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01.
arXiv (CS.CV) 2026-06-16

DeepMine-Mamba: Mitigating Information Dilution in Mamba-Based State Space Models for Document Image Binarization

Document image binarization aims to separate foreground text from degraded backgrounds while preserving thin, broken, and low-contrast strokes. Although deep learning methods have improved binarization performance, most existing approaches rely on convolutional, transformer-based, or generative architectures, while Mamba-based state space models remain largely unexplored for this task. In this work, we investigate Mamba-based feature propagation and observe that direct state-space propagation may dilute weak foreground cues during long-range modeling, especially faint ink traces, fragmented characters, and boundary-sensitive stroke details. To address this problem, we propose DeepMine-Mamba, a Mamba-based binarization framework equipped with a novel Anti-Dilution Gate that estimates propagation-induced feature changes and selectively restores stroke-sensitive local responses while suppressing unnecessary background enhancement. Experiments on DIBCO/H-DIBCO benchmarks under a strict leave-one-year-out protocol show that DeepMine-Mamba achieves competitive overall performance, with strong average FM and Fps across benchmark years. Ablation results further show that the Anti-Dilution Gate is the key component for mitigating propagation-induced foreground dilution and improving stroke preservation.

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

ASTER: Latent Pseudo-Anomaly Generation for Unsupervised Time-Series Anomaly Detection

Time-series anomaly detection (TSAD) is critical in domains such as industrial monitoring, healthcare, and cybersecurity, but it remains challenging due to rare and heterogeneous anomalies and the scarcity of labelled data. This scarcity makes unsupervised approaches predominant, yet existing methods often rely on reconstruction or forecasting, which struggle with complex data, or on embedding-based approaches that require domain-specific anomaly synthesis and fixed distance metrics. We propose ASTER, a framework that generates pseudo-anomalies directly in the latent space, avoiding handcrafted anomaly injections and the need for domain expertise. A latent-space decoder produces tailored pseudo-anomalies to train a Transformer-based anomaly classifier, while a pre-trained LLM enriches the temporal and contextual representations of this space. Experiments on three benchmark datasets show that ASTER achieves state-of-the-art performance and sets a new standard for LLM-based TSAD.

03.
Nature (Science) 2026-06-08

Targeting Cancer-Specific Mutations with RNA-Triggered Chromatin Shredding

Authors:

Genetic mutations that drive cancer often occur in tumor suppressor proteins, including the p53 transcription factor which is altered in ~40-50% of cases1,2. However, current therapies fail to target most such mutations because the mutant proteins typically lack defined drug-binding pockets, and restoring the endogenous function has proven challenging. Here, we programmed CRISPR-Cas12a2, an RNA-guided nuclease with trans-nucleolytic cleavage activities3,4, to selectively kill cancer cells by targeting cancer-specific transcripts. This approach limits cell growth by inducing trans shredding of chromatin, triggering DNA damage responses and cell death. Unlike existing methods, RNA-guided Cas12a2 senses cellular RNA signatures, enabling precise targeting of undruggable mutations. Transcript-activated chromatin shredding provides a new approach to precision disease treatments for undruggable targets.

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

Elastic Queries Reinforcement Learning: Self-Aware Policy Execution for VLA Models

arXiv:2606.14375v1 Announce Type: cross Abstract: Vision-language-action (VLA) models are powerful action generators for robot manipulation, but they are typically executed with fixed inference and replanning schedules. This rigidity ignores the uneven difficulty of robot control: contact-rich or uncertain states may need more computation and fresher feedback, while easier states can often be handled with fewer inference steps and longer open-loop execution. We propose Elastic Queries Reinforcement Learning (EQRL), a framework that makes each VLA policy query elastic. A lightweight latent-schedule adaptor jointly selects the latent input, denoising budget, and action chunk length, without fine-tuning the underlying VLA model. To make scheduling difficulty-aware, EQRL trains a critic over the joint latent-schedule action and derives a state difficulty signal from critic ensemble disagreement. This signal guides compute toward difficult states, while a learned residual allows task-driven correction. We formulate variable chunk execution as query-level macro-action RL with chunk-dependent discounting and an amortized number-of-function-evaluations (NFE) budget. Across simulation and real-robot manipulation, EQRL reduces amortized inference cost while preserving or improving task success.

05.
arXiv (CS.CL) 2026-06-15

Succeeding at Scale: Enterprise Retrieval Benchmark Construction and Index-Preserving Query Adaptation for Multi-Tenant Search

Large-scale multi-tenant retrieval systems generate extensive query logs but lack curated relevance labels for effective domain adaptation, resulting in substantial underutilized "dark data." This challenge is compounded by the high cost of model updates, as jointly fine-tuning query and document encoders requires full corpus re-indexing, which is impractical in multi-tenant settings with thousands of isolated indices. We introduce DevRev-Search, a passage retrieval benchmark for technical customer support built via a fully automated pipeline. Candidate generation uses fusion across diverse sparse and dense retrievers, followed by an LLM-as-a-Judge for consistency filtering and relevance labeling. We further study and systematically evaluate index-preserving query-only adaptation strategies that fine-tune only the query-encoder while keeping the document indices fixed. Experiments on DevRev-Search, SciFact, and FiQA-2018 show that parameter-efficient fine-tuning of the query encoder delivers a remarkable quality-efficiency trade-off, enabling scalable and practical enterprise multi-tenant retrieval.

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

Robust and Interpretable Adaptation of Equivariant Materials Foundation Models via Sparsity-promoting Fine-tuning

arXiv:2606.18691v1 Announce Type: new Abstract: Pre-trained materials foundation models, or machine learning interatomic potentials, leverage general physicochemical knowledge to effectively approximate potential energy surfaces. However, they often require domain-specific calibration due to physicochemical diversity as well as mismatches between practical computational settings and those used in constructing the pre-training data. To address this, we propose a sparsity-promoting fine-tuning method that selectively updates model parameters by exploiting the structural properties of E(3)-equivariant materials foundation models. On energy and force prediction tasks across molecular and crystalline benchmarks, our method matches or surpasses full fine-tuning and equivariant low-rank adaptation while updating only $\sim$3~\% of parameters, and in some cases as little as $\sim$0.5~\%. Beyond energy and force calibration, we further demonstrate task generalizability by applying our method to magnetic moment prediction and magnetism-aware total energy modeling. Finally, analysis of sparsity patterns reveals physically interpretable signatures, such as enhanced $d$-orbital contributions in transition metal systems. Overall, our results establish sparsity-promoting fine-tuning as a flexible and interpretable method for domain specialization of equivariant materials foundation models.

07.
arXiv (CS.AI) 2026-06-16

SCAN: A Decision-Making Framework for Effective Task Allocation with Generative AI

arXiv:2606.15601v1 Announce Type: cross Abstract: We introduce SCAN – a human-centric decision-making framework to facilitate learners for effective task allocation with Generative Artificial Intelligence (GenAI) based on Vygotsky's Zone of Proximal Development and Metacognition. In SCAN, we systematize and formalize AI-human interaction by introducing a task-identification approach with four "sub-zones": Substitute, Complement, Aid, and Non-negotiable. After describing the four sub-zones, we demonstrate how SCAN framework can be applied for knowledge workers in the workplace and students in education to metacognitively "scan" their use of Generative AI. We then discuss how such framework can be related to cognitive load theory, cognitive offloading, sycophancy, three decision-making modes in human-AI interactions (automation, augmentation, and collaboration), future of work such as upskilling and deskilling, and how it accounts for both human-human and human-AI learning. We propose that SCAN offers a great starting point before discussing whether GenAI complements or replaces our abilities when completing a task, with a general objective of sustaining lifelong learning, and a specific goal of reaching hybrid intelligence.

08.
bioRxiv (Bioinfo) 2026-06-17

In silico characterization of lysis and host-recognition modules in Staphylococcus aureus bacteriophage genomes

Background/aim: Antimicrobial resistance in methicillin-resistant Staphylococcus aureus (MRSA) requires precision non-antibiotic therapeutics, yet phage lytic efficacy is poorly predicted by phenotypic assays, as shown by paradoxical biofilm responses. This study characterized the genomic architecture of lytic S. aureus bacteriophages, focusing on the conservation of the lysis module and the variability of host-recognition modules, to provide a rational basis for phage candidate selection. Materials and methods: Twenty-two complete S. aureus phage genomes were retrieved from NCBI GenBank. Genomic features were extracted with custom Biopython scripts. Lysis (endolysin, holin) and host-recognition (tail fiber/receptor-binding protein) modules were annotated and validated by InterPro domain analysis, with disrupted endolysins resolved by tBLASTn. Phylogeny was reconstructed from large terminase subunit (TerL) sequences using maximum likelihood. Results: Genome size spanned three classes, from 17.5 to 148.6 kb. The LysK-type endolysin (CHAP, Amidase, SH3b) was highly conserved, whereas tail fiber/RBP genes were detected in only 14 of 22 phages. Domain analysis reclassified two proteins annotated as endolysins as virion-associated peptidoglycan hydrolases, and identified two independent mechanisms, HNH endonuclease insertion and intron splitting, that interrupt lysis-module genes and confound automated annotation. Maximum likelihood analysis recovered a strongly supported, highly conserved core clade with EW and SA13 as divergent lineages. Conclusion: Lysis modules are conserved whereas host-recognition modules are variable, indicating that host recognition rather than the lytic enzyme is the principal determinant of host range and the more rational target for phage selection and engineering.

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

InfoGeo: Information-Theoretic Object-Centric Learning for Cross-View Generalizable UAV Geo-Localization

Cross-view geo-localization (CVGL) is fundamental for precise localization and navigation in GPS-denied environments, aiming to match ground or UAV imagery with satellite views. Existing approaches often rely on global feature alignment, but they suffer from substantial domain shifts induced by varying regional textures and weather conditions. This issue becomes even more pronounced in UAV-based scenarios, where the broader perspective inevitably introduces dense, fine-grained objects, creating significant visual clutter. To address this, we draw inspiration from Object-Centric Learning (OCL) and propose InfoGeo, an information-theoretic framework designed to enhance robustness and generalization. InfoGeo reformulates the optimization as an information bottleneck process with two core objectives: (i) maximizing view-invariant information by aligning the object-centric structural relations across views, and (ii) minimizing view-specific noisy signals through cross-view knowledge constraints. Extensive evaluations across diverse benchmarks and challenging scenarios demonstrate that InfoGeo significantly outperforms state-of-the-art methods.

10.
Nature Medicine 2026-06-16

<b>Engineered heart muscle passes early clinical milestone</b>

Engineered heart muscle allografts derived from induced pluripotent stem cells show promising early outcomes in patients with treatment-refractory advanced heart failure with reduced left ventricular ejection fraction, in support of further clinical investigation. Engineered heart muscle allografts derived from induced pluripotent stem cells show promising early outcomes in patients with treatment-refractory advanced heart failure with reduced left ventricular ejection fraction, in support of further clinical investigation.

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

Learner-based Concept Drift Detection: Analysis and Evaluation

arXiv:2606.20216v1 Announce Type: cross Abstract: Machine learning algorithms deployed for evolving streaming environments must handle the non-stationary data distributions, commonly referred to as concept drift. The presence of concept drift poses a major challenge for many real-world applications because it can severely degrade their predictive performance, hindering their ability to support robust decision-making. Consequently, the timely and efficient detection of drift events is critical for sustaining high accuracy over time. This study examines theoretically the concept drift characteristics and numerous drift detection algorithms across several categories. Furthermore, we evaluate their performance on both synthetic and real-world datasets exhibiting diverse streaming scenarios and drift characteristics, such as abrupt and gradual changes. This study aims to enhance understanding of the complex notion of concept drift characteristics and behavior of drift detectors, along with their applicability to diverse contexts.

12.
medRxiv (Medicine) 2026-06-15

Filum Terminale Diameter on Routine Pediatric MRI: A Large-Cohort Clinical Reference in 3,406 Children and the Age-Dependent Meaning of the 2-mm Thickened-Filum Threshold

Background. A filum diameter >2 mm is the conventional MRI threshold for a thickened filum, but it derives from small, mostly adult series showing no age dependence; whether one cutoff suits all of childhood is untested. Objective. To build an age-specific filum-diameter reference on routine pediatric MRI and test, adjusting for image resolution, whether the 2-mm threshold is age-stationary. Materials and methods. In this retrospective study an nnU-Net tracer measured the maximal filum diameter on consecutive lumbosacral MRI; versus manual tracing it showed negligible bias but moderate single-measure agreement. After excluding report-confirmed fatty filum, lipoma, or tethered cord, the proportion >2 mm was analysed within one acquisition protocol and by logistic regression adjusting for voxel size and slice thickness. Results. Of 7,245 examinations, 3,869 (53%) were traceable; untraced ones were younger (median 0.75 vs 2.0 years). The presumed-normal cohort had median diameter 1.48 mm. At matched resolution, 2 mm marked the 94th percentile in infants (5.6% exceeded it) but the 83rd by 3-6 years (17.4%); the age effect persisted after adjusting for voxel size and slice thickness (3-6 years vs infants, adjusted OR 4.7; P < .001). Conclusion. Filum diameter clusters near 1.5 mm, and the fixed 2-mm cutoff flags ~5% of infants but ~17% of preschoolers. Caliber should be judged against an age-specific clinical reference, not one fixed cutoff; a thick filum is not itself a diagnosis of tethered cord.

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

Tyler: Typed Latent Reasoning for Language Models – When to Think, What to Compute, and How Much to Allocate

Chain-of-thought (CoT) prompting improves reasoning in large language models (LLMs) by externalizing intermediate computation as discrete text tokens, but this textual interface also introduces redundancy and inference overhead. Latent reasoning offers a promising alternative by carrying part of the computation in continuous representations. However, existing methods typically predefine when latent computation is invoked and how it is allocated during decoding, leaving a key problem unresolved: when to invoke latent computation, what type of computation to perform, and how much budget to allocate. We propose Typed Latent Reasoning (Tyler), a typed and budget-aware framework for latent reasoning during autoregressive decoding. Tyler learns a policy that, at each decoding step, chooses between emitting a text token and switching to a latent computation module specialized for a particular reasoning function. Once invoked, an operator maps the current reasoning state into latent tokens that support global planning, local state updates, or reusable procedural abstraction. Across extensive experiments on three backbone LLMs, Tyler improves accuracy by up to 14.49 points over CoT and by up to 4.30 points over the strongest competing baseline. It further generalizes across diverse reasoning domains and achieves the best final-stage performance with the lowest forgetting.

14.
arXiv (CS.LG) 2026-06-16

How to Score Experts for One-Shot MoE Expert Pruning: A Unified Formulation and Selection Principle

arXiv:2606.15716v1 Announce Type: new Abstract: Mixture-of-Experts (MoE) language models reduce per-token computation through sparse expert activation, yet deployment still requires storing the full expert pool, making one-shot expert pruning a practical approach for reducing memory usage. Although effective, existing criteria are largely heuristic, and no single criterion is universally optimal. Thus, establishing a principle for selecting pruning criteria suited to different deployment objectives remains an important yet largely underexplored problem in one-shot expert pruning. To this end, we introduce a unified formulation for one-shot MoE expert pruning organized around three factors: routing frequency, gate weighting, and activation strength. The formulation yields a criteria selection principle: task-agnostic pruning should favor routed-token-averaged, gate-free activation-based criteria, whereas task-specific pruning can benefit from retaining routing-frequency and gate-weight information. Beyond this principle, the formulation also provides a systematic view of existing heuristic criteria and gives rise to two new task-agnostic criteria, Mean Activation Norm (MAN) and Mean Squared Activation Norm (MSAN). Across four representative MoE models and 16 diverse benchmarks, MAN and MSAN are consistently strong in the task-agnostic setting, obtain the top-two average ranks, and improve average performance by up to 8.8 points over the strongest baseline.

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

Adaptive Nucleus Truncation for Long-Form Reasoning

arXiv:2606.13982v1 Announce Type: cross Abstract: Sampling plays an important role in long-form language-model reasoning. Over thousands of decoding steps, small changes in the candidate token set can compound into different reasoning trajectories, stability profiles, and final answers. Existing truncation methods such as top-$p$, min-$p$, and fixed top-$n\sigma$ sampling improve over unrestricted sampling, but they rely on fixed thresholds that cannot adapt to changes in entropy, task difficulty, training stage, or generation budget. We introduce Adaptive Nucleus Truncation Sampling (ANTS), which extends top-\(n\sigma\) sampling from a fixed decoding rule into an adaptive rollout-control mechanism for long-form generation. ANTS selects standardized neighborhoods around the maximum logit before temperature scaling, adapts the truncation width using an entropy-conditioned controller, and retains a no-truncation fallback arm to stabilize training when truncation becomes unsafe. On a 33B-total / 4B-active sparse Mixture-of-Experts reasoning model, ANTS improves average performance over percentage-based benchmarks by +1.9, +3.8, and +5.2 points at 8K, 16K, and 32K generation budgets, respectively. The strongest gains appear on instruction following and mathematical reasoning, with IFBench improving by more than 10 points at 32K and AIME 2025 improving by 7 points. Code generation reveals an important budget interaction. On Codeforces, ANTS trails the baseline at 8K, but reverses this gap and substantially improves ELO at 16K and 32K. These results suggest that sampler design should be treated not just as a decoding hyperparameter, but as part of how we stabilize and scale long-budget reasoning.

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

Diagnosing and Repairing Shape-Prior Shortcuts in Long-Range Single-Shot Fringe Projection Profilometry

arXiv:2606.17093v1 Announce Type: new Abstract: Learning-based single-shot fringe projection profilometry (FPP) has been studied mostly at close range. The long-range regime (standoff beyond 1 m) remains largely unaddressed: inverse-square intensity falloff lowers fringe signal-to-noise ratio and degrades physical ground truth, the single-shot problem is ill-posed because fringe-order information is absent from one image, and these architectures have not been studied mechanistically. We present a diagnose-repair-verify study using mechanistic interpretability (MI) and conformal uncertainty quantification (UQ) as convergent diagnostics: they agree on one physical failure locus, driving and verifying an architectural repair. On a photorealistic synthetic benchmark (15,600 fringe images, 50 objects at 1.5-2.1 m), a best UNet baseline reaches 14.54 mm object mean absolute error (MAE). Three probes (linear probing, Grad-CAM, flat-plane out-of-distribution test) converge: the baseline solves the task via object-boundary shape priors rather than fringe-phase decoding. We repair this with PhiCalNet, which outputs wrapped phase rather than depth and applies a fixed differentiable calibration layer mapping phase to depth, removing the shape-prior solution from the hypothesis space architecturally rather than by a loss penalty. A physics-informed loss that enforces the same physics as a soft penalty on a depth-regressing network yields no measurable gain, isolating the architecture as the operative factor. PhiCalNet reduces object MAE 3.3x to 4.46 mm; the residual is carried by 0.103% of pixels at the +/-pi wrap discontinuity. Pixel-wise conformal UQ confirms the diagnosis: rejecting the top 5% of object pixels by snapshot disagreement cuts PhiCalNet RMSE by 64% (20.6->7.4 mm) versus 3.5% for the baseline. MI and UQ converge on the same failure locus.

17.
arXiv (CS.LG) 2026-06-12

Towards Provably Fair Machine Learning: Bayesian Approaches For Consistent and Transparent Predictions

arXiv:2606.12615v1 Announce Type: new Abstract: ML classifiers deployed in high-stakes domains produce predictions whose quality varies systematically across subgroups. For granular subgroups defined by intersections of multiple features, predictions are often inconsistent with the observed data: the model's outputs contradict the evidence available for that subgroup. This problem is exacerbated by regularisation, which improves aggregate performance by collapsing small subgroups into larger groups, disproportionately affecting demographic minorities. We define two requirements for consistent prediction: determinism (identical individuals receive identical predictions) and statistical consistency (we cannot reject, at significance level alpha, the hypothesis that the predictions for a subgroup were drawn from the Bayesian optimal target distribution inferred for that subgroup). From these requirements we derive the Fair Bayesian classifier, which enforces both across every group and subgroup simultaneously and abstains whenever no consistent deterministic prediction is possible. On three benchmark datasets (Adult, COMPAS, and Bank Marketing), standard classifiers produce statistically inconsistent predictions for a substantial proportion of subgroups. Our classifier achieves zero consistency error by construction while exceeding baseline accuracy and multicalibration on every dataset tested. Statistical consistency provides a principled foundation for prediction quality with direct implications for algorithmic fairness. Minority demographics are disproportionately concentrated in small subgroups, precisely where frequentist inference is least reliable; addressing this inference problem is therefore a necessary step toward fair ML. By enforcing Bayesian consistency at the finest resolution the data supports, the our classifier demonstrates that exhaustive subgroup fairness with principled abstention is achievable in practice.

18.
medRxiv (Medicine) 2026-06-17

Investigating shared genetic overlap of immune-mediated inflammatory diseases and cardiometabolic diseases

Abstract Background: Immune-mediated inflammatory diseases (IMIDs) are associated with increased risk of cardiometabolic diseases. Investigating genetic overlap among these conditions can provide insights into their clinical management. Methods: Genetic correlation was assessed using linkage disequilibrium score regression (LDSC). Then, a meta-analysis was conducted using Association Analysis Based on SubSETs (ASSET) to pinpoint independent single nucleotide polymorphisms (SNPs) shared across the diseases. Each independent SNP was then used to define a genomic window (+/-500KB) for colocalisation analysis and Local Analysis of [co]Variant Association (LAVA) to offer multiple layers of regional pleiotropic evidence. Over-representation analysis was then run to identify enriched biological pathways, which then were used for drug target analysis. Results: The LDSC analysis showed a significant global genetic correlation for rheumatoid arthritis (RA) and cardiometabolic diseases including hypertension, coronary artery disease (CAD), heart failure (HF), stroke, atrial fibrillation (AF), and type two diabetes mellitus (T2DM) ranging from rg = 0.09 to 0.24. ASSET meta-analysis identified 164 independent SNPs shared across RA and the cardiometabolic diseases with P < 5 x 10- in the overall one-sided meta-analysis P-value, FDR < 0.05 in both individual GWASs, and TRUE phenotype matrix. Colocalisation analysis revealed multiple loci with strong evidence (Posterior probabilities [&ge;] 80) of single causal SNPs between the trait pairs. LAVA analysis was then used as an additional layer of confirmation for the findings generated by ASSET and colocalisation and thus several loci were highlighted. Over-representation analysis showed significant enriched immune-related pathways across RA-hypertension, RA-CAD, RA-AF, and RA-T2DM trait pairs. Drug target analysis highlighted several drugs which could be further tested for their effectiveness in RA and its common comorbidities. Conclusion: The findings revealed a shared genetic architecture and key immune-related biological pathways underlying RA and its associated cardiometabolic comorbidities. The identified genes and drugs provide opportunities for further therapeutic assessment which could improve clinical management strategies.

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

LedgerAgent: Structured State for Policy-Adherent Tool-Calling Agents

Policy-adherent tool-calling agents in customer-service domains must maintain task states across turns while calling tools and obeying domain policies. Task states consist of relevant facts, identifiers, constraints, and conditions observed through user interaction and tool calls. In standard agents, task states are not represented separately. Observations, tool returns, and policy instructions are placed in the prompt, leaving agents to reconstruct the relevant states from the prompt each time they decide what to do next. This design makes state management implicit, creating two common failure modes. An agent may retrieve the right facts but later ground its decision in stale, missing, or incorrect information; and a syntactically valid tool call may still violate a domain policy that depends on the current task state. We introduce \textsc{LedgerAgent}, an inference-time method for tool-calling agents that maintains observed task states in a separate ledger and renders the states into the prompt. The ledger is also used to check state-dependent policy constraints before environment-changing tool calls are executed, blocking policy violations. Across four customer-service domains and a mixed panel of open- and closed-weight models, \textsc{LedgerAgent} improves average pass\textasciicircum{}k over a standard prompt-based tool-calling approach, with the largest gains under stricter multi-trial consistency metrics.

20.
bioRxiv (Bioinfo) 2026-06-11

PhyloZoo: a unified framework for phylogenetic network analysis in Python

Authors:

Reticulate evolutionary processes (events in which lineages merge, such as hybridization, recombination, and horizontal gene transfer) are widespread across nature but cannot be represented by phylogenetic trees alone. Phylogenetic networks have therefore become an important modelling tool, yet existing software is typically tied to specific inference paradigms and provides limited support for working with multiple network representations in a unified and programmable environment. PhyloZoo is an open-source Python framework that lowers the barrier to developing practical, easy-to-use software for phylogenetic network analysis. It provides data structures and algorithms covering the main representations used in the field, together with dedicated visualization tools and robust I/O for all major phylogenetic file formats. A particular emphasis lies on semi-directed phylogenetic networks, which explicitly represent root uncertainty and have so far received limited support in existing software. By offering a shared foundation for developing interoperable tools and a combinatorial layer that supports computational proofs and theoretical exploration, PhyloZoo enables reproducible workflows for applied, methodological, and theoretical studies of reticulate evolution. Availability and implementation: PhyloZoo is implemented in Python and installable from PyPI, with source code, documentation, and examples available at https://github.com/nholtgrefe/phylozoo.

21.
arXiv (math.PR) 2026-06-18

Functional central limit theorems for non-local branching Markov processes

arXiv:2502.19382v2 Announce Type: replace Abstract: The aim of this paper is to study the fluctuations of a general class of supercritical branching Markov processes with non-local branching mechanisms. We establish functional central limit theorems and show that the limiting behaviour falls into three regimes, determined by the size of the spectral gap associated with the first-moment semigroup of the branching process. The main novelty is to develop a unified functional fluctuation theory for spatial branching Markov processes with non-local reproduction, allowing a general finite-dimensional spectral structure for the first-moment semigroup, including non-simple leading eigenvalues and nilpotent Jordan-type components. In doing so, we extend the classical small, critical and large fluctuation trichotomy beyond the finite-type and local spatial settings, and obtain limiting processes that capture the covariance structure induced by non-local offspring displacement.

22.
medRxiv (Medicine) 2026-06-12

High coverage, persistent gaps: quality of Antenatal Care and its determinants in Zambia based on the 2024 Demographic and Health Survey.

Abstract Background Evaluating antenatal care (ANC) quality is critical to reducing maternal and neonatal mortality. In Zambia, despite high basic ANC attendance, comprehensive national evidence on the clinical content and quality of services remains limited. This study assessed the coverage of WHO-recommended ANC interventions and identified factors associated with care quality using the latest national data. Methods A cross-sectional analysis was conducted using data from the 2024 Zambia Demographic and Health Survey. The final analytic sample comprised 4,829 women aged 15-49 with a live birth in the preceding 5 years. A composite index of 15 selected, equally weighted WHO-recommended components evaluated clinical assessment, counseling/screening, preventive interventions, and utilization. Survey-weighted Poisson regression estimated adjusted incidence rate ratios (aIRRs) for the count of ANC components received. Results The mean ANC quality score was 12.5 out of 15 (95% CI: 12.4-12.6), and 78.5% (95% CI: 77.0-80.0) of women achieved adequate ANC ([&ge;] 12/15 components). While individual clinical and counseling coverage generally exceeded 90%, only 47.2% (95% CI: 45.3-49.0) of women initiated care during the first trimester, and just 4.8% (95% CI: 4.1-5.6) achieved [&ge;] 8 ANC contacts. Maternal education was the strongest and most stable predictor of quality across all models. Compared to no education, higher education was associated with an 8.0% higher expected quality score (aIRR = 1.080, 95% CI: 1.051-1.110). Lower ANC quality was significantly associated with unwanted pregnancies (aIRR = 0.970, 95% CI: 0.956-0.993) and with residence in Western (aIRR = 0.923, 95% CI: 0.897-0.951) and North Western (aIRR = 0.966, 95% CI: 0.937-0.996) provinces. Absence of distance barriers and residence in Eastern, Luapula, and Copperbelt provinces were associated with higher quality scores. Conclusion While average ANC component coverage in Zambia is high, critical gaps persist in early initiation and total contact frequency. Care adequacy is strongly influenced by maternal education, relationship status, pregnancy intention, and regional inequities. These findings underscore the need for interventions targeted at uneducated women, preventing unintended pregnancies, and underserved regions such as Western and North Western Provinces. Keywords: Antenatal care quality, ANC content, Zambia, maternal education.

23.
medRxiv (Medicine) 2026-06-22

Panel-level multilocus methylation quantification in native cell-free DNA by PCR-compatible sequential enzymatic processing

DNA methylation is informative for liquid biopsy, but low template abundance, distributed methylation signals and workflow complexity limit implementation. Here we present Delta-HLD, a PCR-compatible methylation assay platform that quantifies methylation directly in native DNA through sequential hybridization, ligation and methylation-sensitive digestion. The assay co-reports methylation-dependent signals from multiple loci through a shared amplification architecture, generating a single panel-level PCR readout. We established the chemistry, optimized panel size and composition through model-guided experiments, and implemented the assay as a triplex qPCR workflow with per-sample internal process controls. Plasma proof-of-concept analyses showed discriminatory signal in CRC and proof-of-concept transferability to hepatocellular carcinoma. Additional platelet-retaining experiments identified a strategy to increase recovery of analyzable circulating templates while reducing genomic DNA recognition. Delta-HLD provides a compact PCR-compatible framework for low-input methylation analysis without base conversion.

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

"That's AI Slop, You Bot!" Studying Accusations, Evidence, and Credibility in Online Discourse Towards LLM-Generated Comments

arXiv:2606.12073v1 Announce Type: cross Abstract: Generative AI has made fluent prose cheap to produce, breaking the old promise to readers that good writing meant real thinking. How have readers responded, and what can this tell us about changing anti-AI attitudes? We analyzed 25 million comments from Hacker News and Reddit (2023-2026), combining LLM judgment on 7,500 sampled accusations of AI use, sentiment trajectories, speech-act coding of 300 confirmed accusations of AI use, and a matched-control test of accused versus non-accused parent comments. We found that the pejorative-label share of accusations rose more than tenfold on both platforms while a placebo vocabulary of pre-2022 inauthenticity terms (shill, astroturf) did not. This shift reflected a fast-growing trend of branding any suspicious or seemingly inauthentic prose as "AI slop". The slop frame now constitutes 94 percent of pejorative mentions, with the dominant comments shifting in tone from mockery toward gatekeeping and structural protest. The key surprise comes from a matched-control test which found that prose features that statistically distinguish AI from human text do not predict which human text gets accused as AI. The new accusations work as social gatekeeping of perceived authenticity without actually screening for AI. This research extends signaling theory by showing that substitute signals used socially can grow even when inaccurate if the underlying detection problem cannot be solved at the non-expert level. It shows that AI's effects on writing from the reader side are distinct from those on the production (writer) side. Detection technology cannot resolve this dynamic because the social function of accusations is increasingly to perform social gatekeeping and in-group signaling as opposed to identifying AI-generated writing.

25.
bioRxiv (Bioinfo) 2026-06-10

ECMME: an atlas of selection pressures on the mammalian extracellular matrix reveals contrasting evolutionary dynamics

The extracellular matrix (ECM) is a fundamental metazoan innovation that provides structural support and regulatory cues essential for multicellular life. While core matrisome components are subject to strong functional constraints, their evolutionary dynamics at the molecular level remain incompletely characterized. Here, we present a comprehensive per-residue analysis of selection pressures across 272 human core matrisome proteins using high-quality orthologous sequences from up to 228 placental mammal species. We developed an automated pipeline integrating ortholog identification, codon-aware alignments, and site-specific selection analyses with the MEME and FUBAR methods from the HyPhy suite. Results reveal pervasive strong purifying selection across the matrisome, consistent with its structural and functional indispensability. This is accompanied by episodic positive selection and rarer pervasive positive selection, with collagens exhibiting significantly elevated episodic positive selection compared to glycoproteins and proteoglycans. To facilitate community access, we developed ECMME (ECM Molecular Evolution) browser, an intuitive open-access web resource that visualizes selection metrics plotted directly onto protein topologies. ECMME allows researchers to seamlessly browse and investigate the data, providing a powerful framework for interpreting functional sites. It is available online and requires no local installation or set-up (https://izzilab-ecmme.share.connect.posit.cloud/).