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

HyDRA: Hybrid Dynamic Routing Architecture for Heterogeneous LLM Pools

Production LLM deployments increasingly maintain heterogeneous model pools spanning order-of-magnitude cost differences. Existing routers make binary strong-vs-weak decisions and couple learned parameters to specific model identities, requiring retraining whenever the catalog changes. We present HyDRA (Hybrid Dynamic Routing Architecture), a framework that predicts fine-grained, multi-dimensional capability requirements per query and matches them against configuration-defined model profiles via shortfall matching. A ModernBERT encoder with K=4 independent sigmoid heads scores each query along reasoning, code generation, debugging, and tool use; a shortfall-matching algorithm then selects the cheapest model whose capabilities meet the predicted requirements. The deployed predictor runs at 86 ms median CPU inference latency in production, and is fully decoupled from the model catalog – adding or removing models requires only a configuration change, with zero retraining. On SWE-Bench Verified (5-model pool: GPT-5.4-mini, Claude Haiku 4.5, GPT-5.3 Codex, Claude Sonnet 4.6, GPT-5.4), HyDRA's tunable shortfall threshold spans three regimes: peak-quality exceeds the always-strong Claude Sonnet 4.6 baseline (75.4% vs. 74.2% resolution) at 12.9% cost savings; iso-quality matches Sonnet at 54.1% cost savings, a 6x improvement over our prior in-house binary router at 9.1%; aggressive pushes savings to 72.5% for a 3.2-point quality trade. Results generalize across LiveCodeBench, BigCodeBench, and tau-bench. HyDRA is deployed to all users in GitHub Copilot's VS Code Chat auto-mode and – to our knowledge for the first time in the LLM routing literature – demonstrates language-invariant routing across CJK, European, and other script families.

02.
medRxiv (Medicine) 2026-06-15

Active commuting, anxiety symptoms and mental wellbeing: a dose-response study

Climate change draws attention to the planetary health perspective in sport and exercise sciences, that is, to physical activity that supports both human wellbeing and environmental sustainability. Active commuting is a sustainable form of physical activity with well-established somatic health benefits. However, more knowledge is needed on its relationship with mental health. We examined dose-response associations between active commuting, anxiety symptoms, and mental wellbeing among Finnish adults, and whether green commuting environment moderates these relationships. We used data from the cross-sectional Environment and Health Survey collected in June-September 2023 in the ten largest cities in Finland. Employed participants with data on anxiety symptoms (Generalized Anxiety Disorder-7, GAD-7), mental wellbeing (World Health Organization-Five Well-Being Index, WHO-5), commuting profile over a year (mode, frequency, distance, and perceived greenness along the commute route), and sociodemographic and lifestyle factors were included (n=1,672; mean age 45.3 years; 53.8% women). Active commuting was defined as travelling the entire commute by walking or cycling (including e-biking) that was converted into approximated annual km/week and MET-h/week. We used linear and logistic regression with restricted cubic splines to evaluate dose-response associations, adjusted for key covariates. The role of perceived greenness was tested using an active commuting x commute greenness interaction term. We found no dose-response relationships between active commuting and anxiety symptoms or mental wellbeing in any of the models. No effect modification by commute greenness was observed. More research on how active commuting may support planetary health from a mental health perspective is needed.

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

How to Detect and Measure the AI Dangers to Democracy

arXiv:2606.16054v1 Announce Type: cross Abstract: Research on artificial intelligence and democracy has grown quickly over the last decade. A shared conclusion in this literature is that AI does not create new democratic problems so much as it makes old ones worse. We now see this across information ecosystems, in elections, and in public administration. However, despite growing evidence, we lack a clear way to prioritize risks in this area, compare them across domains, and identify where democratic control is most likely to break down. So, our problem is: How can we systematize the problems that AI systems pose to democratic processes? This paper argues that principal agent theory may fit the task. In many phases of democratic systems, principals delegate key functions to AI systems and their providers without really being able to monitor how these systems operate or the outputs they produce. Treating AI as a delegation problem helps identify accountability gaps and other governance failures. Most importantly, as we shall illustrate, it provides metrics for empirical assessments of AI impact on democracy. As a second analytical element, we draw on the NIST AI Risk Management Framework and its seven characteristics of trustworthy AI, which supply substantive criteria for evaluating delegated tasks. Operationalized across the three domains through measurable indicators and domain specific trustworthiness criteria, we propose an analytical framework that centers on institutional assessability as the central condition for democratic control over AI. However, we stress that how severe a harm is, and how much risk is acceptable, are evaluative judgments that current methodologies neither acknowledge nor operationalize. This becomes acute when such evaluative judgments are (silently) delegated to private vendors. We identify this as a strong limitation left for future work.

04.
arXiv (CS.AI) 2026-06-19

A Neuromorphic Reinforcement Learning Framework for Efficient Pathfinding in Robotic Mobile Fulfillment Systems

arXiv:2606.20031v1 Announce Type: cross Abstract: Dynamic environmental changes, confined workspaces, and stringent real-time constraints make pathfinding in Robotic Mobile Fulfillment Systems (RMFS) a challenging problem for conventional search- and rule-based methods, which typically suffer from high computational complexity and long decision latency. While reinforcement learning (RL) has emerged as a powerful alternative, deploying learned policies with extreme energy efficiency on resource-constrained hardware remains an open challenge. We present SDQN-RMFS, an end-to-end framework that achieves high-fidelity deployment of an RL-trained policy from a full-precision artificial neural network (ANN) through to a neuromorphic chip. By computing only when triggered by sparse events, this framework unlocks ultra-low-power RMFS pathfinding. Our full-stack pipeline operates as follows: an ANN policy is first efficiently trained via a collision-allowing strategy to densify informative trajectories, and then converted into a spiking neural network (SNN) via a hard-label knowledge distillation approach. This effectively addresses the output distribution mismatch, preserving policy capability across the ANN-to-SNN pipeline while substantially reducing inference latency. Hardware experiments demonstrate up to 11,281$\times$ energy savings and a nearly two-fold reduction in latency compared to a high-performance GPU baseline, while maintaining decision quality on par with the original trained policy. These results establish physical neuromorphic inference as a practical and energy-sustainable pathway for large-scale RMFS operations.

05.
arXiv (CS.CL) 2026-06-12

Entropy-Gradient Inversion: Moving Toward Internal Mechanism of Large Reasoning Models

The advancement of Large Reasoning Models (LRMs) has catalyzed a paradigm shift from reactive ``fast thinking'' text generation to systematic, step-by-step ``slow thinking'' reasoning, unlocking state-of-the-art performance in complex mathematical and logical tasks. However, the field faces the fundamental gap between token-level behavioral analysis and internal reasoning mechanisms, and the instability of reinforcement learning (RL) for reasoning optimization relying on costly external verifiers. We identify and formally define Entropy-Gradient Inversion, a robust negative correlation between token entropy and logit gradients that acts as a definitive geometric fingerprint for LRM reasoning capability. Building on this, we propose Correlation-Regularized Group Policy Optimization (CorR-PO), which embeds this inversion signature into RL reward regularization. Extensive experiments on various reasoning benchmarks across multiple model scales show CorR-PO consistently outperforms state-of-the-art baselines, confirming that stronger inversion directly correlates with superior reasoning performance.

06.
bioRxiv (Bioinfo) 2026-06-11

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

Single-cell multi-omics technologies have recently advanced to enable the profiling of epigenomic, transcriptomic, and proteomic layers within individual cells, offering new opportunities to characterize cellular states as integrated biological systems. However, developing a unified framework that can seamlessly integrate diverse omics modalities and remain robust to heterogeneous modality missingness remains challenging. Here we present HoloCell, to our knowledge the first generative foundation model for joint representation learning and generative modeling across all three major single-cell omics modalities, i.e., epigenomics, transcriptomics, and proteomics. HoloCell contains over 860 million parameters and is pretrained on the Human-Multi-Omics-Corpus, which comprises approximately 468 million single-cell profiles across these three omics layers, corresponding to over 425 billion tokens. HoloCell introduces a simple yet biologically grounded hierarchical tokenization strategy that encodes cis-regulatory elements, genes, and proteins as structured tokens within a shared modeling framework. We evaluated HoloCell across single-omics representation learning, paired multi-omics integration, unpaired multi-omics alignment, and cross-modal generation via iterative diffusion and remasking, demonstrating its superior performance and flexibility across diverse omics tasks. From a representation perspective, HoloCell provides a unified digital mapping of cellular states across multiple omics layers, capturing cell heterogeneity as an integrated system. From a generation perspective, its iterative diffusion and remasking framework accounts for the inherently unordered nature of biological features, enabling in silico simulation of multi-omics information flow. Together, these capabilities position HoloCell as a versatile foundation model toward the emerging concept of a virtual cell, offering both systematic characterization and generative simulation of cellular systems within a unified framework.

07.
arXiv (CS.AI) 2026-06-19

AURA: Adaptive Uncertainty-aware Refinement for LLM-as-a-Judge Auditing

arXiv:2606.19714v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used as judges for open-ended generation, as large-scale human evaluation is often expensive and difficult to scale, yet their preferences remain imperfect proxies for human judgment. Existing auditing pipelines often assume that a reliable subset of examples or clean supervision signals are available beforehand, for example from human annotation, heuristic filtering, or the outputs of strong judges. In LLM evaluation, this assumption is fragile: the initial split may inherit judge bias, while human verification is typically too scarce to define stable groups at scale. We propose AURA, an adaptive uncertainty–aware refinement framework for auditing pairwise LLM–as–a–judge decisions under selected human verification. AURA iteratively learns a human-consistency signal, propagates reliable evidence, and prioritizes uncertain comparisons for human review. The key idea is to treat trust in a judge as a latent quantity that is progressively refined as evidence accumulates. We provide a compact formulation, a stable refinement procedure, and a comprehensive evaluation on both synthetic and real pairwise LLM-answer data.

08.
arXiv (CS.AI) 2026-06-17

MapAgent: An Industrial-Grade Agentic Framework for City-scale Lane-level Map Generation

arXiv:2606.04513v2 Announce Type: replace Abstract: Lane-level maps are critical infrastructure for autonomous driving and lane-level navigation, yet constructing and maintaining standardized lane networks for hundreds of cities remains highly labor-intensive. Recent end-to-end vectorized mapping methods can predict lane geometry and topology directly from sensor data, but they typically treat mapping specifications and traffic regulations as implicit, dataset-dependent supervision. Moreover, in complex scenes (e.g., worn or missing markings and occlusions), correct lane configurations are often under-determined by visual evidence alone, making specification violations a major source of human post-editing. We propose MapAgent, an industrial-grade agentic architecture that augments a vectorization backbone for specification-compliant lane-map production. Rather than merely adding an agent loop to map prediction, MapAgent couples backbone perception with explicit specification verification, constraint-aware reasoning, and deterministic map editing under a bounded, verification-driven Judge-Planner-Worker loop. A vision-language Judge diagnoses errors by jointly inspecting visual evidence and draft vectors, while a tool-calling Planner generates minimal corrective edits with post-edit re-validation. To remain scalable for city-scale production, MapAgent is selectively triggered only on tiles with low backbone confidence, adding modest overhead while preserving throughput. Experiments on real-world datasets show consistent gains over strong production baselines, especially in complex and long-tail scenarios. Additionally, MapAgent has been integrated into Baidu Maps, supporting lane-level map generation for over 360 cities nationwide and elevating the overall production automation to over 95%, demonstrating MapAgent's practicality and effectiveness for large-scale lane-level map generation.

09.
arXiv (quant-ph) 2026-06-17

DRAG-Compatible Leakage Suppression in Landau–Zener Control via Isoprobability Twins

arXiv:2506.19572v4 Announce Type: replace Abstract: Analytically solvable models – particularly the Landau-Majorana-Stückelberg-Zener (LMSZ) and Allen-Eberly-Hioe (AEH) models – underpin many quantum-gate implementations and population-transfer protocols. However, their canonical pulse shapes are incompatible with modern leakage-suppression techniques and some systems. Most notably, the constant Rabi envelope of the LMSZ pulse prevents many leakage-suppression approaches, which require smoothness. We address both limitations by developing the concept of isoprobability twin models: distinct pairs of Rabi frequency $\Omega(t)$ and detuning $\Delta(t)$ that yield identical post-pulse transition probabilities based on the Delos-Thorson transformation. In this work, we formalise the method by experimentally demonstrating the equivalence of multiple LMSZ and AEH twin models on IBM's ibm_kyiv processor. Finally, we show a staggering leakage reduction by more than 3 orders of magnitude using a custom DRAG implementation of a cosine LMSZ isoprobability model.

10.
arXiv (CS.AI) 2026-06-12

Once-for-All: Scalable Simultaneous Forecasting via Equilibrium State Estimation

arXiv:2606.13285v1 Announce Type: cross Abstract: We introduce Equilibrium State Estimation (ESE), a novel paradigm for simultaneous prediction, where multiple interacting systems require separate yet coordinated forecasts. Such scenarios often arise in real-world settings such as economics and healthcare modeling. Unlike existing approaches that predict one system at a time, ESE forecasts all systems in a single pass. It first estimates the equilibrium state across systems, then generates holistic forecasts based on the difference between the current state and the estimated equilibrium. Extensive experiments on synthetic and real-world datasets, including currency exchange and COVID-19 spread modeling, demonstrate that ESE is at least as accurate as state-of-the-art (SOTA) methods while being significantly faster. In addition, ESE integrates seamlessly with conventional predictors, combining their accuracy with its exceptional efficiency and delivering a 10-70x speedup. With linear-time complexity, ESE scales far better than SOTA methods as the number of systems increases. Moreover, it remains accurate under diverse perturbations, establishing ESE as a fast, generalizable, robust, and scalable multi-prediction method.

11.
arXiv (CS.CV) 2026-06-16

Latent Space Reinforcement Learning for Inverse Material Estimation in Food Fracture Simulation

Realistic visual simulation of food manipulation requires accurate material parameters, yet these are difficult to measure directly and vary across the heterogeneous regions of a single food item. We address the inverse problem of estimating material parameters from a target description of fracture behavior in a non-differentiable continuum damage mechanics simulator. Using orange peeling as a test case, we train a neural surrogate on 2,000 forward simulations and compare Covariance Matrix Adaptation Evolution Strategy (CMA-ES, a gradient-free evolutionary optimizer) with Proximal Policy Optimization (PPO, a reinforcement learning algorithm) across the original 9-dimensional parameter space and two learned 4-dimensional latent representations. Since different oranges have different material properties, a practical inverse system must handle arbitrary targets without retraining. We train a goal-conditioned PPO policy that learns a general inverse mapping: given any target description of peeling behavior, the policy produces a material parameter estimate in a single forward pass (8 surrogate evaluations, approximately 10ms). Operating in a normalizing flow latent space with a shared surrogate evaluator, the goal-conditioned policy achieves 0.642 actual recovery when validated through the simulator, outperforming the original parameter space by 23%. A warm-start extension that initializes CMA-ES refinement from the policy's output further improves recovery to 0.828 with 540 evaluations. These findings provide a practical framework for inverse food physics and lay groundwork for vision-driven material identification from video observations of food manipulation.

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

A Unified Latent Space Disentanglement VAE Framework with Robust Disentanglement Effectiveness Evaluation

arXiv:2603.11242v2 Announce Type: replace-cross Abstract: Evaluating and interpreting latent representations, such as variational autoencoders (VAEs), remains a significant challenge for diverse data types, especially when ground-truth generative factors are unknown. To address this, we unify several state-of-the-art disentangled VAE approaches for latent space disentanglement into one framework – bfVAE. To assess the effectiveness of a disentangled VAE model and enhance latent space interpretability, we propose Feature Variance Heterogeneity via Latent Traversal (FVH-LT) and Dirty Block Sparse Regression in Latent Space (DBSR-LS). To ensure robust interpretability of learned latent space, we develop a greedy alignment strategy (GAS) that mitigates label switching and aligns latent dimensions across runs to set the foundation of result aggregation. We also introduce a convenient scalar latent space separation index (LSSI) based on the GAS-aligned outputs of FVH-LT and DBSR-LS to summarize the overall latent structural separation without knowledge of the ground-truth generative factors. We compare bfVAE to five VAE models and validate the effectiveness FVH-LT, DBSR-LS, and LSSI in on seven tabular and image datasets. Under our examined experimental settings, bfVAE provides a more flexible disentanglement framework achieves more favorable overall trade-off between disentanglement and reconstruction than the benchmark VAE models; FVH-LT and DBSR-LS reliably uncover semantically meaningful and domain-relevant latent structures and generally yield consistent results; and LSSI makes an effective quantitative summary of latent structural separation.

13.
medRxiv (Medicine) 2026-06-15

Therapeutic efficacy study on shoulder impingement syndrome in swimmers: a network meta-analysis

Shoulder impingement syndrome (SIS), including subacromial impingement and rotator cuff tendinitis, is commonly caused by repetitive swimming movements and associated shoulder joint dysfunction. Despite numerous available treatment options, no consensus exists on the most effective treatment option. Therefore, this systematic review and network meta-analysis aimed to investigate treatment methods for SIS in swimmers. Using a frequentist framework and Cochrane PICOS principles, we compared SIS treatments, constructed network evidence diagrams, and assessed heterogeneity. A total of 45 studies were included in the qualitative synthesis, and 42 contributed to the network meta-analysis, comprising 1752 participants, 9 treatment categories, and outcome measures. For pain outcomes, some adjunctive interventions combined with exercise showed favorable ranking probabilities, although several estimates were accompanied by wide confidence intervals. For shoulder range-of-motion outcomes, taping, acupuncture, manual therapy, and sport-specific training showed favorable effects in selected comparisons, particularly for external and internal rotation. According to surface under the cumulative ranking curve (SUCRA) rankings, exercise combined with medium-frequency therapy ranked highly for pain reduction, whereas exercise combined with acupuncture or extracorporeal shock wave therapy ranked highly for shoulder flexion. Exercise combined with taping ranked highly for external rotation, and exercise combined with manual therapy ranked highly for internal rotation. However, the interpretation of ranking results should remain cautious because uncertainty and inconsistency were present in some comparisons. Exercise-based rehabilitation appears to remain central to the management of SIS in swimmers. Several adjunctive interventions showed favorable findings for selected outcomes, especially pain relief and shoulder rotational function. However, the available evidence was affected by heterogeneity, inconsistency, and imprecision across some treatment comparisons. More rigorously designed swimmer-specific randomized controlled trials are needed before firm treatment hierarchies can be established. Trial registration: The protocol for this systematic review is registered with PROSPERO (www.crd.york.ac.uk/PROSPERO; registration number: CRD42024498851). The first submission of PROSPERO was on January 15, 2024, and it was revised and updated on March 25, 2026.

14.
arXiv (CS.LG) 2026-06-17

A tensor network approach for chaotic time series prediction

arXiv:2505.17740v2 Announce Type: replace Abstract: Making accurate predictions of chaotic time series is a complex challenge. Reservoir computing, a neuromorphic-inspired approach, has emerged as a powerful tool for this task. It exploits the memory and nonlinearity of dynamical systems without requiring extensive parameter tuning. However, selecting and optimizing reservoir architectures remains an open problem. Next-generation reservoir computing simplifies this problem by employing nonlinear vector autoregression based on truncated Volterra series, thereby reducing hyperparameter complexity. Nevertheless, the latter suffers from exponential parameter growth in terms of the maximum monomial degree. Tensor networks offer a promising solution to this issue by decomposing multidimensional arrays into low-dimensional structures, thus mitigating the curse of dimensionality. This paper explores the application of a previously proposed tensor network model for predicting chaotic time series, demonstrating its advantages in terms of accuracy and computational efficiency compared to conventional echo state networks. Using a state-of-the-art tensor network approach enables us to bridge the gap between the tensor network and reservoir computing communities, fostering advances in both fields.

15.
arXiv (CS.LG) 2026-06-19

Pseudo-Formalization for Automatic Proof Verification

arXiv:2605.20531v2 Announce Type: replace-cross Abstract: Reliable verification of proofs remains a bottleneck for training and evaluating AI systems on hard mathematical reasoning. Fully formal proofs, in languages like Lean, are easy to verify because they are unambiguous and modular. Most proofs, particularly those written by AI systems, have neither property, and translating them into formal languages remains challenging in many frontier math settings. We propose Pseudo-Formalization (PF), a proof format that captures the modularity and precision of formal proofs while retaining the flexibility of natural language. A Pseudo-Formal proof is decomposed into self-contained modules, each stating its premises, conclusion, and proof in natural language. To verify the correctness of a regular natural language proof, an LLM translates it to Pseudo-Formal and then verifies each module independently, an algorithm we call Block Verification (BV). We evaluate PF+BV on two benchmarks spanning olympiad and research-level mathematics, where it pareto-dominates LLM-as-judge baselines on error-finding precision and recall. To support future work, we release our research-level proof verification benchmark ArxivMathGradingBench.

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

Binary Tracking for Spatial QA and Navigation with Open Vision-Language Models

arXiv:2606.16902v1 Announce Type: cross Abstract: This work addresses spatial question answering for service robots traversing long egocentric routes. Given a query such as "where can I find a dry cleaner on the way back home?", the system returns a metric coordinate that downstream navigation components can act on. Prior Spatial Question Answering approaches leverage retrieval-augmented agents built on closed-source models such as GPT-4o for path exploration. However, robots operating in the real world often cannot reliably depend on online closed-source models due to network instability, communication latency, and deployment cost. It creates a need for open-source based Spatial Question Answering approaches that can run onboard the robot, yet prior research in this direction remains limited. This work proposes BinTrack, a simple yet effective, fully open-source spatial-localization agent that leverages the temporal ordering of a robot's trajectory. BinTrack performs a binary search over the trajectory segments between two anchor landmarks identified from a query. It improves overall accuracy by up to 22.8% over other open-source implementations and even matches the reported closed-source model result on the global category of the SpaceLocQA benchmark, the most challenging setting that has so far required strong reasoning agents such as GPT-4o. Furthermore, its optimized inference strategy consistently yields more than a 1.5x inference speedup over previous approaches. Finally, this work releases GangnamLoop, a novel and practical multi-trip outdoor benchmark collected by deploying a real quadruped robot on public streets with the anonymization policy. It revisits the same locations under different outdoor conditions and pairs the robot's low viewpoint with the human owner's. The source codes and datasets are publicly available at https://github.com/ndb796/BinaryTracking

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

Polyp-D2ATL: Deep Domain-Adaptive Transfer Learning for Colorectal Polyp Classification under Label Distribution Shift

Early and highly accurate prediction of colorectal polyps, as an important sign of one of the most dangerous types of cancer, will result in saving more lives. Despite the advancements in colorectal polyp classification, many challenges remain in obtaining an automated polyp prediction system that is able to diagnose the difficult-to-predict polyps accompanied by different features in real scenarios, where the model can handle imbalanced data, label distribution shift, and cross-modality generalization successfully. In this study, we propose Polyp-D2ATL, a novel framework accompanied by a specific training strategy, which mitigates these limitations and effectively predicts the different classes of polyps belonging to the NICE classification. Our extensive experiments on the PICCOLO validation and test sets demonstrate that the proposed Polyp-D2ATL significantly outperforms existing state-of-the-art models across various reliable metrics, achieving an accuracy of 82.38%, a Macro-F1 of 77.49%, and a specificity of 87.47% on the validation set, alongside consistent improvements on the held-out test set which demonstrates the generalization capacity and clinical applicability of the proposed approach.

18.
arXiv (CS.CV) 2026-06-15

VideoWeave: Unlocking Geometric Consistency in Video Generation via Joint Geometry-Video Modeling

Large-scale video diffusion models often fail to preserve 3D structure over time, causing geometric drift and implausible motion under viewpoint changes. Existing methods usually enforce geometric consistency by using explicit geometry reconstructions, such as depth maps, point clouds, or reconstructed 3D structures, to define conditions, supervision, or reward signals, making the generator sensitive to errors from upstream geometry pipelines. We propose VideoWeave, a latent-space post-training framework that uses implicit geometry-model features to constrain the generative distribution, providing a more flexible and non-rigid form of guidance that mitigates the impact of reconstruction errors from geometry models. Specifically, VideoWeave adapts these features into geometry latents and jointly models them with video latents in a shared denoising space, allowing geometry to shape the generative distribution during training. To support this process, we build GeoVid-80K, an 80K-video dataset with paired appearance and geometry representations. Experiments on text-to-video and image-to-video generation show that VideoWeave improves geometric coherence while preserving strong visual quality. VideoWeave project page at https://videoweave.github.io/

19.
PLOS Computational Biology 2026-06-22

Ten simple rules for making the supplement increase your paper’s impact

Authors:

by Volker Grimm, Uta Berger, Stefano Mammola Have you ever lost hours navigating supplementary materials—clicking between the main text and dozens of auxiliary files only to encounter broken links, illegible figures, and undefined variables and acronyms? If so, you’re not alone. What should support scientific communication has instead become an obstacle: supplementary information (SI) increasingly suffers from inconsistent formatting, poor accessibility, and fragmented organization that impedes rather than advances understanding. This is disheartening since the SI, if used effectively, has the power to enhance transparency, credibility, and reproducibility of research. Therefore, we propose 10 simple rules to help authors design SI that genuinely increase the impact of their research. The rules emphasize treating SI with the same care as the main text, using it strategically to support the scientific narrative while preserving clarity and focus. Key recommendations include creating a single, well-structured, self-contained SI master document; ensuring explicit cross-referencing between the main text and SI; making SI machine-readable; and avoiding the misuse of SI as a substitute for proper data repositories. We also highlight the importance of creativity in choosing appropriate formats and strict adherence to journal-specific guidelines. Finally, when available, we advocate the use of standardized templates to improve consistency, readability, and reuse across studies. By following these rules, authors can substantially increase the scientific impact of their work while at the same time contributing to more sustainable research practices.

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

A CEFR-Inspired Classification Framework with Fuzzy C-Means To Automate Assessment of Programming Skills in Scratch

arXiv:2604.00730v2 Announce Type: replace-cross Abstract: Context: Schools, training platforms, and technology firms increasingly need to assess programming proficiency at scale with transparent, reproducible methods that support personalized learning pathways. Objective: This study introduces a pedagogical framework for Scratch project assessment, aligned with the Common European Framework of Reference (CEFR), providing universal competency levels for students and teachers alongside actionable insights for curriculum design. Method: We apply Fuzzy C-Means clustering to 2008246 Scratch projects evaluated via Dr.Scratch, implementing an ordinal criterion to map clusters to CEFR levels (A1-C2), and introducing enhanced classification metrics that identify transitional learners, enable continuous progress tracking, and quantify classification certainty to balance automated feedback with instructor review. Impact: The framework enables diagnosis of systemic curriculum gaps-notably a "B2 bottleneck" where only 13.3% of learners reside due to the cognitive load of integrating Logic Synchronization, and Data Representation–while providing certainty–based triggers for human intervention.

21.
arXiv (CS.CV) 2026-06-15

Gaze Heads: How VLMs Look at What They Describe

How a vision-language model internally solves the task of describing an image is far from obvious. We find that the model develops a specific mechanism for this: a small set of attention heads in its language-model backbone, which we call gaze heads, whose attention tracks the image region the model is currently describing. We find them with a simple correlation score from a few forward passes, using comic strips as a controlled testbed where narrative order is laid out spatially. These gaze heads do not just track the image tokens being described: redirecting their attention to a chosen region forces the VLM to describe that region instead. A single attention-mask intervention on the top-100 gaze heads, fewer than 9% of all heads, steers the model's answer to any chosen comic panel at 83.1% accuracy, while the same intervention on random heads fails to redirect the answer, and intervening on all heads destroys generation. The same lever also extends to continuous control: switching the gaze target mid-generation makes the model wrap up its current panel description and move to the new one within a few tokens. Beyond comics, the same intervention redirects answers to chosen regions in natural COCO images. The mechanism further recurs across model sizes from 2B to 32B parameters and across other VLM architectures, although some frozen-encoder families show no comparable head set. More broadly, this shows that targeted edits identified through mechanistic analysis can serve as practical inference-time levers for steering multimodal model behavior, without any retraining. Our code, interactive demo, and datasets are available at https://gaze.baulab.info/

22.
arXiv (CS.CL) 2026-06-11

DuDi: Dual-Signal Distillation with Cross-Lingual Verbalizer

Small language models (SLMs) are efficient and scalable, but their multilingual capabilities degrade severely at sub-billion scales, especially for Southeast Asian (SEA) languages. We introduce DuDi, a dual-signal multilingual distillation framework that combines an online sequence-level signal with off-policy and on-policy token-level signals. DuDi further uses a cross-lingual verbalizer to refine teacher feedback and improve teacher-student transferability in multilingual settings. Experiments on SEA-HELM across multiple model families, scales, and teacher-student settings show that DuDi consistently outperforms competitive distillation baselines. Ablations and analyses confirm that sequence-level optimization, token-level supervision, and cross-lingual verbalization provide complementary and transferable learning signals for multilingual SLMs.

23.
medRxiv (Medicine) 2026-06-18

Rare Coding Variants Reveal Distinct Genetic Architectures Across Multidimensional Sleep Phenotypes

Sleep and circadian traits have been widely studied using common variants, but the contribution of rare coding variation remains unclear. We analyzed rare coding variants in 397,065 whole-exome sequenced UK Biobank participants across 36 sleep phenotypes from self-report, diagnoses, sleep medication use and accelerometry, and meta-analyzed results with 171,536 whole-genome sequenced All of Us participants of diverse ancestries, with replication in the Mass General Brigham Biobank (N = 31,275). We identified 260 genes associated with sleep phenotypes, including novel associations with sleep medication use in 29 genes and 24 out of 29 have not previously been reported with any sleep phenotypes. We observed modest but significant rare variant heritability and strong genetic correlations between sleep medication use, insomnia and fatigue. Temporal gene expression trajectory analyses indicate that genes associated with self-reported sleep traits show constant high prenatal expression, whereas genes linked to sleep medication phenotypes exhibit peak expression in the late prenatal period. These findings highlight distinct biological mechanisms captured by different measurement sources of sleep phenotypes and reveal rare-variant-informed targets for therapeutic discovery.

24.
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

25.
arXiv (math.PR) 2026-06-18

Kemeny's constant minimization for reversible Markov chains via structure-preserving perturbations

arXiv:2510.24679v4 Announce Type: replace-cross Abstract: Kemeny's constant measures the efficiency of a Markov chain in traversing its states. We investigate whether structure-preserving perturbations to the transition probabilities of a reversible Markov chain can improve its connectivity while maintaining a fixed stationary distribution. Although the minimum achievable value for Kemeny's constant can be estimated, the required perturbations may be infeasible. We reformulate the problem as an optimization task, focusing on solution existence and efficient algorithms, with an emphasis on the problem of minimizing Kemeny's constant under sparsity constraints.