Academic Intelligence · Curated Daily

探索全球前沿学术脉络

AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。

01.
medRxiv (Medicine) 2026-06-24

Multifactorial tuberculosis severity score for people living with HIV based on the Rand Appropriateness Method

Background In people living with Human Immunodeficiency Virus (PLWH), tuberculosis (TB) is the leading cause of death and is often associated with substantial morbidity. Better identifying PLWH with severe forms of TB could help target early interventions to reduce mortality and severe morbidity. Existing TB severity assessment tools may be sub-optimal for assessing disease severity in PLWH, since they incompletely integrate key determinants of disease severity. We aimed to develop a consensus-based TB severity score tailored to PLWH. Methods We developed a multifactorial TB severity score (TBSS) for PLWH using a modified Delphi process with a multidisciplinary group of international TB experts as the second part of a RAND/UCLA Appropriateness Method, following a previously published systematic review. Results Eight of 15 invited experts (53%) participated in both Delphi rounds. Of 62 candidate factors, 15 reflecting TB-related characteristics, host-related characteristics as well as characteristics related to both TB and host were rated as having high appropriateness for inclusion in the final TBSS. The total score ranges from 0 (no severity) to 61 (highest severity). Conclusion This study represents a first step towards the development of a multidimensional TB severity assessment tool for PLWH. However, its clinical usefulness, feasibility, and added value compared with existing severity scores remain to be demonstrated through validation studies before routine implementation can be considered. Key words: tuberculosis, HIV, severity.

02.
arXiv (CS.AI) 2026-06-16

Bayesian 3D Steerable CNNs: Enabling Equivariance and Uncertainty Quantification Simultaneously

arXiv:2606.15479v1 Announce Type: cross Abstract: Steerable convolutional neural networks (Steerable-CNNs) guarantee SE(3)-equivariance by parameterizing kernels as linear combinations of steerable basis functions, but their deterministic nature precludes uncertainty quantification - limiting their use in settings where confidence estimates are essential. We propose a Bayesian Steerable-CNN that places posterior distributions over the basis coefficients, yielding stochastic kernels while preserving equivariance exactly. The loss function of the model is obtained via variational inference and minimized by Bayes-by-Backpropagation. The framework admits a decomposition of predictive uncertainty into epistemic and aleatoric components. Empirically, the model attains competitive classification accuracy alongside an expected calibration error of 0.0263 and outperforms its deterministic counterpart by up to 6.17% under distributional shift induced by additive Gaussian noise. Furthermore, we leverage the model's uncertainty estimates to enhance its performance significantly, achieving a notable gain - approximately 4% higher accuracy across 84% of the test dataset. A statistically significant negative correlation between epistemic uncertainty and prediction error confirms that the learned posterior variance is semantically meaningful. The framework unifies Bayesian uncertainty quantification with the inductive bias of equivariant CNNs.

03.
arXiv (CS.AI) 2026-06-19

Evaluating and Enhancing Negation Comprehension in Remote Sensing MLLMs

arXiv:2606.20177v1 Announce Type: cross Abstract: Multimodal Large Language Models (MLLMs) have demonstrated remarkable success in various Remote Sensing (RS) tasks. However, their ability to comprehend negation remains underexplored, limiting deployment in real-world applications where models must explicitly identify what is false or absent, e.g., emergency responders need to locate non-flooded routes for evacuation. To comprehensively study this limitation, we introduce RS-Neg, the first benchmark to evaluate negation understanding across region-level to scene-level tasks. Specifically, we design an automated data generation pipeline for RS imagery, using LLMs to synthesize diverse negation queries, and introduce a dynamic visual focus module for verification. Our evaluation reveals that advanced RS MLLMs struggle with negation, exhibiting hallucinations and substantial performance degradation. To close this gap, we propose NeFo, a novel test-time learning method that explicitly incorporates the logical role of negation into the model optimization. Remarkably, using about 5\% unlabeled test samples, NeFo significantly improves the negation understanding of models and shows strong generalization to unseen tasks. Code and data will be released upon acceptance.

04.
arXiv (CS.CL) 2026-06-24

MorfFlex: Handling Rich Morphology

We present MorfFlex, a morphological dictionary architecture suitable for languages with extensive regularity in both inflection and derivation. As the primary example of MorfFlex in use we introduce MorfFlex CZ, a morphological dictionary of Czech. It is distributed as a simple, unstructured list of triplets, however, its manually maintained, unpublished source files and conversion scripts encode a sophisticated system of inflectional and derivational patterns. These patterns dramatically reduce the otherwise enormous size of the dictionary, which currently contains over 100 million wordforms and more than 1 million lemmas. The MorfFlex CZ dictionary serves as an essential resource for ensuring the consistency of manual morphological annotation in the Prague Dependency Treebanks and underpins state-of-the-art automatic tools such as MorphoDiTa. In this paper, we focus on: (i) presenting an effective method for managing the rich morphological system within the dictionary, and (ii) demonstrating the utility of such a language resource for maintaining annotation consistency in corpora and supporting the development of advanced NLP applications.

05.
arXiv (CS.AI) 2026-06-17

WallZero: Mastering the Game of WallGo with Strategic Analysis

arXiv:2606.17847v1 Announce Type: new Abstract: WallGo is a recently introduced strategic board game popularized by the 2025 Netflix series The Devil's Plan. Although played on a small 7 x 7 board, its combination of stone movement and wall placement yields high game-tree complexity and intricate strategic interactions. Despite its growing popularity, WallGo remains underexplored. This paper presents WallZero, an AlphaZero-based agent for the two-player WallGo setting. We introduce tailored action and feature designs to improve playing performance significantly. In the evaluation, WallZero defeats two professional Go players who participated in this study, securing on average 1.98x more territory per game. Beyond its strength, we use WallZero to assess game fairness and identify key strategies for mastering WallGo. Interestingly, our results show that the opening used in the Netflix series yields a more balanced game. Our code is available at https://rlg.iis.sinica.edu.tw/papers/wallzero.

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

Overcoming Labelled Data Scarcity for Defect Classification in Scanning Tunneling Microscopy

arXiv:2506.01678v2 Announce Type: replace-cross Abstract: Scanning tunnelling microscopy (STM) is a powerful technique for imaging surfaces with atomic resolution, providing insight into physical and chemical processes at the level of single atoms and molecules. A regular task of STM image analysis is the identification and labelling of features of interest against a uniform background. Performing this manually is a labour-intensive task, requiring significant human effort. To reduce this burden, we propose an automated approach to the segmentation of STM images that uses both few-shot learning and unsupervised learning. Our technique offers greater flexibility compared to previous supervised methods; it removes the requirement for large manually annotated datasets and is thus easier to adapt to an unseen surface while still maintaining a high accuracy. We demonstrate the effectiveness of our approach by using it to recognise atomic features on three distinct surfaces: Si(001), Ge(001), and TiO$_2$(110), including adsorbed AsH$_3$ molecules on the silicon and germanium surfaces. Our model exhibits strong generalisation capabilities, and following initial training, can be adapted to unseen surfaces with as few as one additional labelled data point. This work is a significant step towards efficient and material-agnostic, automatic segmentation of STM images.

07.
arXiv (CS.LG) 2026-06-15

Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction

arXiv:2606.14217v1 Announce Type: new Abstract: Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery. Recent geometric deep learning methods have achieved promising performance by representing protein-ligand complexes as three-dimensional graphs. However, most existing approaches mainly rely on static interaction geometry from a single bound conformation, while neglecting molecular flexibility and binding-induced conformational changes. To address this limitation, we propose a curvature-informed potential energy surface (CPES) graph neural network for protein-ligand binding affinity prediction, which incorporates physics-informed curvature representations to model conformational flexibility. CPES first derives curvature spectral descriptors from the Hessian of the potential energy surface evaluated at equilibrium configurations, whose eigenvalues define the local principal curvatures of the potential energy surface. It then uses spectral cross-attention to compare the unbound ligand and protein with the bound complex, thereby capturing binding-induced changes in conformational dynamics. In parallel, hierarchical protein-ligand interaction representations are learned from static structural features through geometry-aware message passing, soft clustering, and bidirectional cross-attention. Finally, CPES fuses the curvature-informed dynamic representations with static interaction representations for affinity regression. Extensive evaluations on multiple benchmark datasets demonstrate that CPES achieves improved predictive performance and offers physical interpretability.

08.
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/

09.
arXiv (quant-ph) 2026-06-15

Inhomogeneous Light-Matter Coupling as a Resource for Noiseless Quantum Memories

arXiv:2605.26783v3 Announce Type: replace Abstract: Inhomogeneous ensembles of two-level systems are central to both fundamental light-matter physics and quantum-network applications. Understanding and optimizing ensemble-based quantum memories and entanglement protocols requires a unified framework that describes how to store quantum states of light as collective matter excitations and retrieve them on demand. Here we develop such a framework, the waveguide model, by mapping the dark collective modes of the ensemble onto an effective waveguide with well-defined input-output relations, valid in both the weak-excitation regime and near population inversion. This model reveals that inhomogeneous coupling – often regarded as a limitation – is instead the physical origin of noisy-echo suppression by adiabatic pulses, a key ingredient for realizing noiseless quantum memories. For entanglement generation, the same mechanism exposes a previously unexplored shortcoming of robust control pulses and leads to a new composite-pulse protocol that overcomes it. These results establish the waveguide model as a practical bridge between fundamental collective physics and quantum-network protocol design, recasting inhomogeneous coupling from an obstacle into a control knob for collective emission.

10.
arXiv (CS.AI) 2026-06-18

Target-confidence Recourse Using tSeTlin machines: TRUST

arXiv:2606.18832v1 Announce Type: cross Abstract: Counterfactual explanations are widely used to provide algorithmic recourse in high-stakes decision-making systems. Most existing methods seek the smallest change to an input that flips a model's decision. However, decision-makers often rely not only on predicted labels but also on confidence thresholds and risk margins. Counterfactuals that barely cross a decision boundary can be fragile and unstable under noise or model variation. In this paper, we propose Target-confidence Recourse Using tSeTlin machines (TRUST), a framework in which users explicitly specify the desired prediction confidence for recourse. Rather than generating counterfactuals and evaluating confidence afterward, TRUST directly searches for minimal changes that satisfy a user-defined confidence target, enabling comparison of recourse options in terms of cost, confidence, and robustness. We instantiate TRUST using a Probabilistic Tsetlin Machine (PTM) combined with Bayesian optimization. The probabilistic clause-based structure of PTM links prediction confidence to the stability of decision rules. We show that counterfactuals satisfying the same rules can still differ substantially in reliability depending on how securely they satisfy those rules, revealing whether decisions are supported by robust or fragile clause activations. Experiments on synthetic and real-world datasets demonstrate that target-confidence counterfactuals produce more robust and interpretable recourse than conventional boundary-based approaches. Across multiple benchmarks, TRUST achieves perfect robustness while maintaining low recourse cost, including an L2 distance of 0.10 on the Haberman dataset at 0.92 confidence. By explicitly controlling confidence and exposing rule-level stability, TRUST provides actionable recourse for high-stakes decision support.

11.
medRxiv (Medicine) 2026-06-15

Fanconi Anemia as a Window into Premalignant Field Cancerization of the Oral Mucosa

Head and neck squamous cell carcinoma (HNSCC) evolves through stepwise clonal expansion within genetically altered mucosa fields, yet actionable biomarkers remain undefined. Leveraging Fanconi anemia (FA), a cancer predisposition syndrome with extreme HNSCC risk due to defective DNA interstrand crosslink repair, we profiled premalignant changes in the oral cavity using noninvasive brush biopsies. Consistent with our prior demonstration of genomic instability in FA-associated SCCs, we detected pathogenic TP53 variants in 26% and copy number alterations in 60.5% in clinically normal-appearing oral mucosa of individuals with FA. These subclinical clonal expansions define candidate biomarkers of early clonal evolution amenable to serial sampling for risk stratification and prevention studies. Since FA-associated SCCs share genomic features with sporadic HNSCC, these findings may extend to the broader population. We also identify somatic reversion of a pathogenic FANCB variant, providing evidence of genomic self-correction and suggesting a potential avenue for gene-based cancer prevention in FA.

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

SorryDB: Can AI Provers Complete Real-World Lean Theorems?

arXiv:2603.02668v2 Announce Type: replace Abstract: We present SorryDB, a dynamically-updating benchmark of open Lean tasks drawn from 78 real world formalization projects on GitHub. Unlike existing static benchmarks, often composed of competition problems, hillclimbing the SorryDB benchmark will yield tools that are aligned to the community needs, more usable by mathematicians, and more capable of understanding complex dependencies. Moreover, by providing a continuously updated stream of tasks, SorryDB mitigates test-set contamination and offers a robust metric for an agent's ability to contribute to novel formal mathematics projects. We evaluate a collection of approaches, including generalist large language models, agentic approaches, and specialized symbolic provers, over a selected snapshot of 1000 tasks from SorryDB. We show that current approaches are complementary: even though an agentic approach based on Gemini Flash is the most performant, it is not strictly better than other off-the-shelf large-language models, specialized provers, or even a curated list of Lean tactics.

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

Repeated Bilateral Trade: The Quest for Fairness

arXiv:2606.15369v1 Announce Type: new Abstract: We study repeated bilateral trade from a fairness perspective. At each round, a fresh seller-buyer pair arrives, and the platform posts a price before observing the traders' valuations. Trade occurs only if both agents accept the price. Rather than maximizing only the gain from trade, we consider platforms that seek balanced divisions of the generated surplus. We show that natural fairness desiderata lead to a one-parameter Rawls-to-Nash family of fair-gain objectives, obtained by aggregating the seller's and buyer's net gains through nonpositive Hölder means. Unlike the standard gain-from-trade objective and the Rawlsian fair-gain objective studied in prior work, our proposed objectives induce a new statistical structure in which expected rewards are recovered from threshold feedback through a two-dimensional singular-kernel integral identity. This leads to a nonstandard pure-exploration problem whose natural estimators are rectangular double sums with row-column dependence and singular weights. Assuming independent i.i.d. seller and buyer valuation sequences with arbitrary unknown marginals, we characterize the optimal learning rates for the whole Rawls-to-Nash family of fair-gain objectives, giving matching fixed-confidence sample-complexity and regret bounds up to polylogarithmic factors.

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

Continuous Language Diffusion as a Decoder-Interface Problem

Gaussian-corrupted sentence embeddings have no direct linguistic interpretation, yet continuous diffusion language models can generate fluent text from them. We study this puzzle through Embedded Language Flows (ELF) and identify a decoder-basin mechanism: our evidence suggests that denoising becomes reliable when trajectories reach regions where the native decoder can read stable tokens. We introduce a diagnostic protocol for denoisability, semantic recoverability, order sensitivity, decoder compatibility, and trajectory reliability. It exposes failures hidden by scalar metrics: low mean-squared error can discard linguistic content, low perplexity can reflect low-entropy collapse, and clean latent reconstruction can coexist with a narrow decoder basin. A decoder-margin bound explains why token recovery depends on margin and local decoder sensitivity, not latent error alone. Auditing public ELF checkpoints reveals an interface phase diagram: early predictions are weakly readable, mid-trajectory disagreement marks a competition region, and late predictions enter a high-margin decoder basin. Once inside, token realization is surprisingly simple on generated ELF states: frozen T5 (Text-to-Text Transfer Transformer) token-embedding lookup recovers $93$–$96\%$ of native decoder decisions, and a single linear readout reaches $97.9\%$ agreement at 32k samples, leaving an $\approx1.1$–$1.2$ perplexity gap in a structured residual tail. Under conservative held-out gates, a margin rule exits roughly $17$–$28\%$ earlier in denoising steps under an explicit diagnostic monitor. Boundary checks on LangFlow, BitstreamDiffusion, and the Continuous Latent Diffusion Language Model (Cola-DLM) show that the same interface questions remain meaningful when the state object and decoder change. Continuous and latent diffusion language models should therefore be evaluated as representation-decoder systems.

15.
arXiv (CS.AI) 2026-06-17

Temporal Motif-aware Graph Test-time Adaptation for OOD Blockchain Anomaly Detection

arXiv:2605.29526v2 Announce Type: replace-cross Abstract: Ever-evolving transaction patterns have significantly hindered anomaly detection on emerging cryptocurrency blockchains due to the vast number of addresses and diverse anomalous behaviors. Recently, advanced Graph Anomaly Detection (GAD) approaches applied to blockchains have faced two critical challenges: adversarial pattern evolution by malicious actors and the out-of-distribution (OOD) problem caused by varied transaction semantics on blockchains. To address these challenges, we propose a novel framework termed TEmporal Motif-aware Graph Test-Time Adaptation (TEMG-TTA). First, we comprehensively capture the 3-node temporal motif distribution of each active address using an efficient computational mechanism, enabling downstream temporal motif-aware graph learning. Second, we design a simple yet effective test-time adaptation strategy to facilitate the sharing of common patterns between training and testing graphs. Extensive experiments on 5 real-world datasets demonstrate that our proposed TEMG-TTA outperforms state-of-the-art GAD approaches by an average of 54.88\%. A further case study on interpretable motif patterns reveals that TEMG-TTA explicitly characterizes the complex transaction patterns of anomalous addresses, thereby verifying the effectiveness of our technical designs. Our code is publicly available at https://github.com/LuoXishuang0712/TEMG-TTA/.

16.
bioRxiv (Bioinfo) 2026-06-15

AliceDB database and pipeline for identification of natural protein variants based on mass spectrometry measurement data

The natural variation that distinguishes living organisms within a single species is currently being studied intensively, primarily at the genetic level. Unfortunately, studies of natural variants at the level of protein gene products are not very common, mainly due to the lack of appropriate databases and bioinformatics tools. The main research technique used to study proteomes/peptidomes is mass spectrometry (MS). A classic method for interpreting raw mass spectrometry data in proteomic/peptidomic studies involves the use of databases containing representative (canonical) sequences that define the proteome of the organism under study. In this paper, we present the AliceDB database, which contains information on over 7 million natural variants of protein sequences described in the scientific literature for Homo sapiens. The data contained in the AliceDB database can be utilized using widely available and commonly used software for interpreting proteomic data. Test results regarding the use of the AliceDB database for the interpretation of proteomic data indicate that accounting for the presence of natural variants increases both the number and quality of identified proteins. Furthermore, it is easy to identify protein sequence variants that may, for example, be of significance in medicine.

17.
bioRxiv (Bioinfo) 2026-06-19

ContinuumCellAgent: A Framework-Guided Agent for Long-Horizon Scientific Research

AI-scientist systems are beginning to automate parts of scientific research. We present ContinuumCellAgent, an autonomous agent that executes literature review, hypothesis formation, computational experimentation, manuscript drafting, and adversarial peer review as a single unattended run. Existing AI scientist systems remain difficult to diagnose because they lack modularity, systematic prompt grounding, and observability into long-running behavior. ContinuumCellAgent addresses these gaps with a modular supernode architecture for stage-wise backend swapping, protocols grounded in curated research-method checklists that also define reviewer rubrics, and a diagnostics layer that records file-based artifacts, message traces, and state transitions. We evaluate the system on open-domain QA benchmarks and biomedical/longevity case studies, showing that it can produce checkable research artifacts while exposing pipeline dynamics for rigorous AI co-scientist research.

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

Fast LLM-Based Semantic Filtering: From a Unified Framework to an Adaptive Two-Phase Method

arXiv:2606.08090v2 Announce Type: replace-cross Abstract: Evaluating a natural-language yes/no predicate over a document corpus under an accuracy target - the semantic filter - is a cornerstone of LLM-based data processing. Calling the LLM on every document (the oracle) is prohibitive, so cascades pair the oracle with a fast proxy. As deployed today, they leave four limitations on the table. (1) Each cascade family - model-free clustering, prebuilt small-LLM proxies, online-trained proxies - commits to a single representation and pipeline, and wins on only a narrow query regime. (2) The strongest online proxy invests in a custom training scheme on a bi-encoder over dense embeddings, missing the token-level evidence richer predicates require. (3) The proxy is trained against binary yes/no labels, wasting the LLM's per-document confidence at the boundary documents it most needs to learn. (4) Existing calibrations add a uniform safety margin, conflating genuine proxy uncertainty with small-sample noise and inflating cascade cost. We address these by (1) composing families adaptively - model-free clustering first, online proxy only when needed, with oracle calls shared across phases; (2) replacing the cosine bi-encoder with a hybrid of off-the-shelf token-aware models; (3) training the proxy with the oracle's per-document confidence as a soft label; and (4) a calibration that adds the safety margin only where the labeled sample is sparse. We are also the first to use the oracle's per-document confidence for three purposes: a query-level difficulty compass, a lower bound on the minimum oracle calls any proxy-based cascade can make, and the proxy's soft training label. At a 90% accuracy target on three 10K-document corpora, our methods are 1.6-2.0x faster than the best prior method per corpus and meet the target on 95% of queries; the BER-derived lower bound indicates a further ~4-20x of headroom for future work.

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

Maximum entropy principle for quantum processes

arXiv:2506.24079v3 Announce Type: replace Abstract: The maximum entropy principle, as applied to quantum systems, is a fundamental prescript positing that for a quantum system for which we only have partial knowledge, the maximum entropy state consistent with the partial knowledge is a valuable choice as the system's state. An intriguing result is that in case the only prior knowledge is of a fixed energy, the maximum entropy state turns out to be the thermal state, a ubiquitous state in several arenas, especially in statistical mechanics. We extend the consequences of this principle from static quantum states to dynamic quantum processes. We establish that a quantum channel attains maximal output entropy under a fixed energy constraint if and only if it is an absolutely thermalizing channel, where the fixed output is the thermal state corresponding to that energy. Our results have potential implications for understanding the informational and thermodynamic utility of quantum channels under physical constraints. As an application, we examine the consequences for private randomness distillation from fixed energy constrained quantum processes.

20.
arXiv (CS.CL) 2026-06-15

Fractured Chain-of-Thought Reasoning

Inference-time scaling techniques have significantly bolstered the reasoning capabilities of large language models (LLMs) by harnessing additional computational effort at inference without retraining. Similarly, Chain-of-Thought (CoT) prompting and its extension, Long CoT, improve accuracy by generating rich intermediate reasoning trajectories, but these approaches incur substantial token costs that impede their deployment in latency-sensitive settings. In this work, we first show that truncated CoT, which stops reasoning before completion and directly generates the final answer, often matches the full CoT sampling while using dramatically fewer tokens. Building on this insight, we introduce Fractured Sampling, a unified inference-time strategy that interpolates between full CoT and solution-only sampling along three orthogonal axes: (1) the number of reasoning trajectories, (2) the number of final solutions per trajectory, and (3) the depth at which reasoning traces are truncated. Through extensive experiments on five diverse reasoning benchmarks and several model scales, we demonstrate that Fractured Sampling consistently achieves superior accuracy-cost trade-offs, yielding steep log-linear scaling gains in Pass@k versus token budget. Our analysis reveals how to allocate computation across these dimensions to maximize performance, paving the way for more efficient and scalable LLM reasoning. Code is available at https://github.com/BaohaoLiao/frac-cot.

21.
arXiv (CS.AI) 2026-06-17

LongWebBench: Evaluating Structural and Functional Webpage Generation in Long-Horizon Settings

arXiv:2606.17727v1 Announce Type: new Abstract: Recent vision-language models (VLMs) have shown promising progress in generating webpages from visual inputs, yet existing evaluations mainly focus on short, single-screen, and largely static webpages. We introduce LongWebBench, a benchmark for evaluating long-horizon webpage generation from both structural and functional perspectives. LongWebBench contains 490 real-world long webpages for structural fidelity evaluation and 507 goal-oriented interaction tasks over 129 webpages for functional evaluation. It employs two complementary protocols: a multi-dimensional VLM-based metric for assessing long-range structural coherence, and a DOM-augmented agent-based pipeline for end-to-end functional verification. We further examine the automatic evaluation protocols through human agreement analysis. Experiments with state-of-the-art open-source and proprietary VLMs under single-image and multi-image settings reveal that structural fidelity degrades as webpage length increases, while visually plausible generations often fail to support executable multi-step interactions. These results highlight the need to evaluate long webpage generation beyond visual similarity, with executable interaction as a core criterion. Our code and data are available at https://github.com/zheny2751-dotcom/LongWebBench.

22.
bioRxiv (Bioinfo) 2026-06-23

Multi-Scale Machine Learning for Antibody-Antigen Binding Affinity Prediction Using Deep Mutational Scanning and Structural Features

Predicting how mutations alter antibody-antigen binding affinity is essential for antibody engineering and vaccine design, yet current methods generalize poorly to unseen complexes. We present a multi-scale machine learning framework integrating 93 descriptors across four modalities: physicochemical, structural, ESM-2 protein language model, and solvent-accessible surface area (SASA)/{Delta}{Delta}G_fold features. Under leave-one-complex-out deep mutational scanning (LOCO-DMS) cross-validation on AbAgym (36,541 mutations, 68 experiments, 13 pathogens), gradient boosting achieved MCC = 0.206; a confidence-stratified ensemble reached MCC = 0.374 (83.5% accuracy, 25.5% coverage). No single modality exceeds the majority baseline alone; only multi-scale fusion succeeds. Boltzmann ceiling analysis shows 45.9% of mutations are near-neutral (|{Delta}{Delta}G| < k_BT), bounding theoretical maximum MCC at 0.473; our method achieves 79.1% of this limit. Five deep learning architectures benchmarked under LOCO-DMS showed self-attention matching gradient boosting (MCC = 0.200). Cross-pathogen transfer failed systematically (mean 46.7%), confirming universal binding predictors remain an open challenge.

24.
arXiv (CS.CV) 2026-06-16

Where Does Texture Evidence Live in SAM? Features, Proposal Masks, and Texture Segmentation

Texture segmentation stresses foundation segmentation because meaningful regions are defined by material or repeated appearance rather than object identity. Segment Anything Models (SAMs) often fail by default on such texture-defined partitions, but this failure is ambiguous: the texture evidence may be absent, missing from the proposal bank, or present but selected or assembled incorrectly by an object-centric readout. We ask what texture-relevant evidence is already preserved in frozen SAM before adaptation. We study two frozen evidence spaces: multiscale features, probed with a minimal clustering readout, and the automatic proposal bank, treated as evidence for a supervised consolidation readout. SAM is frozen throughout; we do not fine-tune the backbone or retrain the proposal generator. Across RWTD, STLD, an ADE20K-selected refined-crop complement, and a ControlNet-stitched PTD bridge archive, frozen SAM is not a texture segmenter by default, but its failures are not simple texture blindness. Coarse frozen features preserve texture organization, and proposal banks often contain texture-aligned masks or fragments. Natural scenes more often require assembly and commitment over fragments, while cleaner synthetic cases more often reduce to selecting an already coherent proposal. Default mask failure should therefore be decomposed into representation evidence, proposal-bank support, readout mismatch, and commitment failure.

25.
Science (Express) 2026-04-23

Structural N- and O-glycans revealed by high-resolution cryo-EM analysis of tubular mastigonemes | Science

作者: 未知作者

The chemical complexity and non-templated biosynthesis of glycans have posed significant challenges for establishing sequence-structure relationships. Here we report cryo-EM structures of tubular mastigonemes from a golden alga species, Ochromonas danica , in which a large number of N- and O-glycans are resolved at 1.8-2.2 Å resolution. Beyond high-mannose and complex N-glycans, we identify a non-canonical N-glycan on the Ala- Asn -Asp (A N D) motif. The surface spikes comprise dense O-glycans coating PSXX tetrapeptide repeats, with two glycans linked on trihydroxylated proline and one on serine per repeat. In addition to various types of sugars and their covalent modifiers, water molecules (>10% of resolved volume) and cations are clearly resolved and mediate the structural assembly. Our study establishes a framework for investigating glycan folding in high-order biological assemblies.