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01.
arXiv (CS.AI) 2026-06-18

A Hybrid LSTM–Vision Transformer Architecture for Predicting HRRR Forecast Errors

arXiv:2606.19026v1 Announce Type: cross Abstract: Forecast errors in high-resolution numerical weather prediction (NWP) systems are often linked to unresolved planetary boundary layer (PBL) processes, convection, terrain-induced circulations, and other vertically structured atmospheric phenomena. Previous work demonstrated that Long Short-Term Memory (LSTM) networks can successfully predict forecast errors in the High-Resolution Rapid Refresh (HRRR) model using mesonet observations, but we believe performance degradation is linked to periods of complex vertical atmospheric evolution. To address this limitation, we develop a hybrid LSTM-Vision Transformer (LSTM-ViT) framework that combines temporal sequence learning from surface observations with atmospheric profiles from the New York State Mesonet profiler network. The LSTM-ViT framework is trained to predict HRRR hourly precipitation, 10 m wind speed, and 2 m temperature forecast errors at individual mesonet stations. Across all three predictors, incorporation of profiler-derived atmospheric structure improves forecast error prediction skill relative to the baseline LSTM architecture, with the largest gains occurring at shorter forecast lead times and during periods of enhanced PBL activity. Improvements are particularly pronounced for precipitation forecast error, where the LSTM-ViT framework achieves approximately a twofold increase in predictive skill relative to the baseline LSTM while better capturing convectively driven error evolution and reducing degradation associated with PBL processes. These results demonstrate that combining temporal sequence learning with vertically informed attention mechanisms provides a physically meaningful pathway for improving forecast error prediction in operational NWP systems. Our research offers forecasters enhanced guidance regarding model bias and forecast confidence.

02.
medRxiv (Medicine) 2026-06-15

ICD-10 Code Ambiguity Obscures Treatment-Eligible Adults with Spinal Muscular Atrophy: A Single-Center Chart Review and Patient Outreach Study

Background. Three disease-modifying therapies (DMTs) for spinal muscular atrophy (SMA) have been approved since 2016, yet many adults remain untreated. Identifying them depends on ICD-10 codes that capture SMA but do not reliably distinguish it from other related conditions. We examined, in one U.S. health system, both patients' engagement with therapy and the accuracy of the codes used to find them. Methods. We conducted a retrospective chart review of adults in an academic health system identified by SMA-associated ICD-10 codes, with manual adjudication of diagnosis and DMT status. Confirmed SMA-positive, DMT-naive patients were invited to a structured telephone interview on treatment awareness and barriers. Results. Of 60 charts, 22 (36.7%; 95% CI 25.6-49.3%) were appropriately coded for SMA or a related disorder; only 16 (26.7%) had molecularly confirmed SMA. The other 38 (63.3%) were miscoded, spanning spinal and bulbar muscular atrophy, asymptomatic carriers, prenatal screening, and conditions unrelated to SMA. Ten of the 16 confirmed patients (62.5%) were DMT-naive; one was interviewed, one declined, and eight could not be reached. The non-response is itself a finding: the patients least visible to administrative data are the hardest to reach. Conclusions. ICD-10 ambiguity is a barrier to treatment access in adult SMA, as is loss to follow-up. We make two recommendations: continuous documentation-coding alignment that uses natural language processing to verify the genetic precondition, and type-specific SMA codes (subcodes for Types 0-4) anchored on molecular SMN1 confirmation. Together these would support cohort identification, outreach, and evidence generation without adding to clinician burden.

03.
arXiv (CS.CL) 2026-06-11

Augmenting Molecular Language Models with Local $n$-gram Memory

Transformer-based language models for SMILES strings suffer from a locality gap: standard character-level tokenization fragments chemically meaningful motifs, forcing models to repeatedly learn local syntax at the expense of long-range dependencies. To address this without disrupting standard tokenizers, we propose MolGram, which integrates a conditional $n$-gram memory module into molecular language models. MolGram maps local string patterns to learned embeddings via scalable hash lookups and dynamically injects this regional context into hidden states. Evaluations across three tasks, including unconditional molecule generation, forward reaction prediction, and single-step retrosynthesis, show that MolGram consistently improves performance. Crucially, our analyses demonstrate that MolGram outperforms baselines with 3$\times$ more parameters, establishing explicit local pattern memory as a highly efficient inductive bias.

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

Spectrum Aware Illumination Estimation Using Multispectral Image

Multispectral (MS) imaging extends beyond conventional RGB imaging by capturing more spectral bands, thereby improving illuminant spectrum estimation (ISE). However, existing methods often fail to fully exploit spectral information, resulting in suboptimal performance under diverse lighting conditions and across different sensor domains. Hence, we propose a deep learning framework with a spatio-spectral feature extraction block, which incorporates spectral attention mechanisms to enhance spectral correlation and preserve illuminant-relevant spatial features. Through the inclusion of an illuminant prior (IP), our approach prioritizes specific channels that provide more meaningful information in an MS image. We also propose a spectral-domain transform across different MS sensor spaces. The results demonstrate that illuminant spectra learned in high-dimensional sensor spaces can be effectively transformed to various lower-dimensional camera sensor spaces without any additional training. To facilitate evaluation, we introduce a real-world MS dataset containing high-dimensional ground-truth illumination spectra captured under diverse lighting conditions. Through extensive experiments, we demonstrate that our method achieves superior accuracy compared to existing models, thus providing a practical solution for real-world ISE. The code and dataset are available at https://github.com/hyejin5/Spectrum-Aware-Illumination-Estimation-Using-Multispectral-Image.

05.
arXiv (CS.LG) 2026-06-19

Algebraic Dead Directions in LayerNorm Transformers: A Forward-Pass-Only Diagnostic at LLM Scale

arXiv:2606.19491v1 Announce Type: new Abstract: Pretrained transformers sit near singular minima of the loss, where the Fisher information metric degenerates along dead directions: directions in parameter space along which the directional Fisher vanishes. Locating such a direction normally needs a forward pass and an eigendecomposition of activations, or a sampling-based complexity estimate; none returns a direction computable from the network's parameters alone. We give one, for LayerNorm transformers. The inverse-scale direction $\gamma^{-1}/\|\gamma^{-1}\|$ of the LayerNorm affine is an exact algebraic kernel of the post-final-norm centred activation covariance, for any input distribution, and induces a corresponding dead direction in parameter space. It is read from the LN scale parameter alone, with no forward or backward pass and no eigensolve: the cheapest dead-direction read, specific to LayerNorm. We test it on $14$ pretrained transformers ($9$ LayerNorm, $5$ RMSNorm; $160$M-$35$B; language and vision objectives). At random initialisation the predicted direction matches the measured bottom singular direction (one forward pass, direct SVD) to four decimal places on $9/9$ LayerNorm models, and is correctly absent on $5/5$ RMSNorm models, which lack the mean-subtraction projector that creates it. On the trained checkpoint the covariance eigenvalue along this direction deepens by ${\sim}10^3\times$ and further dead directions open; the random-init-to-trained gap is a one-forward-pass, per-checkpoint readout of singular structure along the predicted coordinate. Two consequences follow in closed form: the residual stream's smallest singular value is preserved block-to-block on $13/14$ transformers measured on their own input distribution, the one exception (Gemma$4$-$31$B) a genuine dead direction the same read pinpoints; and the kernel direction's presence classifies a transformer's normalisation from the parameters alone.

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

Diffusive Dynamics of Nonstabilizerness

arXiv:2606.13606v1 Announce Type: new Abstract: Symmetries shape the quantum-information dynamics of many-body systems, but their effect on nonstabilizerness, the resource complementary to entanglement, is less understood. We compute the stabilizer Rényi entropy, a measure of nonstabilizerness, in $\mathrm{U}(1)$-symmetric one-dimensional random circuits. The disorder-averaged dynamics is captured by a four-replica tensor network, which we evaluate by $S_4$-adapted infinite time-evolving block decimation (iTEBD) directly in the thermodynamic limit. Together with a hydrodynamic argument, our results identify a diffusive universality class for the late-time approach of nonstabilizerness to its random-state value, with the stabilizer Rényi entropy gap closing as $1/t$. The same scaling is verified in an energy-conserving nonintegrable Ising chain. More broadly, our framework provides a hydrodynamic perspective on nonstabilizerness generation and offers insight into the design of approximate Haar-random states in Hamiltonian dynamics.

07.
arXiv (CS.CL) 2026-06-17

Scaling Enterprise Agent Routing: Degradation, Diagnosis, and Recovery

Production LLM assistants route user requests to growing libraries of specialized tools, but how does routing accuracy degrade as the catalog scales? We study single-step routing on a 110-agent, 584-tool catalog from a deployed enterprise productivity assistant, evaluating three frontier models from 10 to 110 agents. Routing F1 on under-specified requests drops 16–23 percentage points across models. An oracle analysis decomposes the degradation into a retrieval gap (the model cannot surface the right tool) and a confusion gap (even with perfect retrieval, the oracle ceiling drops 10pp). Embedding-based shortlisting recovers +10–11pp F1 at full scale across all three models and two providers. A production annotation study (1,435 human-labeled utterances, three annotators) confirms the recovery on real traffic at +10–17pp despite 10–15pp lower absolute performance.

08.
arXiv (CS.CL) 2026-06-15

SciDef: Datasets and Tools for Automated Definition Extraction from Scientific Literature with LLMs

Scientific concepts are often defined inconsistently across papers, making it difficult to compare findings, reuse terminology, and build reliable downstream resources. We present SciDef, a resource suite for scientific definition extraction. The suite contains DefExtra, a benchmark of 268 human-validated author-stated definitions from 75 academic papers; DefSim, 60 human-labeled definition-pair similarity judgments; and an open LLM-based pipeline for PDF preprocessing, chunking, definition extraction, prompt optimization, and evaluation. We validate the resources by benchmarking 16 language models across prompting strategies and chunking schemes. The strongest set-level configuration achieves a score of 0.397, while the highest-coverage configuration matches at least one prediction to 86.4% of gold definitions but over-generates candidate definitions. We further show that an NLI-based matching metric agrees strongly with human DefSim judgments. These results position SciDef as a reusable benchmark and tooling layer for definition-centric literature analysis, while highlighting relevance-aware filtering as the key bottleneck for fully automatic definition extraction. Code & datasets are available at https://github.com/Media-Bias-Group/SciDef.

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

GenAutoML: An Agentic Framework for Dynamic Architecture Generation and Optimization in Time-Series Analysis

arXiv:2606.05860v2 Announce Type: replace Abstract: Designing neural architectures for time-series forecasting and anomaly detection remains a resource-intensive task that often requires substantial domain expertise. Traditional Automated Machine Learning (AutoML) systems typically rely on static, predefined search spaces, limiting their ability to adapt to diverse data characteristics. We present GenAutoML, an agentic framework that leverages Large Language Models (LLMs) as neural architects to bridge natural-language requirements and executable PyTorch implementations. The framework incorporates a Sandboxed Reflection Loop for autonomous code refinement and a Signature-Aware Runtime that enforces architectural consistency and execution safety. To improve robustness under non-stationary conditions, we further introduce a Dynamic Reversible Instance Normalization (Dyn-RevIN) wrapper. Experiments on the ETTh1, ETTm1, and Weather benchmarks demonstrate that GenAutoML can dynamically generate task-specific neural architectures tailored to dataset characteristics. Among the generated models, WaveInterferenceNet achieves inference latency below 0.01 ms per sample while maintaining competitive predictive performance. By emphasizing computational efficiency, architectural adaptability, and stable optimization behavior, GenAutoML enables the creation of ultra-lightweight neural networks suitable for resource-constrained and latency-sensitive Edge AI deployments.

10.
arXiv (CS.LG) 2026-06-15

Machine Learning for Biomedical Raman Spectroscopy: From Spectral Acquisition to Clinical Translation

arXiv:2606.14169v1 Announce Type: new Abstract: Raman spectroscopy provides label-free, chemically specific characterization of biological systems and has become an important tool for cancer diagnosis, molecular subtyping, microbiological identification, and intraoperative decision support. Biomedical Raman spectra are, however, high-dimensional, noisy, and affected by fluorescence background, acquisition variability, and biological heterogeneity, making robust computational analysis essential. This review examines the role of machine learning across the biomedical Raman spectroscopy pipeline, from preprocessing and signal correction to unsupervised structure discovery, supervised diagnosis and molecular stratification, representation and transfer learning, explainability, biomarker discovery, and multimodal integration with imaging, pathology, and molecular profiling. Emphasis is placed on the use of machine learning not only for diagnostic classification, but also for biologically interpretable and clinically actionable analysis. We also discuss the main barriers to clinical translation, including limited dataset sizes, inter-instrument variability, inconsistent preprocessing, insufficient external validation, reproducibility concerns, and limited sharing of software, data, and metadata. We argue that progress will require methodological advances together with standardization, robust validation, explainability, and deployment-ready analytical frameworks. By integrating methodological, biomedical, and translational perspectives, this review outlines key directions for developing reliable and clinically deployable Raman-AI systems.

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

AfriSUD: A Dependency Treebank Collection for Evaluating Models on African Languages

Despite their linguistic diversity and global significance, African languages remain underrepresented in research and resources to support NLP. We aim to bridge this gap by introducing AfriSUD, the first large-scale collection of syntactically annotated treebanks for nine diverse African languages spanning major language families and regions across Sub-Saharan Africa. Using the Surface-Syntactic Universal Dependencies (SUD) framework, our community-led effort provides high-quality, native-speaker verified data that capture typological key features such as agglutination and tone. We evaluate a range of models on AfriSUD for part-of-speech tagging and dependency parsing including non-transformer baselines, multilingual pretrained encoders, and LLMs. Our results reveal a significant syntax gap, where models still show clear limitations across the nine languages, suggesting that existing architectures may not fully capture the structural diversity of African-language syntax.

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

ScholarQuest: A Taxonomy-Guided Benchmark for Agentic Academic Paper Search in Open Literature Environments

arXiv:2606.20235v1 Announce Type: cross Abstract: Academic paper search is a core step in scientific research, and LLM-based search agents are emerging as a promising paradigm for iterative, intent-driven literature exploration. However, existing benchmarks are insufficient for systematically evaluating agentic academic search under realistic open literature environments. We propose ScholarQuest, a large-scale, taxonomy-guided benchmark for agentic academic paper search. ScholarQuest is constructed from over 1,000 computer science topics and four representative research intents, including method-oriented, setting-anchored, comparison-based, and scope-controlled queries. It further provides scalable answer construction and a shared retrieval backend ScholarBase for reproducible evaluation. Benchmarking results show that agentic methods outperform single-shot retrieval baselines, yet the best-performing agent only achieves 0.314 Recall@100 and 0.355 Recall@All, indicating substantial room for improvement. In addition, analyses of search efficiency, intent-level robustness, and failure cases further highlight the benchmark's ability to provide multi-dimensional evaluation signals for academic paper search agents.

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

Beyond Safe Data: Pretraining-Stage Alignment with Regular Safety Reflection

arXiv:2606.19168v1 Announce Type: new Abstract: To achieve deeper safety alignment for large language models (LLMs), recent efforts have studied how to push safety interventions earlier into the pretraining stage, primarily by filtering unsafe data or rewriting it into safer forms. We argue that pretraining-stage alignment should go beyond making the data safe: LLMs may compose seemingly benign knowledge and capabilities into unsafe behaviors. To this end, we propose Safety Reflection Pretraining, a pretraining-stage alignment method which regularly inserts short safety reflections into pretraining corpora to integrate self-monitoring directly into language modeling, establishing a foundational capability that is subsequently reinforced by compatible post-training. Our experiments with 1.7B models pretrained on FineWeb-Edu show that Safety Reflection Pretraining improves safety classification accuracy and substantially reduces the success rates of inference-stage and finetuning attacks. Complementary to our real-world experiments, we also introduce a fully controlled synthetic environment, MedSafetyWorld, with a clear definition of safety and a reasoning structure under which models can easily generalize unsafe behaviors from safe data. Ablations in MedSafetyWorld further demonstrate a clear advantage of Safety Reflection Pretraining in preventing models from acting on unsafe behaviors generalized from safe data, compared with data filtering and rewriting. Taken together, our findings suggest that pretraining alignment should not only make the training data safe, but also shape the behaviors that models are likely to acquire from safe data.

14.
arXiv (quant-ph) 2026-06-19

Approximating optimal decoding of quantum LDPC codes with narrow frontiers

arXiv:2606.20513v1 Announce Type: new Abstract: We introduce the Frontier decoder, a pruned dynamic-programming decoder for sparse quantum decoding problems. Frontier processes error variables in a chosen order, merges prefixes with the same residual syndrome and logical label, and approximates logical-coset posterior masses by retaining only a narrow scored frontier. Without pruning, the recursion is exact ordered inference with exponential complexity. In the code-capacity setting, the decoder reaches thresholds close to optimal for the surface code and the color code. In the circuit-level noise model, it achieves state-of-the-art performance with a very small average retained list size: less than 100 for the gross code $[[144,12,12]]$ at a physical error rate of $0.001$. When the list size is constant, the decoder has linear complexity, suggesting the possibility of low-latency implementations.

15.
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/

16.
arXiv (CS.CV) 2026-06-19

Neural Events: Discrete Asynchronous Autoencoders for Event-Based Vision

Event cameras capture dynamic scenes with exceptional temporal fidelity by representing them as a continuous stream of microsecond resolution events. Each individual event, however, only carries minimal semantic value, merely signaling a localized brightness change. To derive meaningful signals, downstream algorithms need to quickly integrate cues from a potentially massive torrent of low-information events. Current architectures, however, are easily overwhelmed, struggling to balance capturing fine-grained temporal dynamics and maintaining a manageable data throughput. This paper proposes a framework to re-tokenize event streams into a small set of highly informative neural events, each representing a local spatio-temporal context window with a discrete learnable code. Every time this code flips, a neural event is triggered, yielding a highly compressed data stream. We demonstrate that, across object detection and classification, networks trained on neural events are on par or surpass the performance of state-of-the-art approaches while reducing the event rate by a factor of 2.0.

17.
arXiv (quant-ph) 2026-06-12

Efficient certification of intractable quantum states with few Pauli measurements

arXiv:2511.07300v2 Announce Type: replace Abstract: Efficient verification of quantum computational resources is crucial as experiments advance toward fault-tolerance. Universal quantum computation can be achieved by consuming resource states through simple Pauli measurements, yet a significant gap remains between states that are easy to certify and those required for universality. We focus on Clifford-enhanced Product States, a class of resource states obtained by applying Clifford circuits to a product of single-qubit, potentially magic, states. While essential for universal computation, the certification of such states has previously relied on query oracles that are \#P-hard to implement, leaving their efficient, oracle-free verification an open challenge. In this work, we demonstrate that such classically intractable resource states can be efficiently verified using only Pauli measurements. Our protocol achieves sample- and time-efficiency in both i.i.d.\ and adversarial settings. This work fills a gap in Pauli-based certification, providing a new practical pathway to verify resource states that drive universal Pauli-based quantum computation.

18.
arXiv (quant-ph) 2026-06-16

Symmetry Breaking through Superselection by Boundary Conditions

arXiv:2606.15272v1 Announce Type: cross Abstract: Spontaneous symmetry breaking (SSB) is central to modern physics but is conventionally defined only for infinite systems, raising challenges for its interpretation in finite, real-world setups. This paper argues that the key to resolving this issue lies in the underappreciated role of boundary conditions in quantum systems. Inspired by both the relational approach to symmetries and the physical mechanism behind symmetry breaking, we formulate a relational interpretation of SSB: a finite system exhibits SSB relative to a reference environment which can induce perturbations across the boundary. This eliminates the need for the thermodynamic limit, offering a more physical picture of SSB that emphasizes the observable consequences of the interactions that real-life systems inevitably have with their environment. We show how, in this relational interpretation, SSB for both lattice systems and (gauge) field theories should be understood as subtle, rather than spontaneous, symmetry breaking, still in contrast to explicit symmetry breaking. We also explain how algebraic definitions of SSB for infinite systems relate to the intuitive picture of SSB in finite systems and illustrate how asymptotic boundary conditions push the environment "to infinity". In this way, our relational interpretation of SSB provides a unified conceptual framework applicable to symmetry-breaking in systems of any size.

19.
arXiv (CS.CV) 2026-06-16

Wavelength-Multiplexed 2D Beam Steering via a Passive Diffractive Network

We introduce a wavelength-addressable diffractive optical network that transforms illumination wavelength into a high-dimensional control parameter for arbitrarily programmable 2D beam steering. The proposed passive architecture comprises cascaded spatially optimized diffractive layers, jointly designed using deep learning, to rapidly map distinct wavelengths to predefined/desired output angles. Unlike conventional single-layer dispersive optical elements, which are physically restricted to 1D linear mapping, this framework harnesses complex wavefront transformations to utilize the illumination wavelength as an intrinsic addressing key for arbitrary 2D beam steering, eliminating the need for mechanical scanning or electronic phase control. We numerically demonstrate wavelength-controlled beam steering across 625 wavelength channels spanning 400-750 nm, realizing a 25 x 25 array of independently addressable beam positions with subwavelength positioning accuracy and high channel fidelity. Unlike conventional gratings, which constrain wavelength routing to a linear trajectory, the proposed diffractive network performs nonlocal wavefront transformations, enabling arbitrary wavelength-to-angle mappings across a 2D field of view. We further validate the proposed framework experimentally in both the terahertz and visible spectral regimes, demonstrating wavelength-multiplexed beam steering using 3D fabricated passive diffractive layers at terahertz frequencies and phase-only spatial light modulators in the visible spectrum. This wavelength-addressable diffractive architecture establishes a compact and scalable paradigm for high-speed programmable beam steering, with potential applications in optical communications, routing, imaging, sensing, and emerging photonic information-processing systems.

20.
arXiv (quant-ph) 2026-06-17

Matrix Product States for Modulated Symmetries: SPT, LSM, and Beyond

arXiv:2603.19189v2 Announce Type: replace-cross Abstract: Matrix product states (MPS) provide a powerful framework for characterizing one-dimensional symmetry-protected topological (SPT) phases of matter and for formulating Lieb-Schultz-Mattis (LSM)-type constraints. Here we generalize the MPS formalism to translationally invariant systems with general modulated symmetries. We show that the standard symmetry "push-through" condition for conventional global symmetry must be revised to account for symmetry modulation, and we derive the appropriate generalized condition. Using this generalized push-through structure, we classify one-dimensional SPT phases with modulated symmetries and formulate LSM-type constraints within the same MPS-based framework.

21.
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.

22.
bioRxiv (Bioinfo) 2026-06-17

DNA-binding specificity recognition from predicted homologous protein-DNA structures

Predicting protein DNA-binding specificity is essential for understanding gene regulation and disease mechanisms. Existing deep learning methods typically infer specificity from a single protein-DNA complex structure, which limits their ability to capture the diverse geometric patterns underlying protein-DNA recognition. Homologous protein-DNA interfaces provide complementary structural evidence and richer geometric features related to interatomic interactions. To address the limited diversity and coverage of experimentally determined complexes, we constructed a large-scale library of predicted homologous protein-DNA complex structures. Building on this resource, we propose HomoDSP, a template-retrieval-based framework for accurate DNA-binding specificity prediction. Benchmark evaluations and validation on newly released JASPAR 2026 samples indicate that HomoDSP outperforms existing methods in both accuracy and generalization, with particularly substantial gains on high-error samples. Moreover, this performance is largely retained when AlphaFold3-predicted complex structures are used as input. Template- and residue-level interpretability analyses suggest that HomoDSP improves prediction by focusing on DNA-affinity residues across multiple homologous templates. Finally, universal Protein Binding Microarrays evaluations on AI-designed DNA-binding proteins show that HomoDSP rescues a baseline failure mode in which the baseline method produces incorrect predictions because of training-set bias. Together, these results support the use of homologous template interfaces as informative structural priors for decoding protein DNA-binding specificity.

23.
arXiv (CS.LG) 2026-06-17

SpatioTemporal Causal Network Diagnostics for Geographic Tipping Point Early Warning

arXiv:2606.17553v1 Announce Type: new Abstract: Geographic tipping points in ecosystems, climate subsystems, or ice sheets pose severe challenges for localized early warning. Classical spatial indicators such as Moran's I summarize global spatial structure, but they struggle with three issues: spatial dilution, Euclidean assumptions, and correlated noise. This paper introduces SpatioTemporal Causal Network Diagnostics (ST-CND), a framework that addresses these three issues by representing the geographic field as a time-evolving directed causal network. The core workflow is as follows: (1) infer which spatial nodes help predict other nodes via transfer entropy, replacing fixed Euclidean neighborhoods with data-driven information-flow topology; (2) estimate local recovery rates within each candidate subnetwork via dynamic mode decomposition; and (3) identify the most vulnerable subnetwork by combining three signals, namely high internal fluctuation, high internal synchronization, and low external coupling, thereby suppressing false alarms from spatially correlated noise. Validated on synthetic bifurcations and two observational sea-surface temperature benchmarks, namely Indo-Pacific SST and North Atlantic AMOC, ST-CND delivers localized and interpretable warnings. On the AMOC task, it achieves an AUROC of 0.783 and a critical-subnetwork IoU of 0.378, outperforming recurrence-network and lambda-AR1 baselines. The framework provides an interpretable and scalable pipeline for spatial early warning in Earth system science.

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

Agent Skill Evaluation and Evolution: Frameworks and Benchmarks

The growth of agent skills has transformed how agentic systems are built, evaluated, and deployed. As skill libraries continue to scale, rigorous evaluation becomes critical to ensuring their utility, quality, and safety in real-world applications. Consequently, the field is undergoing an emerging paradigm shift from isolated skill creation to automated, evaluation-driven skill evolution. In this survey, we systematically examine the landscape of skill evolution and evaluation beyond foundational skill creation. We categorize evolution into four distinct paradigms, spanning execution feedback, trajectory distillation, compression, and reinforcement learning, showing how each element contributes to improving skill utility and reliability. We also provide an analysis of six skill-centric benchmark categories, identifying structural gaps in benchmark coverage, trade-offs, and metric richness to advance skill research. Finally, we identify open directions for building skill ecosystems that are generalizable, efficient, and verifiably safe. The project URL is https://github.com/Cassie07/AgentSkill_Survey

25.
bioRxiv (Bioinfo) 2026-06-11

A systematic imputation framework for sparse, multimodal space biology datasets: application to retinal imaging and omics from the RR9 mission

Space biology experiments are expensive, logistically complex, and inherently limited in sample size, resulting in datasets that are frequently incomplete and highly heterogeneous (2). Missing data is a fundamental barrier to building reliable computational models of how the human body responds to spaceflight. This work introduces a systematic framework for addressing missing data through imputation. We developed a validated four-stage framework for imputation specifically designed to preserve biological signal needed for digital twin development, while quantifying trade-offs in downstream analyses. Using retinal imaging and omics data from the NASA RR9 mission as a case study (9), we demonstrate how to diagnose why data is missing(10), select and optimize appropriate imputation strategies (5,10), and rigorously evaluate whether imputed data remains biologically meaningful. A key finding of this work is that while imputation substantially improves the performance of predictive models, it can simultaneously obscure subtle biological patterns; a critical trade-off that researchers must understand before applying these methods (11). This framework provides practical, actionable guidance for space biologists and data scientists working with sparse, multimodal datasets in space biology, and represents a foundational step toward more complete and reliable data-driven models of human physiology in extreme environments.