also explore trade-offs between expanding existing stations and deploying new sites, informing future ground network design for operational constellations.

23.
arXiv (CS.CL) 2026-06-16

SimSiam Naming Game: A Unified Approach for Emergent Communication and Representation Learning

Emergent Communication (EmCom) investigates how agents develop symbolic communication through interaction without predefined language. Recent frameworks, such as the Metropolis–Hastings Naming Game (MHNG), formulate EmCom as the learning of shared external representations negotiated through interaction under joint attention, without explicit success or reward feedback. However, MHNG relies on sampling-based updates that suffer from high rejection rates in high-dimensional perceptual spaces, making the learning process sample-inefficient for complex visual datasets. In this work, we propose the SimSiam Naming Game (SSNG), a feedback-free EmCom framework that replaces sampling-based updates with a symmetric, self-supervised representation alignment objective between autonomous agents. Building on a variational inference–based probabilistic interpretation of self-supervised learning, SSNG formulates symbol emergence as an alignment process between agents' latent representations mediated by message exchange. To enable end-to-end gradient-based optimization, discrete symbolic messages are learned via a Gumbel–Softmax relaxation, preserving the discrete nature of communication while maintaining differentiability. Experiments on CIFAR-10 and ImageNet-100 show that the emergent messages learned by SSNG achieve substantially higher linear-probe classification accuracy than those produced by referential games, reconstruction games, and MHNG. These results indicate that self-supervised representation alignment provides an effective mechanism for feedback-free EmCom in multi-agent systems.

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

Quantum enhancement and Doppler suppression of Kasevich-Chu atom interferometer with motional squeezing states

arXiv:2606.16632v1 Announce Type: new Abstract: Hybridization of internal and external atomic degrees of freedom in a Kasevich-Chu interferometer enables the possibility to enhance the sensitivity significantly even under quantum-standard limit. By introducing motional squeezing state as an input, we systematically derive the computational framework of quantum and classical Fisher information of two measurement protocols for arbitrary strength of Doppler effects. Through maximizing the corresponding classical Fisher information, we obtain the optimal control parameters and the corresponding quantum Fisher information. For population measurement, the largest sensitivity can be as large as four times than the semi-classical limit through enlarging the atom coherence length. For joint measurement of population and position, the competition between quantum enhancement and Doppler suppression induces two three behaviors, in one regime, the quantum enhancement dominates even in presence of strong Doppler broadening effects where the sensitivity is significantly enhanced; while in another regime, an optimal squeezing parameter is observed where the classical Fisher information reaches the maximum. Our results clearly demonstrate the robustness of external quantum enhancement against Doppler suppression. Our proposal can be readily applied to gravimeter of mobile platform where decoherence from noise will damage the many-body entanglement of internal spin squeezing.

25.
arXiv (quant-ph) 2026-06-16

High-fidelity two-qubit gates in a 7-qubit register for quantum networks

arXiv:2606.14847v1 Announce Type: new Abstract: Quantum networks based on optically active solid-state spins may enable quantum technologies including long-range quantum communication and distributed quantum computing. Network nodes containing multiple high-fidelity qubits can facilitate large-scale fault-tolerant operation. However, the stringent error thresholds remain out of reach for multi-qubit registers. In this work, we demonstrate high-fidelity two-qubit gates in a 7-qubit register, based on nuclear spins coupled to a nitrogen-vacancy (NV) center in diamond. We analyze crosstalk in highly connected spin systems, develop an efficient optimization procedure, and characterize the gates using gate set tomography. The two-qubit gate fidelities (best: 99.61(5)%, average: 99.18(2)%) demonstrate a multi-qubit register at the threshold for distributed quantum computation. Finally, as an example application, we perform a variational quantum eigensolver (VQE) simulation of the ground-state energy of H2 and LiH molecules. These results demonstrate one of the key prerequisites for scalable quantum networks based on solid-state spins.