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01.
medRxiv (Medicine) 2026-06-11

Impact of Out-Migration and Remittances on Food Consumption Outcomes among Rural Households in Tigray, Ethiopia

Authors:

This study examines the effects of rural out-migration and remittance inflows on food consumption outcomes among rural households in the Tigray region of Ethiopia. Utilizing household survey data collected from 521 rural households across three distinct Weredas (districts) (Tahtay Maichew, Kola Tembien, and Kilte-awlaelo). A Binary Probit model was employed to identify factors influencing migration decisions, while an Endogenous Switching Regression (ESR) model was used to estimate the impact of migration on food consumption outcomes while controlling for selection bias and unobserved heterogeneity. Food security was measured using the Food Consumption Score (FCS) and dietary diversity indicators. The empirical results reveal that severe food insecurity is widespread, with over 60% of all surveyed households falling into the "Poor" food consumption category. Descriptive baseline comparisons show that migration and remittance transfers marginally shift the raw average FCS upward from 23.86 to 25.48. However, this impact is profoundly nuanced: remittances serve as an immediate consumption-smoothing safety net but run parallel to a "labor-lost" constraint that reduces own-production capacities, forcing households to rely increasingly on market purchases for staple foods. The findings reveal that migration creates short-term labor shortages in agricultural production; however, remittance inflows substantially improve household food consumption frequencies, particularly for pulses, vegetables, and other nutrient-rich foods. After accounting for self-selection bias and unobserved traits, the rigorous ESR estimates indicate that migration increases the Food Consumption Score of participating households by an average Treatment Effect on the Treated (ATT) of 10.75 points, shifting them into more secure dietary tiers. Moreover, remittances help households mitigate the adverse effects of drought and other shocks by relaxing liquidity constraints and supporting both food purchases and agricultural investments. The study recommends establishing target food security safety nets for non-remittance households, promoting scale-appropriate labor-saving agricultural technologies, expanding traditional communal labor-sharing innovations, and boosting irrigation and agricultural input support programs to enhance rural food security and livelihood resilience.

02.
arXiv (CS.CV) 2026-06-12

Modality Forcing for Scalable Spatial Generation

Text-to-image (T2I) models contain rich spatial priors. Synthesizing photorealistic, cluttered scenes requires an understanding of geometry, including perspective and relative scale. Prior works adapt T2I models to leverage this prior for depth prediction, but they require dense depth data and involve complex recipes. We propose Modality Forcing, a simple, scalable post-training recipe for joint image-depth generation using a single DiT trained on sparse depth data. Modality Forcing enables conditional and joint generation of image and depth in any permutation by assigning separate noise levels per modality. Per-modality decoders let us train on sparse, real-world depth and achieve strong, generalizable depth prediction. We further show that Modality Forcing inherits the scalability of T2I pre-training: by training a set of T2I models from scratch (370M to 3.3B parameters), we find that larger models trained on more image data produce more accurate depth. Our strongest model is competitive with state-of-the-art monocular depth estimators and reduces AbsRel by 57% relative to existing joint image-depth generative models. These results provide strong evidence that image generation is a scalable pre-training objective for spatial perception. https://modality-forcing.github.io/

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

NEST3D: A High-Resolution Multimodal Dataset of Sociable Weaver Tree Nests

Sociable weaver nests function as complex ecological structures offering thermoregulatory microhabitats and sustaining diverse species; however, datasets used in prior studies lack fine-grained 3D structural detail. Producing usable and accurate 3D weaver nest data is challenging due to their irregular geometry and integration with complex host vegetation. We bridge this gap with an open-access, 1.4 TB multimodal drone dataset of 104 nest-bearing trees, comprising 27,945 RGB images, 111,780 multispectral images, approximately 781 million 3D points, and expert-annotated semantic segmentation labels. We benchmark semantic segmentation using KPConv, RandLA-Net, and Point Transformer V3, with PT-v3 achieving an mIoU of 86.35% on the test set. While the results demonstrate strong performance for transformer-based and point-wise methods, they also highlight architecture-dependent challenges, particularly for convolution-based approaches such as KPConv. By uniquely combining spectral, spatial, and structural information, the presented dataset advances 3D reconstruction, segmentation, and classification algorithms, enabling ecological applications from nest volume estimation to species conservation, and serves as a demanding benchmark that exposes architecture-dependent performance under extreme class imbalance.

04.
arXiv (quant-ph) 2026-06-16

REGRID-QAOA: A Resource-Efficient Graph-Reduced Hybrid QAOA Framework for Physics-Constrained Power System Islanding

arXiv:2606.15083v1 Announce Type: new Abstract: Quantum computing has rapidly emerged as a powerful paradigm for tackling computationally demanding problems. In particular, quantum optimization shows strong promise for hard combinatorial problems in power systems, where increasing distributed energy penetration heightens the need for intentional islanding to maintain grid reliability and resilience. However, power system islanding is an NP-hard combinatorial optimization problem that becomes computationally prohibitive for classical solvers as network size grows, motivating the use of quantum computing as a promising alternative pipeline. This study develops a resource-efficient hybrid QAOA islanding framework that brings physics-constrained power-system partitioning into the quantum optimization workflow. The framework combines coherency-informed graph reduction, physics-aware constraint modeling, and structured post-processing to efficiently convert shallow-circuit QAOA samples into high-quality feasible islanding decisions without deep circuits or large shot budgets. The proposed framework is validated on the standard IEEE benchmark systems (9-, 14-, 24-, 30-, 39-, and 57-bus), demonstrating that the hybrid workflow achieves Gurobi-optimal solution quality with a clear quantum resource advantage over vanilla QAOA, while the resulting islanding solutions satisfy all physical feasibility requirements after network separation. This study establishes QAOA-based islanding as a viable quantum approach for critical infrastructure, with structured post-processing as the key enabler of quantum resource efficiency.

05.
arXiv (CS.CV) 2026-06-24

Revealing Training Data Exposure in Vision Language Large Models via Parameter Gradients

Vision-Language Large Models (VLLMs) trained on massive crawled corpora raise pressing copyright and data-provenance concerns. These concerns are particularly acute in healthcare, where patient medical images paired with clinical reports demand rigorous privacy safeguards. However, existing training data detection methods either fail in cross-modal scenarios or rely on superficial output signals with insufficient discriminative power. We introduce GradAudit, a gradient-based auditing framework that examines internal optimization dynamics rather than treating VLLMs as black boxes. Our approach builds on a key observation: model parameters converge to regions where gradients on training samples become stable and well-aligned, whereas gradients on non-training samples remain noisy and inconsistent. By analyzing these gradient signatures, GradAudit achieves strong separability and detects genuine image-text associations learned during training, not merely individual modality membership. Empirically, across both medical and general-domain datasets, GradAudit substantially outperforms state-of-the-art baselines in both pretraining and fine-tuning VLLMs. In a case study employing copyrighted content, we show that existing training data detection methods not only underestimate the extent of unauthorized data usage, but that this underestimation becomes more pronounced as models become more recent and more advanced.

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

Linear-Time Encodable and Decodable Quantum Error-Correcting Codes

arXiv:2603.04543v2 Announce Type: replace Abstract: Recent years have seen rapid development in the subject of quantum coding theory, with breakthroughs on many exciting classes of codes, including quantum LDPC codes, quantum locally testable codes, and quantum codes with interesting transversal gates. However, a natural class of quantum codes, which has been well-studied classically, has not yet been treated: those which can be quickly encoded and decoded. This problem concerns the channel capacity setting, where a noise channel sits between perfect encoding and unencoding/decoding operations; this is the setting that is relevant for communication between fault-tolerant quantum computers. In this work, we construct asymptotically good quantum codes that can be encoded and unencoded by quantum circuits of logarithmic depth and consisting of a linear total number of gates. The classical decoding algorithms also run in logarithmic depth and use $\mathcal{O}(n \log n)$ gates, or alternatively a linear number of gates but with higher depth. We further construct explicit and asymptotically good quantum codes whose encoding, unencoding and decoding all use a linear number of gates, and additionally whose encoding and unencoding may be run in logarithmic depth.

07.
arXiv (CS.AI) 2026-06-24

Maestro Order: A Model-Agnostic Orchestration Harness

Authors:

arXiv:2606.23983v1 Announce Type: cross Abstract: A single forward pass of a capable model is a fast, fluent, and unreliable problem-solver: it is right often enough to be useful and wrong often enough to be dangerous; in language models, such confident errors are known as hallucinations. We present Maestro Order, a model-agnostic orchestration harness that turns unreliable solvers into reliable problem-solving systems by composing them according to four structural primitives (decompose, ensemble, verify, and recurse) and a budget-aware controller that decides where to spend compute. The harness treats any model as a black-box base solver behind a uniform interface, layers a verifier ensemble whose discrimination is measured online, and allocates verification and voting to the stages with the highest marginal reliability per unit cost. We give the architecture, the message and state schema, the controller algorithm, and the engineering that makes it deterministic, observable, and fault-tolerant. We then specify an evaluation methodology (reliability at fixed cost, coverage, calibration, and ablations) and report results from a faithful Monte Carlo simulation of the harness over a parameterized solver/verifier model. The simulation reproduces the predicted laws quantitatively: verification amplifies reliability geometrically (e.g. $0.55\to0.98$ with two gates, $\to0.999$ with four), voting helps only above chance and is limited by shared errors, and a budget-aware controller reaches a target reliability at a small fraction of the cost of voting alone by selecting the cheapest mechanism for each regime. We close with failure modes (verifier gaming, correlated errors, and decomposition error compounding) and concrete guidance: build robust checkers, diversify solvers, and let the controller put compute where the information is.

08.
arXiv (quant-ph) 2026-06-16

Excited-State Quantum Chemistry on Qumode-Based Processors via Variational Quantum Deflation

arXiv:2604.13457v3 Announce Type: replace Abstract: Variational quantum algorithms on bosonic quantum processors are an emerging paradigm for quantum chemistry calculations, exploiting the natural alignment between molecular structure and harmonic oscillator-based hardware. We introduce the qumode-based variational quantum deflation framework (QumVQD) for finding both electronic and vibrational excited state energies on qumode-based architectures. We validate the approach through electronic structure calculations on H$_{2}$ and linear H$_{4}$, where we introduce Hamming-weight filtering of the Fock basis to enforce particle number conservation and eliminate spurious eigenstates by reducing the required Hilbert space, which reduces the required number of qumodes in turn. We achieve agreement with full configuration interaction (FCI) using the STO-3G basis set within the chemical accuracy threshold at most points along the potential energy surfaces. Extending to the vibrational structure, we combine QumVQD with an existing Hamiltonian fragmentation approach based on Cartan subalgebra, allowing us to compute the vibrational eigenenergies of CO$_{2}$ and H$_{2}$S to spectroscopic accuracy with per-fragment circuits that scale as $O(N)$ in single-qumode gates and $O(N^2)$ in beam-splitter gates for $N$ qumodes. For the case of CO$_{2}$, we get total gate counts more than an order of magnitude smaller than those reported for qubit-based vibrational algorithms at this system size. These results demonstrate that bosonic quantum devices are a viable platform for excited-state quantum chemistry, particularly for vibrational problems where qubit-based methods incur substantial boson-to-qubit mapping overhead.

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

Flex4DHuman: Flexible Multi-view Video Diffusion for 4D Human Reconstruction

We present Flex4DHuman, a multi-view video diffusion model that transforms a monocular or sparse multi-view video of a dynamic subject into synchronized dense multi-view videos using only relative camera-pose conditioning. Unlike prior human-centric methods that rely on skeletons, depth maps, normals, or rendered target-view geometry, Flex4DHuman requires no explicit geometry priors and instead conditions generation through relative camera-pose positional encoding. The generated videos can be directly ingested by downstream reconstruction pipelines to create dynamic 4D Gaussian splats. Built on the Wan 2.1 1.3B text-to-video model, Flex4DHuman preserves the backbone architecture and encodes camera and view information through a five-axis positional encoding that extends spatio-temporal RoPE with view indices and continuous SE(3) relative camera geometry. A three-stage curriculum progressively trains the model for pose following, flexible reference-to-target view generation, and temporal rollout. To support temporal rollout, we train with clean historical target-view tokens. We also add multi-view captions to enable test-time text control. Combined with an off-the-shelf 4D Gaussian Splatting stage, our framework lifts monocular static-camera videos into dynamic 4D Gaussian splats. Experiments on DNA-Rendering and ActorsHQ show that Flex4DHuman surpasses prior state-of-the-art methods, while the same formulation generalizes to animal categories after mixed human-animal training. These capabilities make Flex4DHuman a practical step toward scalable 4D content creation from casual monocular videos for simulation, gaming, AR/VR, and video re-shooting.

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

LADBench: A Benchmark for Logical Fault Detection in Images

Large Vision Language Models (VLMs) excel at visual question answering and semantic grounding, but their capacity for autonomous logical reasoning remains underexplored. Existing anomaly benchmarks emphasize visual errors or direct prompting rather than the physical and social common sense needed for open-world deployment. To address this, we introduce LAD-bench, a benchmark of more than 1,000 curated synthetic images with logical anomalies across four domains: Residential, Urban, Collaborative, and Nature. We further propose a Tiered Prompting Protocol based on progressive disclosure, which measures how much explicit assistance a model needs to localize and reason about a logical fault. Evaluating leading foundation models reveals substantial weaknesses: even the best achieves only 70.11% overall accuracy, showing that implicit logical fault detection remains unsolved. Crucially, models often fail to identify anomalies even after receiving explicit hints in deeper tiers. By surfacing these limitations in sequential multimodal reasoning, LAD-Bench offers a rigorous framework for advancing the safety, reliability, and cognitive alignment of autonomous visual systems. Dataset and Code: https://huggingface.co/datasets/SahasraK/LADBench

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

Prague Dependency Treebank – Consolidated 2.0: Enriching a Complex Annotation Scheme

The Prague Dependency Treebank framework is unique in its attempt to systematically include and link different layers of language, including a meaning representation with several types of inter-sentential phenomena, especially coreference and discourse relations. We present its second consolidated version (PDT-C 2.0), which concludes almost 30-years long project of sustained development of the resource to a uniformly and coherently annotated, genre-diversified, almost 4 million token language resource of Czech language, with accompanying fully compatible lexicons. In addition to continuous linguistic research, the richly linguistically annotated corpus is also widely used in international comparisons of the development of traditional and novel NLP tools as well as in conversions into other formalisms. The corpus and the trained parsers are available under the CC BY-NC-SA licence.

12.
bioRxiv (Bioinfo) 2026-06-16

FlowBench: separating planning, fault recovery and interpretation in agentic bioinformatics

Agentic large language model (LLM) systems are being deployed in bioinformatics faster than they are understood, and single-metric evaluations conflate capabilities that fail independently. We introduce FlowBench, a benchmark that decomposes agentic bioinformatics performance into planning, fault recovery, biological interpretation, and end-to-end output-fidelity. Existing systems achieve high plan completeness, but their closed, single-provider designs prevent attribution of performance to scaffolding versus the underlying model. We therefore built FlowAgent, a modular, provider-agnostic framework whose components can be selectively disabled and whose backbone model can be swapped across providers on a shared harness, and used it to evaluate 23 models from three main providers. Three findings emerge. First, generating a valid workflow plan from a named toolchain is largely solved, whereas inferring an appropriate toolchain from biological intent alone is uniformly difficult regardless of model tier, compressing all models into a narrow 44-57% pass-rate band. Second, ablation shows that the dependency-structured plan and a completeness-reflection step drive performance, while adding a same-context validator-driven retry makes structural quality worse. Third, fault recovery and data-grounded interpretation remain unsolved. Models frequently propose fixes that force a clean exit while leaving the underlying data invalid, and data-grounded interpretation lags internal-knowledge recall by a consistent margin. Safety does not emerge from capability, and reasoning-tier models were among the least reliable at recognising unrecoverable faults. Once planning saturates, agent architecture and refusal calibration, not model scale, are the productive frontier.

13.
arXiv (CS.CL) 2026-06-15

WorkBench Revisited: Workplace Agents Two Years On

Authors:

The best agent on WorkBench in March 2024, GPT-4, completed 43% of tasks and took an unintended harmful action, such as emailing the wrong person, on 26% of them. We re-visit the benchmark in June 2026 and find that the best agent to date, Claude Opus 4.8, completes 89% and takes an unintended harmful action on 2.5%. Aside from this considerable progress in frontier agent performance, three things stand out. First, capability and safety go together on WorkBench rather than trade off, so the models that finish the most tasks also do the least unintended damage. Second, while several classes of error have been totally eliminated, frontier models still make some basic mistakes that occasionally result in irreversible harm, such as sending an email to the wrong person. Third, the rise of open-weight models has drastically lowered costs for a performance level that was previously only accessible to proprietary models, while frontier costs have stayed relatively stable. We release an updated version of the benchmark with data and code quality improvements, new model scores, and analysis of agent progress on WorkBench since 2024.

14.
PLOS Computational Biology 2026-06-22

A lactylation- and autophagy-associated prognostic signature reveals LSEC-derived CLEC3B as a novel mediator of hepatocellular carcinoma suppression

Authors:

by Youai Song, Yinkuan Ning, Meihui Li, Jianwei Lan, Liangchen Lei, Yufei Han, Zhuo Meng, Binjie Li, Pengpeng Liu, Quanyan Liu The crosstalk between lactylation and autophagy within the hepatocellular carcinoma (HCC) microenvironment is a burgeoning field with profound implications. By integrating multi-omics data from public cohorts, we delineated two molecular subtypes of HCC with divergent clinical outcomes and established a lactylation-autophagy-related prognostic signature. This signature highlighted CLEC3B as a pivotal gene. Subsequent single-cell RNA sequencing and experimental validation unequivocally pinpointed liver sinusoidal endothelial cells (LSECs) as the principal cellular source of CLEC3B, which was significantly downregulated in HCC tissues. Functionally, conditioned media derived from CLEC3B-overexpressing LSECs potently inhibited HCC cell proliferation. Mechanistic investigations revealed that this tumor-suppressive effect was orchestrated through the concurrent suppression of autophagy and diminution of lactylation levels. Our findings position LSEC-secreted CLEC3B as a novel metabolic mediator in HCC, bridging two key pathways in tumor suppression, and endorse its clinical value both as a prognostic indicator and a promising therapeutic target.

15.
arXiv (quant-ph) 2026-06-19

Optimized Quantum States for Sensing in the Presence of Loss and Phase Noise

arXiv:2606.19649v1 Announce Type: new Abstract: Squeezed vacuum lets gravitational-wave detectors and other quantum sensors surpass the standard quantum limit, and is optimal in the loss-limited regime; phase noise breaks this optimality. Numerically optimizing the quantum Fisher information across the loss and phase-noise landscape, we identify non-Gaussian states that outperform any Gaussian state. These fall into three classes: Fock-like, cubic-phase-like, and states with discrete rotational symmetry. Limiting the average number of photons in the input state to $\bar{n}=5$, with $1-\eta = 5\%$ photon loss and 200 mrad phase noise, the non-Gaussian advantage reaches up to 2.2 dB. Furthermore, we observe that the non-Gaussian advantage can persist even when the measurement strategy is homodyne detection.

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

From Spectral Singularities to Multipartite Entanglement Scaling at Higher-Order Exceptional Points

arXiv:2606.24205v1 Announce Type: new Abstract: Exceptional points (EPs) are non-Hermitian spectral singularities exhibiting fractional-power responses, yet their implications for multipartite entanglement of interacting quantum many-body systems remain largely unexplored. Here we develop a general framework that links higher-order non-Hermitian degeneracies to the scaling behavior of genuine multipartite entanglement in interacting identical-qubit systems. Permutation symmetry of the identical qubits decomposes the exponentially large Hilbert space into independent irreducible-representation sectors, thereby constraining the maximal EP order of $N$ qubits to $N+1$ rather than $2^N$. Near an $n$th-order EP, genuine multipartite entanglement inherits the spectral response and generically exhibits a fractional-power scaling under weak perturbations. Explicit examples show that conventional two-body interactions support third- and fourth-order EPs with the corresponding entanglement responses, whereas higher-order EPs with genuine multipartite-entangled coalesced states require additional independent interaction channels, such as three-body interactions. Our results establish a fundamental connection among non-Hermitian degeneracies, multipartite entanglement, and symmetry, extending higher-order EP physics from spectral singularities to genuine many-body quantum correlations.

17.
arXiv (CS.CV) 2026-06-16

Structural Energy Guidance for View-Consistent Text-to-3D Generation

Text-to-3D generation based on diffusion models often suffers from the Janus problem, leading to inconsistent geometry across viewpoints. This work identifies viewpoint bias in 2D diffusion priors as the main cause and proposes Structural Energy-Guided Sampling (SEGS), a training-free and plug-and-play framework to improve multi-view consistency. SEGS constructs a structural energy in the PCA subspace of U-Net features and injects its gradient into the denoising process. It can be easily integrated into SDS/VSD pipelines without retraining. Experiments show that SEGS reduces the Janus Rate by about 10% on average and improves View-CS scores across multiple baselines, including DreamFusion, Magic3D, and LucidDreamer. This method effectively alleviates viewpoint artifacts while preserving appearance fidelity, providing a flexible solution for high-quality text-to-3D content generation.

18.
arXiv (quant-ph) 2026-06-11

Entanglement generation between field modes mediated by a fluctuating conducting wall

arXiv:2606.12338v1 Announce Type: cross Abstract: We consider a movable conducting plate of finite mass, between two fixed ones, whose mechanical degrees of freedom are treated quantum-mechanically and bound to its equilibrium position by a harmonic potential. The movable wall is thus subjected to quantum fluctuations of its position. This creates a system of two sub-cavities separated by the movable fluctuating plate, and two massless one-dimensional scalar fields, one in each sub-cavity. This system is described by an appropriate generalization of the Law Hamiltonian. The presence of the movable wall yields an effective plate-fields interaction, as well as an effective interaction between the field modes. We obtain, at the second order in perturbation theory, the ground state of the interacting system and the reduced density operator of the fields in each sub-cavity by tracing out the wall's degrees of freedom. We calculate the entanglement between two field modes, one in each cavity, by evaluating analytically the negativity; we then evaluate numerically also the total multimode negativity. Our results show that in both cases the fields in the two sub-cavities are entangled, in contrast to the case in which the wall is fixed in space. We discuss the amount of the field entanglement present as a function of relevant physical parameters of the system such as the mass and oscillation frequency of the movable wall, its distance from the fixed walls and the frequencies of the field modes considered.

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

Promise and challenges of heart chamber segmentation from non-contrast CT scans using contrastive unpaired image translation: a feasibility study

arXiv:2606.23879v1 Announce Type: cross Abstract: Purpose: To evaluate the feasibility and challenges of heart chamber segmentation from non-contrast CT scans using contrastive unpaired image translation and deep learning-based segmentation. Approach: We developed ChameleonNet, a framework utilizing the Contrastive Unpaired Translation (CUT) network with decoupled contrastive learning (DCL) loss to synthesize non-contrast CT from contrast CT scans. Using annotations of four heart chambers (left atrium (LA), left ventricle (LV), right atrium (RA), and right ventricle (RV)) from contrast scans, we trained a Hausdorff distance loss-enhanced nnU-Net on synthesized non-contrast images. The translation model was trained with 35,538 contrast-enhanced and 37,197 non-contrast CT slices. The segmentation model was trained with 292 synthesized non-contrast scans. Performance was evaluated using Dice similarity coefficient (DSC) and 95th Hausdorff distance (HD95) on 36 synthesized non-contrast scans, and volume agreement on 36 real non-contrast CT scans was assessed using Pearson correlation, mean absolute percentage error (MAPE), and mean percentage error (MPE). Results: The segmentation model achieved DSC of 0.94 (0.01), 0.91 (0.04), 0.92 (0.03), 0.93 (0.02), and HD95 of 3.63 (1.49), 5.74 (4.08), 5.18 (1.77), 5.51 (3.21) mm on synthesized non-contrast images for LA, LV, RA, and RV, respectively. On real non-contrast CT scans, Pearson correlations were 0.93, 0.82, 0.87, and 0.89 (all p

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

Discovery and inference beyond linearity for epidemiological data by integrating Bayesian regression, tree ensembles and Shapley values

arXiv:2505.00571v3 Announce Type: replace-cross Abstract: Machine Learning (ML) is gaining popularity in epidemiology and healthcare studies for hypothesis-free discovery of risk and protective factors. ML is strong at discovering nonlinearities and interactions, but this power is compromised by a lack of reliable inference. Although Shapley values provide local measures of features' effects, valid uncertainty quantification for these effects is typically lacking, thus precluding statistical inference. We propose RuleSHAP, a framework that addresses this limitation by combining a dedicated Bayesian sparse regression model with an improved tree-based rule generator and Shapley value attribution. RuleSHAP provides detection of nonlinear and interaction effects, with uncertainty quantification at the individual level as a key contribution. We derive an efficient formula for computing marginal Shapley values within this framework. We apply RuleSHAP to data from an epidemiological cohort to detect and infer several effects for high cholesterol and blood pressure, such as nonlinear interaction effects between features like age, sex, ethnicity, BMI and glucose level. To conclude, we demonstrate the validity of our framework on simulated data.

21.
PLOS Computational Biology 2026-06-17

Machine learning-driven identification of virulence determinants in <i>Borrelia burgdorferi</i> associated with human dissemination

by Hoa Thanh Nguyen, Catherine A. Brissette Lyme disease, the most common tick-borne infectious disease in the United States, presents with highly variable clinical outcomes, ranging from localized erythema migrans to severe disseminated complications affecting the heart, joints, and nervous system. The bacterial determinants underlying this phenotypic variation remain largely unknown, limiting our ability to predict disease progression and optimize treatment strategies. Here, we applied machine learning (ML) approaches to identify specific amino acid residues within surface-exposed virulence factors that predict human dissemination phenotypes. Utilizing the published whole genome sequences from 299 clinical Borrelia burgdorferi isolates collected from the United States and Slovenia over a 30-year period (1992–2021), we extracted and characterized translated amino acid sequences (variants) of seven known virulence factors (BB_0406, BBK32, DbpA, OspA, OspC, P66, and RevA). Protein variants were classified based on their association with disseminated versus localized infections using clinical metadata. Cramér’s V analysis revealed possible strong associations between dissemination phenotypes and five adhesins: BBK32, DbpA, OspC, P66, and RevA. We developed ML models using five algorithms with multiple feature selection strategies, achieving robust predictive performance for DbpA, OspC, and RevA variants (all performance metrics > 0.7). Feature importance analysis identified 57, 29, and 42 key predictive residues for DbpA, OspC, and RevA, respectively. Notably, B-cell epitope prediction revealed significant enrichment of ML-identified residues within predicted epitope regions for OspC (11 overlapping residues, OR = 3.57, p = 0.006) and RevA (12 overlapping residues, OR = 2.37, p = 0.048), suggesting these residues may influence immune recognition and bacterial persistence. This study establishes the first computational framework linking Borrelia protein sequence variants to clinical dissemination phenotypes, providing molecular insights into Lyme disease pathogenesis that may inform the development of improved diagnostics and therapeutic targets.

22.
arXiv (CS.CL) 2026-06-17

When English Isn't the Best Teacher: Source Language Effects in Cross-Lingual In-Context Learning

Cross-lingual transfer in multilingual NLP has been widely explored in supervised fine-tuning contexts, where factors like data availability and linguistic similarity largely determine transfer quality. As the field shifts toward few-shot In-Context Learning (ICL), it is often presumed that insights from fine-tuning carry over unchanged. Yet this assumption has not been rigorously evaluated, leaving open the question of how to choose source languages for cross-lingual ICL. We conduct a broad empirical study of cross-lingual transfer in ICL spanning seven tasks, six models, and a typologically diverse set of languages. We further analyze language confusion, a key obstacle for generative tasks in cross-lingual ICL. Our results show that conventional fine-tuning-based expectations do not consistently apply in the ICL regime and point to alternative heuristics for selecting source languages effectively.

23.
arXiv (CS.CL) 2026-06-19

Analyzing Error Propagation in Korean Spoken QA with ASR-LLM Cascades

We analyze how automatic speech recognition (ASR) errors propagate through ASR-LLM cascades in Korean spoken question answering (SQA), focusing on downstream semantic failures that conventional ASR metrics cannot fully capture. Our analysis shows that the relative downstream degradation caused by ASR errors is consistent across LLMs with different absolute performance, suggesting that cascade degradation largely tracks ASR-stage information loss. We further identify single-character Korean ASR errors as a Korean-specific loss channel, where even a minimal transcription difference can change the intended question and degrade downstream QA performance. Finally, an auxiliary comparison shows that a large audio language model outperforms an ASR-LLM cascade with an approximately matched language backbone in noisy Korean SQA, indicating the potential of direct audio input to mitigate transcript-induced information loss.

24.
arXiv (CS.AI) 2026-06-25

Specifying AI-SDLC Processes: A Protocol Language for Human-Agent Boundaries

Authors:

arXiv:2606.20615v2 Announce Type: replace Abstract: AI agents now participate as first-class team members across the software development lifecycle, yet no specification language exists for expressing the human-agent responsibility boundaries, approval gates, and governance constraints this collaboration requires. Existing approaches encode process in agent prompts (subject to drift), target adjacent domains (workflow management, business processes), or address only fragments (access control, approval gates). We propose a domain-specific language for specifying AI-SDLC processes as protocols, with formal syntax, well-formedness conditions, operational semantics, and enforcement invariants. The language distinguishes policy (declared intent) from mechanism (structural enforcement), enabling implementations to bound process non-determinism through primitives such as validation tokens and capability boundaries. Three results follow. A failure rate analysis shows that structural enforcement bounds system failure rates at a weighted product of agent and validator rates, while behavioral compliance permits cumulative or near-saturating growth. The 2+N team pattern (two human-in-control roles plus N specialized agent members) formalizes classical Separation of Duties for AI-SDLC. Kleene closure of orchestration loops and reflexive protocol-adherence validation emerge as design properties rather than special-case constructs. We position the contribution against multi-agent frameworks (MetaGPT), workflow specification (FlowAgent, BPMN extensions), and capability-based security (SAGA): the novelty lies in the specific integration, not any single primitive. A working implementation demonstrates feasibility; empirical evaluation is future work.

25.
bioRxiv (Bioinfo) 2026-06-24

Systematic benchmarking of multi-modal approaches for tumor-naive ctDNA detection and quantification

Longitudinal monitoring of circulating tumor DNA (ctDNA) has emerged as a promising framework for characterizing treatment response dynamics in cancer. Scalable tumor-naive approaches for quantifying ctDNA often involve whole-genome sequencing (WGS) or DNA methylation profiling, but their comparative performance and capacity for complementary integration remain poorly understood. Here we systematically benchmarked tumor-naive WGS- and methylation-based ctDNA quantification methods using plasma from 150 patients with colorectal, lung and breast cancer. Using paired high-depth WGS and EM-seq data, we generated 40,000 in silico samples and evaluated detection accuracy, limits of detection (LoD) and quantification (LoQ) across cancer types and sequencing depths (0.1x-30x). We further assessed single- and multimodal method combinations, identifying conditions under which integrated approaches enhance analytical performance for detection and quantification relative to single modalities. This benchmark delineates key performance trade-offs and provides a practical framework to support method development and guide future research applications in ctDNA-based biomarker studies.