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01.
medRxiv (Medicine) 2026-06-15

Midwifery Practice in Conflict Contexts: Lived Experiences from Somalia and Nigeria

Background: Midwives are a central cadre in the health system, particularly in conflict-affected settings where they are sometimes the primary or even only skilled providers available. Yet, despite their critical role, there is limited qualitative evidence capturing their lived experiences and how these shape workforce entry, retention, and overall well-being. Methods: Drawing on a phenomenological research methodology, this qualitative study was embedded within a larger prospective longitudinal cohort of midwifery students and graduates in Somalia and Nigeria. We conducted focus group discussions with graduate midwives (n=48 in Nigeria; n=63 in Somalia) to explore their experiences transitioning into the workforce and their realities working in health systems impacted by conflict and violent insecurity. Data were analysed using inductive thematic analysis. Results: Five themes emerged from the data: (1) job search and workforce entry, which was described as fraught with challenges and shaped by a set of formal systems in Nigeria but informal networks and structural barriers in Somalia (2) working conditions that were marked by resource scarcity, infrastructural challenges, and heavy and unreasonable workloads, (3) safety, security and coping strategies that differed across the two contexts but reflected persistent exposure to violence and a reliance on ad hoc and personal coping in lieu of systematic protection, (4) community perceptions of midwives, shaped and constrained by social and gender norms and (5) mental health and emotional wellbeing, highlighting stress, burnout and moral injury experienced by this cadre. Conclusion: Our findings highlight the profound challenges faced by midwives working in conflict-affected settings, and they shine a light on the urgent need to support and invest in this critical and predominantly female health workforce.

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

OmniBioTwin: A System-of-Twinned-Systems Framework for Health Digital Twins

arXiv:2606.11264v1 Announce Type: cross Abstract: Health digital twins (HDTs) promise patient-specific modeling and decision support but current approaches remain structurally fragmented: monolithic models that address a single organ or task lack cross-scale fidelity, while system-level twins lack generalizable architectural frameworks. We propose OmniBioTwin, a System-of-Twinned-Systems (SoTS) framework that organizes HDTs as modular computational entities coupled through explicit interaction operators within a multi-layer network architecture. The framework comprises seven coordinated layers - spanning data integration, autonomous twin modeling, cross-scale coupling, temporal synchronization, and human-in-the-loop decision support. We demonstrate OmniBioTwin by instantiating a multiscale twin for glucagon-like peptide-1 (GLP-1) signaling pathways in Alzheimer's disease, illustrating how molecular, cellular, and organ-level twins can be composed and coupled within a unified system.

03.
arXiv (CS.AI) 2026-06-16

STRIDE: Strategic Trajectory Reasoning via Discriminative Estimation for Verifiable Reinforcement Learning

arXiv:2606.15866v1 Announce Type: new Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) has become an effective post-training paradigm for improving the reasoning abilities of large language models. However, existing RLVR methods typically rely on final-answer correctness to assign trajectory-level rewards, providing sparse supervision and treating all tokens uniformly regardless of their actual contribution to reasoning. Although recent studies introduce intermediate signals such as process rewards, high-entropy tokens, and semantic uncertainty, these signals are often not inherently verifiable and may fail to distinguish beneficial strategic patterns from harmful ones. To address this limitation, we propose STRIDE (Strategic Trajectory Reasoning with Discriminative Estimation), a fine-grained RLVR framework that derives strategic reasoning supervision from verifiable outcomes. STRIDE contrasts successful and failed trajectories within each response group to estimate the outcome-discriminative preference of each $n$-gram strategic pattern, and further combines this signal with reasoning saliency entropy to identify decision-relevant strategic patterns. These patterns are assigned differentiated advantage values during RL optimization, enabling more precise credit assignment while preserving the verifiability of RLVR. Extensive experiments demonstrate that STRIDE consistently improves reasoning performance across diverse models, tasks, and extended settings, including VLMs and agent-based systems.

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

Is Code Better Than Language for Algorithmic Reasoning

arXiv:2606.15589v1 Announce Type: cross Abstract: For tool-augmented language models, comparing natural-language reasoning with code-execution pipelines is difficult because the comparison changes both the intermediate representation and the execution mechanism. We separate these factors with an intermediate intervention: the model expresses its reasoning as executable code, and the language model simulates that code in context to produce an answer. On a 40-task verifiable algorithmic benchmark, deterministic code execution outperforms natural-language reasoning by +31.6pp. We observe that the intermediate intervention is not meaningfully different from natural-language reasoning (+0.15pp). These results suggest that, in our evaluated setting, changing the intermediate representation alone does not explain the tool-use advantage, providing evidence for the performance gains requiring reliable external execution. We formalize this intuition with a simple statistical decision-theoretic model that characterizes when execution dominates end-to-end risk in our disentangled trace-generation/execution regime. We validate our theory using a reconstruction intervention that leverages a proxy language model to infer natural-language reasoning traces from code representations, recovering performance comparable to the original natural-language reasoning pipeline. All experiments are at https://github.com/TerryTong-Git/ToolProj.

05.
PLOS Medicine 2026-05-20

Associations between hematologic dynamics during pregnancy and obstetric complications: A retrospective observational study

by Veronica Tozzo, Rachel Petherbridge, Kaitlyn James, Sarah Hsu, Deepti Pant, Chloe Michalopoulos, Brody H. Foy, Tanayott Thaweethai, Christopher Mow, Jacqueline Maya, Carolina Batlle Camero, Lydia Shook, Kathryn J. Gray, Logan Mauney, John M. Higgins, Camille E. Powe Background Pregnancy alters hematologic state as measured by complete blood count (CBC), but the longitudinal changes in CBC indices that define healthy pregnancies are not well established. In a large cohort based at an academic health system in the United States, we aimed to define reference intervals and typical longitudinal changes in CBC indices during pregnancy. We then tested for associations between extreme CBC values for gestational age or extreme longitudinal changes in CBC indices and obstetric complications. Methods and findings We studied nine CBC indices in individuals with singleton pregnancies who delivered after 30 weeks’ gestation and presented for prenatal care prior to 20 weeks. The electronic health record (EHR)-based Maternal Health Cohort (Massachusetts General Hospital; 1998–2016) formed our discovery cohort of 45,992 pregnancies, 18% of which had relevant complications. We developed a validation cohort of 48,868, 27% with complications from EHR data in the Mass General Brigham healthcare system from 2016 to 2024. In pregnancies without complications in the discovery cohort, we derived gestational-age-specific reference intervals (2.5th–97.5th percentile) and established typical intra-pregnancy longitudinal changes. In the validation cohort, we then tested CBC values outside of the 26–29 weeks’ gestation reference interval and CBC rare changes (uncommon changes in magnitude and direction) between 7–14 and 26–29 weeks’ gestation for association with a composite outcome (hypertensive disorders of pregnancy, small for gestational age birthweight, preterm birth) and its individual components using generalized estimating equations. Derived reference intervals differed from those in the literature for mean red cell volume, mean red cell hemoglobin, red cell count, and mean red cell hemoglobin concentration; reference intervals for other indices were similar to those previously published. In validation, hematocrit, hemoglobin, and red cell count values above their gestational-age specific reference intervals were associated with increased risk of the composite obstetric outcome: odds ratios (ORs) of 1.4 (95% CI [1.2, 1.5] p 

06.
PLOS Medicine 2026-05-22

Differences in tuberculosis prevalence by sex in low- and middle-income countries over 1993–2025: A systematic review and meta-analysis

by Nicole A. Swartwood, Nanki Singh, Seyed Alireza Mortazavi, Melike Hazal Can, Hening Cui, Do Kyung Ryuk, Peter MacPherson, Katherine C. Horton, Nicolas A. Menzies Background Global and national initiatives to combat tuberculosis (TB) have expanded over recent years. Despite this, the TB burden remains high in some population groups, with men recognized as having elevated TB risks. Summary measures of sex differences in TB prevalence were last estimated in 2016. Since then, many additional prevalence surveys have been conducted, including in the highest TB burden countries. We conducted a systematic review of sex-stratified TB prevalence survey data published over 1993–2025, to provide updated estimates of male-to-female (M:F) TB prevalence ratios and determine whether sex-related disparities in TB burden have closed over time. Methods and findings We identified surveys reporting community-representative, sex-stratified estimates of pulmonary TB prevalence in low- and middle-income countries (LMICs), including surveys from an earlier review (covering January 1993–March 2016) and a new systematic review (covering 1st December 2015–13th October 2025). This review was prospectively registered with PROSPERO (CRD42024503853) and included searches of PubMed, Embase, Global Health, the Cochrane Library, Africa Index Medicus, LILACS, and SciELO. We extracted data on bacteriologically confirmed and smear-positive TB prevalence among adults (aged ≥ 15 years), stratified by sex. Risk of bias was evaluated using eight criteria specific to prevalence surveys. We fit multi-level Bayesian regression models with study- and country-level random effects to estimate the M:F ratio of TB prevalence (male prevalence divided by female prevalence), overall and for key subgroups. In meta-regression analyses, we estimated how prevalence ratios varied over time and according to known TB risk factors and TB case definitions.We identified 10,124 publications and extracted data from 100 eligible studies representing 102 unique prevalence surveys and 4,658,310 participants (45.6% male) in 33 LMICs. TB prevalence was higher in men than women in 90/102 of the included surveys, with a pooled M:F prevalence ratio of 2.02 (95% credible interval (CrI): 1.71, 2.34) for bacteriologically confirmed TB and 2.38 (95% CrI: 1.91, 2.90) for smear-positive TB. Time trend analyses showed a 2.0% (95% CrI: −0.2, 4.5%) average annual change in the M:F ratio of bacteriologically confirmed TB over the study period. The M:F prevalence ratio was estimated to be higher for countries with greater excess HIV prevalence among men, and countries with greater gender equity (as measured by the United Nation’s Gender Development Index). The estimated M:F prevalence ratio was also higher for surveys that did not restrict testing to individuals reporting TB symptoms. Study limitations include heterogeneity in survey methods and definitions, as well as limited data from the Americas, Eastern Mediterranean, and Europe WHO world regions and post-COVID-19 period. Conclusions Men in LMICs consistently experience TB at a higher prevalence than women. Time trend estimates are uncertain, but consistent with widening sex differences in TB prevalence over the last three decades, despite efforts to address the risk factors underlying this excess TB burden.

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

GRACE: Step-Level Benchmark for Faithful Reasoning over Context

Many reasoning tasks require models to reason over input context, from document-grounded question answering to rule-based deduction. Chain-of-Thought (CoT) prompting produces traces that appear transparent, yet individual steps can silently deviate from the source evidence, even when the final answer is correct. Existing methods detect hallucinations at the response level but fail to identify where in the chain a failure occurs or what type it is. We introduce GRACE, the first human-annotated step-level faithfulness benchmark with a data-driven error taxonomy for context-grounded textual reasoning. GRACE covers CoT traces from 10 models across 4 source datasets, with each step annotated for faithfulness, error category, and natural language explanation. A data-driven taxonomy, discovered bottom-up via unsupervised clustering, organizes failures into two tracks: GRACE-Inference (deductive errors) and GRACE-Grounding (factual grounding errors), with four categories each. The evaluation set is human-annotated and challenging by design. Our experiments reveal substantial headroom for current models. In addition, integrating step-level faithfulness signals into reinforcement learning pipelines improves both downstream accuracy and reasoning reliability.

08.
Nature (Science) 2026-06-24

Dietary cholesterol activates a Ral-dependent pathway driving LDLR turnover

作者:

Metabolism of the hepatic low-density lipoprotein receptor (LDLR) is a key determinant of cholesterol homeostasis1,2. The molecular switches that coordinate LDLR trafficking and turnover in response to nutritional cues, including high dietary cholesterol, remain poorly defined3–6. Here we identify a new pathway regulated by Ral GTPases that links extracellular cholesterol signals to the intracellular trafficking machinery controlling LDLR turnover. Chronic dietary cholesterol activates the Ral proteins by increasing RAS activity, routing LDLR to lysosomes for degradation and inhibiting its recycling independently of transcriptional regulation or PCSK9. Constitutive activation of Ral via RalGAPB deletion or overexpression of constitutively active Ral mutants in hepatocytes reduces LDLR levels and impairs cholesterol clearance. Ral engages the endocytic RalBP1–REPS1 complex to promote LDLR internalization and lysosomal routing, where LDLR is degraded by the lysosomal protease cathepsin A (CTSA). Ral activation directs CTSA towards lysosomes for maturation while limiting its secretion, further promoting LDLR degradation in lysosomes. Genetic variants in this pathway significantly associate with altered cholesterol in humans. Pharmacological inhibition of CTSA activity increases hepatic LDLR function and improves cholesterol clearance, offering a potential new therapeutic strategy for hypercholesterolaemia and cardiovascular disease. Chronic dietary cholesterol activates Ral GTPases, which promote LDLR internalization and lysosomal degradation through RalBP1–REPS1 and CTSA, thereby reducing cholesterol clearance, whereas CTSA inhibition restores LDLR function and may offer a therapeutic strategy for cardiovascular disease.

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

Physics-conforming Latent Twins

arXiv:2606.15053v1 Announce Type: new Abstract: Surrogate models are central to scientific machine learning, where they enable fast prediction, simulation, inference, and control for complex physical systems. For time-dependent problems, however, accurate interpolation of training trajectories is not sufficient: reliable surrogates should also respect the conservation laws, invariants, admissibility conditions, and dissipative structures that give those trajectories physical meaning. We introduce Physics-conforming Latent Twins, a framework for learning latent surrogate solution operators whose dynamics satisfy selected physical principles by design. The method builds on the Latent Twin formulation by jointly learning an encoder, a decoder, and a latent flow map between arbitrary time-indexed states, while constraining the latent dynamics to preserve or dissipate prescribed structural quantities. We develop a constraint-transfer viewpoint that connects physical structure in the original state space with compatible constraints in latent space, and prove structure-preservation bounds showing how latent enforcement improves control of physical defects after decoding. We also derive algebraic conditions for latent flow maps that preserve linear and quadratic invariants or enforce dissipative inequalities. Numerical experiments on representative ODE and PDE benchmarks demonstrate improved constraint satisfaction, structural fidelity, and qualitative long-time behavior while maintaining accurate surrogate prediction.

10.
arXiv (quant-ph) 2026-06-19

Topological Codes Based on Space Groups

arXiv:2606.20548v1 Announce Type: new Abstract: Topological codes form one of the most important classes of stabilizer codes. Most existing algebraic constructions and analyses of topological codes assume translation invariance. Here we show that topological codes can arise in more general settings by incorporating point group operations. The central construction is a class of Calderbank-Shor-Steane (CSS) codes called space-group codes, whose check operators are built from group-algebra templates over space groups that combine translations with point-group operations. We develop methods for analyzing topological properties of space-group codes using ring-modules and their invariant theory. At first glance, space-group codes might appear to complicate practical implementation; however, we find that they can exhibit greater locality than previous codes based purely on translations. Our framework thus extends the landscape of topological codes and opens up a broader design space for the co-design of topological codes with quantum computing platforms.

11.
arXiv (CS.LG) 2026-06-12

Interpretable Factor Decomposition for Decision Intelligence in Large-Scale Financial Markets: Evidence from China's A-Share Market

arXiv:2606.12843v1 Announce Type: new Abstract: We present an interpretable machine learning pipeline to decompose Cross-Sectional Equity Return Predictability into auditable factor contribution. We apply an XGBoost model with TreeSHAP attribution and conduct stress testing on 3632 Chinese A-share stocks from 2009 until 2019. Using 60-month, rolling windows over 55 months of out-of-sample data, XGBoost obtains a mean AUC of 0.547 and +2.38%/month (Newey-West t = 5.94; Annualized Sharpe 2.23) long-short spread for the top vs bottom quintiles. This alpha is persistent after adjusting for the Carhart four-factor model (+2.31%/month; t = 7.48). SHAP Decomposition indicates that behavioral signals (turnover and momentum) account for 58.2% of predictive attribution compared to 10.7% for valuation ratios, on average, across 55 industry groups. Ablation analysis serves to cross-validate this ranking and provides evidence that SHAP and ablation diverge in a manner that highlights feature substitutability structure that is largely invisible to either method used in isolation.

12.
arXiv (CS.CV) 2026-06-16

Toward the Whole Picture: Accumulative Fingerprint Mapping and Reconstruction for Small-Area Mobile Sensors

Small-area fingerprint sensing on mobile devices creates a fundamental mismatch between acquisition and recognition: each touch captures only a tiny, pose-varying local patch, while reliable biometric matching ultimately requires a stable and sufficiently complete fingerprint representation. Existing pipelines largely cope with this mismatch by treating repeated touches as independent partial templates, which leads to repeated registration, repeated matching, and no guarantee of adequate global coverage. In this paper, we advocate a different formulation, namely accumulative fingerprint mapping and reconstruction for small-area mobile sensing. Rather than matching every partial patch separately, the proposed perspective converts a sequence of local observations into a unified fingerprint state that is progressively refined as new touches arrive and can be matched only once after consolidation. As a concrete baseline, we present a classical pipeline that performs patch-wise structural feature extraction, feature-level registration and fusion, fingerprint map construction, and phase-based ridge reconstruction. More importantly, we position this baseline within a broader mobile fingerprint framework that integrates structured token learning, two-stage pose reasoning, and diffusion-based generative reconstruction. This viewpoint reframes mobile fingerprint recognition from multi-capture multi-match processing to accumulative map building, state refinement, and one-shot matching, offering a principled route toward efficient, pose-robust, and deployment-friendly biometrics for small-area mobile platforms. The baseline implementation has been publicly released at https://github.com/XiongjunGuan/FpReconstruction.

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

DifFRACT: Diffusion Feature Reconstruction and Attribution for Circuit Tracing

Mechanistic interpretability seeks to explain neural network behavior by decomposing model computations into interpretable features and circuits. While transcoder-based circuit tracing has recently enabled detailed causal analyses of large language models, multimodal diffusion transformers for image generation remain comparatively opaque. We still lack tools for understanding how semantic information propagates across denoising steps and how text and image representations interact within double-stream MM-DiT architectures. Existing methods provide only partial insight: attention maps expose a limited view of token interactions, while sparse autoencoders can discover interpretable features but do not directly reveal how these features are transformed and composed through nonlinear MLP layers. In this work, we extend transcoder-based circuit tracing to multimodal diffusion transformers. We train timestep-conditioned transcoders that faithfully approximate the input-output behavior of MLP sublayers in FLUX.1[schnell]. By replacing MLPs with transcoders and linearizing the remaining computation, we obtain exact feature-to-feature attribution and recover compact, interpretable circuits. Empirically, our transcoders match or slightly outperform sparse autoencoders on the sparsity-faithfulness tradeoff. The resulting circuits reveal mechanisms underlying attribute binding and cross-stream semantic propagation, and provide causal explanations for systematic generation errors. Moreover, circuit-guided interventions are substantially more precise and effective than standard SAE-based steering. Our results demonstrate that transcoder-based circuit analysis is feasible for state-of-the-art diffusion transformers and provides a powerful framework for understanding and controlling multimodal generative models. The code is available at https://github.com/Artalmaz31/DifFRACT

14.
arXiv (CS.CL) 2026-06-25

What Intermediate Layers Know: Detecting Jailbreaks from Entropy Dynamics

Jailbreak attacks reveal a persistent weakness in aligned Large Language Models: carefully crafted prompts can elicit policy-violating responses despite safety training. While most defenses operate at the prompt or output level, it remains unclear how harmful intent is encoded within the model's internal representations. We investigate this question by analyzing token-level predictive entropy trajectories across layers of a frozen LLM using the logit lens. We find that static aggregate statistics of prompt-level entropy (e.g., mean, variance) carry little discriminative signal, whereas features capturing how entropy evolves across token positions, such as monotonic rank-based trend scores, are substantially more informative. Importantly, this signal is not uniform across model depth: it is concentrated in intermediate layers and degrades at the final layer, indicating that jailbreak-relevant structure is most pronounced in mid-network representations rather than at the output head. Across multiple models (Llama, Qwen, Gemma) and adversarial benchmarks, these entropy dynamics provide architecture-consistent separation without additional training. Together, our findings show that jailbreak behavior is reflected in structured intermediate uncertainty dynamics, clarifying both which entropy-derived features encode harmful intent and where in the network that signal is most pronounced.

15.
medRxiv (Medicine) 2026-06-22

Referral pathways, ETAT triage acuity, and inpatient outcomes among children presenting to a national tertiary paediatric emergency unit in Ghana: a prospective cohort study

Emergency referral systems in sub-Saharan Africa are fragmented, and children reaching tertiary facilities through different referral pathways often arrive in advanced clinical states. Prospective data simultaneously characterising referral patterns, triage acuity at presentation, diagnostic case mix, and inpatient mortality at a national tertiary paediatric emergency unit are lacking from West Africa. This prospective cohort study enrolled 675 consecutively presenting children aged one month to 12 years at the Paediatric Emergency Unit of Korle Bu Teaching Hospital, Accra, Ghana, from February to December 2019. The primary outcome was all-cause inpatient mortality. Key variables collected included referral status and facility tier, Emergency Triage Assessment and Treatment (ETAT) triage category, ICD-10 diagnostic classification, Oyedeji socioeconomic classification, and time from symptom onset to PEU registration. Crude odds ratios were computed for all candidate predictors. Multivariable logistic regression was conducted using complete case analysis (n = 613). Of 675 children, 63.0% (n = 425) were referred from another health facility; referred children had higher ETAT emergency triage category rates than self-presenting children (32.7% vs 27.6%, p < 0.001). Overall inpatient mortality was 9.9% (67/675). Mortality varied by referral source: 16.7% among secondary/regional hospital referrals, 11.0% among lower-tier facility referrals (district, municipal, CHAG, polyclinic, private, health centre, and maternity home facilities combined, n = 356), 7.6% among self-presenting children, and 7.4% among tertiary referrals. Overall, 30.8% of children were classified as ETAT emergencies on arrival, with case fatility rate of 21.6%. The three most common diagnostic domains were respiratory conditions (17.2%), blood and haematological disorders (17.0%), and digestive presentations (16.4%). Inpatient mortality was highest in neoplastic disease (33.3%, n = 30) and circulatory presentations (31.0%, n = 29). In the primary multivariable analysis (n = 613, 51 events; events-per-variable ratio 4.2), no referral tier was independently associated with inpatient mortality after adjustment. Referral from secondary/regional hospitals showed a borderline non-significant association (adjusted odds ratio 3.09, 95% CI 0.96 to 9.90, p = 0.058). School going children (60-119 months) had higher odds of inpatient death than infants (adjusted odds ratio 5.56, 95% CI 1.16 to 26.53, p = 0.032), as did adolescents (adjusted odds ratio 10.01, 95% CI 2.15 to 46.69, p = 0.003). ETAT emergency category and lower socioeconomic status were not independently significant in this model. A pre-specified sensitivity analysis using the full analytic cohort (n = 674, events-per-variable ratio 6.7) with collapsed referral categories did not confirm any referral tier association; ETAT emergency category and lower SES were independently associated in the sensitivity model. All multivariable estimates should be regarded as exploratory. This prospective cohort provides simultaneous characterisation of referral patterns, ETAT triage acuity, diagnostic case mix, and inpatient mortality at a national tertiary paediatric emergency unit in West Africa. The referral-mortality gradient and high ETAT emergency category proportion document the severity of illness arriving through different referral pathways at this facility. The association between secondary/regional hospital referral and inpatient mortality is hypothesis-generating and requires replication in an adequately powered multicentre study before any service-level conclusions can be drawn.

16.
medRxiv (Medicine) 2026-06-17

Proteomics Uncovers Cryptic JPH2 Loss in Paediatric Dilated Cardiomyopathy

Despite recent advances in next-generation sequencing, genetic diagnostic rates for dilated cardiomyopathy (DCM) remain low. Among paediatric DCM, causes are often heritable, with a greater frequency of de novo, recessive and syndromic causes of disease. Novel diagnostic methods are therefore required to solve monogenic cases. To assess the value of proteomics as a diagnostic tool for paediatric DCM, we obtained left ventricle myocardial samples from paediatric patients undergoing heart transplantation at the Royal Children's Hospital, Melbourne. We performed genome sequencing and proteomics and leveraged this multi-omics dataset to uncover the molecular cause of disease in a gene elusive proband. The proband carried a heterozygous JPH2 frameshift variant identified on clinical exome sequencing. However, proteomic analysis showed a pronounced downregulation of JPH2, suggestive of biallelic loss-of-function. Closer inspection of the genomic data revealed a large inversion (~8.34 Mb) with a breakpoint falling within intron 5 of JPH2 that displaces the 3'UTR from the coding transcript. The two variants were confirmed to be in trans using long read DNA sequencing, consistent with a diagnosis of JPH2 autosomal recessive DCM. Finally, we applied RNA sequencing with total RNA library preparation to show that transcripts containing a 3'UTR were reduced to ~10% relative to controls. As a proof-of-principle, we present the first reported use of proteomics from explanted cardiac tissue to provide a genetic diagnosis. Our methodology has broad relevance to patients with genetically unsolved Mendelian diseases, who might undergo organ transplantation as part of clinical management.

17.
arXiv (CS.CL) 2026-06-11

Beyond Fully Random Masking: Attention-Guided Denoising and Optimization for Diffusion Language Models

Diffusion large language models (dLLMs) offer an efficient alternative to autoregressive models through parallel decoding, yet existing post-training methods largely rely on random masking strategies that overlook intrinsic token dependencies. In this work, we present an empirical analysis of attention in dLLMs and show that tokens attending more strongly to unmasked context exhibit greater generation stability and play a critical role in reasoning. Motivated by these findings, we propose AGDO, an attention-guided denoising and optimization framework that aligns both training and optimization with attention-derived dependencies. AGDO determines the denoising order based on attention structure and emphasizes attention-critical tokens during supervised fine-tuning and reinforcement learning. Experiments on mathematical and coding benchmarks demonstrate that AGDO consistently improves reasoning performance, outperforming state-of-the-art post-training methods for dLLMs.

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

MolE-RAG: Molecular Structure-Enhanced Retrieval-Augmented Generation for Chemistry

arXiv:2606.05693v2 Announce Type: replace Abstract: Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained. To bridge this semantic and chemical knowledge gap, we propose MolE-RAG, a training-free, molecule-centric retrieval-augmented generation framework for LLM-based molecular property prediction. MolE-RAG augments each prediction with three complementary sources of inference-time context: retrieved chemistry literature, molecule-specific information including compound synonyms, identifiers, functional group annotations, and physicochemical descriptors, and structurally similar molecules retrieved from the training set. We evaluate MolE-RAG across nine molecular property prediction tasks using proprietary, chemistry-specialized, and open-source LLMs. Across general-purpose LLMs, MolE-RAG improves ROC-AUC by up to 28 percentage points on classification tasks and reduces regression RMSE by up to 67% relative to a SMILES-only baseline. We further find that the utility of each context source varies across models and tasks, with different models benefiting most from textual retrieval, molecular context, or structural retrieval. These results suggest that molecule-centric retrieval can improve LLM-based molecular property prediction without model fine-tuning while providing a flexible framework for integrating heterogeneous chemical knowledge at inference time.

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

Select and Improve: Understanding the Mechanics of Post-Training for Reasoning

arXiv:2606.13125v1 Announce Type: cross Abstract: Reinforcement learning has rapidly emerged as a key component in the training of reasoning and coding models, yet it remains poorly understood from a mechanistic perspective. We study how and through what underlying processes capabilities are acquired or enhanced via reinforcement learning post-training. Our analysis, based on controlled math reasoning experiments with Qwen-2.5-1.5B, reveals two core mechanisms: strategy selection and strategy improvement. Our results highlight the role of SFT data and reinforcement learning data in activating these mechanisms, in particular showing how supervising the model on diverse reasoning strategies can enable strategy selection and how increasing difficulty in reinforcement learning data can enable strategy improvement. Taken together, our results provide mechanistic insight into RL training and suggest practical interventions to continue scaling reasoning capabilities.

20.
arXiv (CS.AI) 2026-06-16

Learning to Share: Selective Memory for Efficient Parallel Agentic Systems

arXiv:2602.05965v2 Announce Type: replace-cross Abstract: Agentic systems solve complex tasks by coordinating multiple agents that iteratively reason, invoke tools, and exchange intermediate results. To improve robustness and solution quality, recent approaches deploy multiple agent teams running in parallel to explore diverse reasoning trajectories. However, parallel execution comes at a significant computational cost: when different teams independently reason about similar sub-problems or execute analogous steps, they repeatedly perform substantial overlapping computation. To address these limitations, in this paper, we propose Learning to Share (LTS), a learned shared-memory mechanism for parallel agentic frameworks that enables selective cross-team information reuse while controlling context growth. LTS introduces a global memory bank accessible to all teams and a lightweight controller that decides whether intermediate agent steps should be added to memory or not. The controller is trained using stepwise reinforcement learning with usage-aware credit assignment, allowing it to identify information that is globally useful across parallel executions. Experiments on the AssistantBench and GAIA benchmarks show that LTS significantly reduces overall runtime while matching or improving task performance compared to memory-free parallel baselines, demonstrating that learned memory admission is an effective strategy for improving the efficiency of parallel agentic systems. Project page: https://joefioresi718.github.io/LTS_webpage/

21.
arXiv (quant-ph) 2026-06-11

Strong-field control of the $Z$-boson resonance in $e^+e^-$ collisions

arXiv:2606.09394v2 Announce Type: replace-cross Abstract: Resonant $Z$-boson production is a cornerstone of precision electroweak physics, with its vacuum line shape set by the $Z$ mass, width, and collision kinematics. We show that a strong laser field can significantly alter this picture. By treating the field nonperturbatively, we find that laser dressing of the incoming fermions alters the effective collision kinematics and opens laser-photon exchange channels, including multiphoton processes, in $e^{+}e^{-}$ collisions. As a result, the $Z$-resonance profile develops distinct intensity-dependent regimes, evolving from the vacuum limit to saturation at intermediate field strengths and to an approximately quadratic enhancement at higher intensities. Additionally, the polarization composition of the produced $Z$ bosons is redistributed. In particular, at high intensities the laser-induced contribution can compensate the intrinsic chiral asymmetry of the electroweak interaction, leading to nearly parity-balanced $Z$-boson production. Our results identify that strong classical fields can dynamically control electroweak resonance phenomena, opening a bridge between strong-field QED and high-energy collider physics.

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

Discrete Autoregressive Transformer for Generative Mechanism Synthesis

arXiv:2606.17409v1 Announce Type: cross Abstract: Planar path synthesis requires mechanisms whose coupler curves match a prescribed trajectory; the mapping from curve to linkage is inherently one-to-many across four-, six-, and eight-bar topologies. We address this design problem with simulation-grounded evaluation on a curated corpus of over one million mechanisms, reporting Chamfer distance and dynamic time warping after forward kinematics and geometric alignment. We formulate synthesis as conditional autoregressive sequence modeling: joint coordinates are uniformly quantized to tokens and generated by a decoder-only transformer with a variational-autoencoder (VAE) latent of the target curve and an explicit mechanism-type token. Training combines token cross-entropy with a Gaussian-smoothed bin auxiliary loss that respects ordinal structure among bins. At inference, a bounded latent-noise schedule decodes all mechanism types at each noise level; we retain the top five candidates by geometric error, yielding diverse accurate families without dataset lookup. On held-out tests, aggregate mean Chamfer distance is $0.0132$ and mean dynamic time warping is $0.153$; a latent $k$-nearest-neighbor baseline that conditions on training-set neighbor latents in VAE space achieves matched-topology mean Chamfer distance $0.0071$ and mean dynamic time warping $0.117$ using the same decoder.

23.
arXiv (CS.CL) 2026-06-24

The Sparse Frontier: Sparse Attention Trade-offs in Transformer LLMs

Sparse attention offers a promising strategy to extend long-context capabilities in Transformer LLMs, yet its efficiency-accuracy trade-offs remain unclear due to the lack of comprehensive evaluation. We address this gap with the largest-scale empirical analysis to date of training-free sparse attention, evaluating six methods across multiple model families and sizes, sequences up to 128K tokens, and sparsity levels up to 0.95 (i.e., $1/20$ attention budget) on nine diverse tasks. We first organise the rapidly evolving landscape of sparse attention methods into a taxonomy along four design axes. Our analysis then yields actionable insights: 1) sparse attention is effective: larger sparse models outperform smaller dense ones at equivalent cost, improving the Pareto frontier; 2) for the training-free methods we study, fine-grained per-query importance estimation during prefilling remains impractical-due to both the cost of estimation and the lack of sparse kernels that translate fine-grained sparsity into wall-clock gains-forcing a task-dependent choice between global-to-token and block-to-block selection. Instead, during decoding, token-to-page selection becomes feasible, enabling better generalisation and higher sparsity tolerance; 3) longer sequences tolerate higher sparsity, suggesting that fixed-budget methods in production are suboptimal. Together, these findings provide practical guidance for deploying sparse attention and methodological recommendations for future evaluations. Our code is available at https://github.com/PiotrNawrot/sparse-frontier.

24.
arXiv (CS.CV) 2026-06-12

Comparing Commercial Depth Sensor Accuracy for Medical Applications

Depth estimation has numerous medical and surgical applications. We benchmark four depth sensors on a porcine bone specimen, a porcine belly specimen, and a silicone kidney phantom using stylus-sampled references. These objects contain several real-world challenges, including homogeneous surfaces, specular surfaces, and subsurface scattering. The comparison includes stereo, structured-light, and time-of-flight sensors at a distance of approximately 50 cm. Specifically, the Intel RealSense D405 (Intel RealSense, United States), PMD Flexx2 (pmdtechnologies, Germany), Stereolabs ZED 2i (Stereolabs, France), and Zivid 2M+ 60 (Zivid, Norway) are compared. The Zivid 2M+ 60 performed best across all objects and metrics considered in this work. The ZED ranked second for real tissue, but last on the phantom.

25.
arXiv (CS.AI) 2026-06-11

Engineering Robustness into Personal Agents with the AI Workflow Store

arXiv:2605.10907v3 Announce Type: replace-cross Abstract: The dominant paradigm for AI agents is an "on-the-fly" loop in which agents synthesize plans and execute actions within seconds or minutes in response to user prompts. We argue that this paradigm short-circuits disciplined software engineering (SE) processes – iterative design, rigorous testing, adversarial evaluation, staged deployment, and more – that have delivered the (relatively) reliable and secure systems we use today. By focusing on rapid, real-time synthesis, are AI agents effectively delivering users improvised prototypes rather than systems fit for high-stakes scenarios in which users may unwittingly apply them? This paper argues for the need to integrate rigorous SE processes into the agentic loop to produce production-grade, hardened, and deterministically-constrained agent *workflows* that substantially outperform the potentially brittle and vulnerable results of on-the-fly synthesis. Doing so may require extra compute and time, and if so, we must amortize the cost of rigor through reuse across a broad user community. We envision an *AI Workflow Store* that consists of hardened and reusable workflows that agents can invoke with far greater reliability and security than improvised tool chains. We outline the research challenges of this vision, which stem from a broader flexibility-robustness tension that we argue requires moving beyond the ``on-the-fly'' paradigm to navigate effectively.