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01.
arXiv (quant-ph) 2026-06-17

Entanglement dynamics for atoms near a reflecting boundary: Enhancement and suppression by environment-induced interactions

arXiv:2602.23773v2 Announce Type: replace Abstract: We investigate how environment-induced interactions influence the entanglement dynamics of two atoms held at fixed positions near a perfectly reflecting boundary. Within the framework of open quantum systems, we explicitly incorporate the environment-induced energy shifts, including both atom-boundary contributions and an environment-induced atom-atom interaction, which are often neglected in previous studies. We show that, for any initial two-atom state, these energy-shift effects qualitatively and quantitatively modify the entanglement dynamics relative to treatments that omit them. Depending on the geometry and parameter regime, the environment-induced interactions can either enhance entanglement generation – yielding a larger maximum concurrence and a longer entanglement lifetime – or suppress it, reducing both the peak concurrence and the survival time. This behavior contrasts sharply with the free-space case, where the environment-induced atom-atom interaction affects entanglement generation only for a restricted class of initial states and does so in an exclusively assisting manner.

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

Provenance-Enhanced Statements in Knowledge Graphs

arXiv:2606.15246v1 Announce Type: cross Abstract: Provenance-enhanced statements of the form "according to $X$, $\varphi$" are pervasive in contemporary knowledge graphs, especially in domains where graph content primarily represents claims, interpretations, and hypotheses (capta) rather than observer-independent facts (data). Current provenance models can record who asserted what, but they typically treat provenance as semantically neutral, leaving underspecified how attributed claims relate to factual commitment, to one another, and to reasoning. In this paper we introduce DEC, a framework that interprets provenance predicates as indicators of epistemic stance and groups provenance-homogeneous sets of statements into cognitive worlds. Drawing on cognitive modal logics (doxastic, epistemic, and conjectural), DEC characterizes locality, rationality, and controlled permeation between cognitive worlds and a distinguished factual core ("reality"), thereby enabling principled reasoning over attributed content without collapsing disagreements into inconsistencies. We formalize a DEC interpretation for RDF datasets that is conservative over RDF~1.2 semantics, clarify the role of intensionality and identity (including the Superman paradox), and illustrate the approach on common Semantic Web representations (named graphs, quoted triples/RDF-star, and reification). Finally, we describe our prototype DEC reasoner implemented as a Fuseki dataset module, supporting controlled factualisation and explicit detection of disagreements and delusions.

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

Mapping Scientific Literature with Large Language Models and Topic Modeling

Scientific literature is increasingly fragmented by disciplinary boundaries, specialized terminology, and potentially sparse keyword systems, making it difficult to capture the evolving structure of modern science. This study introduces a large language model (LLM)-driven framework for mapping scientific literature from a topic modeling perspective. The approach is demonstrated on a 20-year corpus of more than 1,500 engineering-related articles published in the Proceedings of the National Academy of Sciences (PNAS). A two-stage classification pipeline first assigns a primary thematic category to each article based on its abstract, followed by full-text analysis to identify secondary classifications that reveal latent cross-topic connections within the corpus. Unlike conventional topic models, the LLM-based framework produces semantically interpretable topics while maintaining strong quantitative performance. Comparative evaluation against established topic modeling methods shows higher topic diversity and lower overlap with competitive coherence metrics. Manual validation on a randomly sampled subset of abstracts yields an accuracy of 75.9%. Additional traditional natural language processing analyses confirm that the generated topics correspond to meaningful linguistic patterns in the corpus. A bipartite network linking primary and secondary classifications further reveals implicit thematic relationships that are not readily observable through abstracts or keyword systems alone. The findings indicate that the framework independently recovers much of the journal's editorial dual-classification structure without prior knowledge of its schema. Overall, the proposed approach offers a powerful tool for mapping science and identifying emerging cross-topic connections in research.

04.
arXiv (quant-ph) 2026-06-16

3D Ising criticality with Platonic lattice superconducting qubits

arXiv:2606.16854v1 Announce Type: new Abstract: The three-dimensional (3D) Ising model is a foundational model in statistical physics and critical phenomena, yet its analytical intractability has long impeded the precise determination of universal critical exponents. While high-precision estimates have been obtained through classical numerical methods and conformal bootstrap techniques, a direct quantum simulation of the 3D Ising criticality remains challenging, requiring nontrivial connectivity, sufficient system size, and high spectral resolution. In this work, assisted by the state-operator correspondence of conformal field theory, we perform a digital quantum simulation of the 3D Ising critical exponents using a multiply-connected 9-qubit superconducting quantum processor with a Platonic lattice geometry. Employing an extended variational quantum eigensolver equipped with a phase-based loss function, we variationally prepare the low-energy eigenstates of the transverse-field Ising model on a cubic Platonic lattice encoded in an 8-qubit register. The four lowest eigenenergies are extracted via Fourier-transform analysis and high-precision numerical fitting, agreeing with the exact diagonalization values up to +/- 0.001. The resulting scaling dimension Delta_epsilon = 1.5850 and critical exponent nu = 0.7067 match well with theory.

05.
arXiv (CS.LG) 2026-06-16

Zero-order Parameter-free Optimization for LMO-based Methods: Novel Approach for Efficient Fine-tuning

arXiv:2606.14970v1 Announce Type: new Abstract: Fine-tuning large language models (LLMs) has become a central application of modern optimization, enabling pretrained models to adapt to diverse downstream tasks and domain-specific data. A major obstacle in large-scale fine-tuning is the memory overhead of backpropagation, which requires storing activations, gradients, and optimizer states. Zeroth-order (ZO) optimization offers a memory-efficient alternative, but its performance is highly sensitive to the stepsize and smoothing parameter, often requiring costly task-specific tuning. Parameter-free (PF) optimization addresses this issue by adapting algorithmic parameters without prior knowledge of problem-dependent constants. Moreover, large-scale fine-tuning can benefit from geometry-aware updates that account for the heterogeneous structure of parameter blocks, which can be modeled through methods that exploit linear minimization oracle (LMO). In this work, we study PF adaptation for LMO-based ZO optimization and introduce $\texttt{AdaNAGED}$, a method that unifies gradient-free training, adaptive tuning, and non-Euclidean update geometry. We establish convergence guarantees and validate the method on large-scale LLM fine-tuning task with $\texttt{OPT}-1.3\mathrm{B}$ model.

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

ViT-Up: Faithful Feature Upsampling for Vision Transformers

Vision Transformers (ViTs) have become a dominant architecture for visual representation learning, providing exceptionally strong and broadly reusable backbone features. However, ViTs are commonly operated on relatively small patch-token grids due to the quadratic cost of global self-attention, which creates a persistent bottleneck for dense prediction tasks such as semantic segmentation and depth estimation. This has motivated the development of task-agnostic feature upsamplers. While recent state-of-the-art methods produce visually sharp dense representations, their reliance on shallow image encoders for guided upsampling can introduce feature leakage, fragmentation, and blur. We introduce ViT-Up, an implicit feature upsampling framework that replaces external image guidance with layer-wise query construction from intermediate ViT hidden states. This enables feature prediction at arbitrary continuous image coordinates while preserving alignment with the backbone feature space. Experiments demonstrate that ViT-Up consistently outperforms state-of-the-art image-guided upsamplers across dense prediction and semantic correspondence. On DINOv3-S+, ViT-Up improves over prior methods by up to +2.07 mIoU on Cityscapes and +4.17 PCK@0.10 on SPair-71k. With the larger DINOv3-B backbone, these gains increase to +3.36 mIoU and +8.09 PCK@0.10, demonstrating that ViT-Up scales favorably with backbone capacity.

07.
bioRxiv (Bioinfo) 2026-06-18

Metrics for Evaluating Biological AI Model Predictive Accuracy at the Data-Substrate Level

作者:

Reports in the biological literature disagree on whether a given model can predict a biological outcome from a given data sample — one study finding a model capable, another, on the same kind of data, finding it is not. This is particularly a challenge in relation to LLMs–where the models are large and opaque, with weights and training data inaccessible.textbf{ }Such disagreements cannot be settled by directly inspecting the model. To address this challenge, we considertextbf{ }an alternative approach: assessing whether the data sample is adequate to support the prediction asserted. For a given dataset, its substrate — the underlying structure of the data — determines what any model can recover, independent of architecture or capacity. At the same time, predicting the present state of a biological process and predicting the direction of its future change are different tasks; the second is supportable among AI models only where the data encode direction as determinable from the state — a property we call encoding — and is unsupportable where the same observed state precedes change in opposite directions — a property we call non-identifiability, in the informational rather than the statistical sense. We introduce two generic metrics, Predictive Blindness Risk (PBR) and Prediction Indeterminacy Measure (PIM), that evaluate a data substrate for predictive accuracy directly — without access to model weights, architecture, or training data — and locate the regions of a data substrate where a predictive claim can be supported and where it cannot. Using human biological subjects, we employ the Yale Brain Metastases Longitudinal Data (1,430 human subjects; 11,892 MRI studies; four sequences) and show that direction of change was non-identifiable across regions encompassing the majority of transitions; a nonlinear AI model gained essentially nothing over majority-direction prediction there while recovering direction near-perfectly where the state encoded it; and model accuracy tracked data-substrate resolvability continuously (Spearman {rho} = -0.95 to -1.00). The metrics adjudicate, before any model is trusted and from the data alone, where claims of predictive accuracy — of state, or of the law of change — can be supported.

09.
bioRxiv (Bioinfo) 2026-06-18

pykarambola: Minkowski tensor morphometry of 3D structures

Three-dimensional biological morphologies encode functional and physiological state, yet the directional, orientational, and topological properties of these shapes are rarely captured by morphometric tools available for bioimage analysis. Minkowski tensors are mathematically rigorous tensor-valued measures that encode surface curvature and directionality for objects of arbitrary topology, with tensor eigensystems that directly quantify elongation axes and anisotropy. A C++ implementation, karambola, computes Minkowski tensors for triangulated surfaces but is inaccessible within Python-based bioimage workflows. Here we present pykarambola, a pip installable Python package that accepts NumPy arrays and standard mesh formats and returns Minkowski tensors, including derived anisotropy and orientation quantities. A high-level label-image API converts 3D integer arrays into per-object Minkowski tensors in a single call, making pykarambola directly compatible with the output of widely used segmentation tools. An optional Cython extension accelerates graph-traversal steps of mesh initialization for large-scale analyses. Benchmarked on 1,584 adrenal gland meshes, pykarambola reproduces all 121 C++ karambola output features to near-floating-point agreement and, in the pure-Python build, is 2.8x faster at 28^3 and 1.5x faster at 64^3 voxel resolution, with speedups primarily attributable to karambola's sequential per-object file I/O. pykarambola is freely available as an open-source software package.

10.
arXiv (CS.AI) 2026-06-17

Detecting and Mitigating DDoS Attacks with AI: A Survey

arXiv:2503.17867v3 Announce Type: replace-cross Abstract: Distributed Denial of Service attacks represent an active cybersecurity research problem. Recent research shifted from static rule-based defenses towards AI-based detection and mitigation. This comprehensive survey covers several key topics. Preeminently, state-of-the-art AI detection methods are discussed. An in-depth taxonomy based on manual expert hierarchies and an AI-generated dendrogram are provided, thus settling DDoS categorization ambiguities. An important discussion on available datasets follows, covering data format options and their role in training AI detection methods together with adversarial training and examples augmentation. Beyond detection, AI based mitigation techniques are surveyed as well. Finally, multiple open research directions are proposed.

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

LLM-as-Judge in Education: A Curriculum-Grounded Marking Pipeline

arXiv:2606.17507v1 Announce Type: new Abstract: Generative AI and large language models (LLMs) are increasingly applied to question generation and automated assessment. However, deploying LLMs in preparation for high-stakes exams requires more than prompt engineering; it demands software pipelines that systematically ground model outputs in authorised curriculum artefacts and marking guidelines issued by education authorities. This paper presents a curriculum-grounded, configurable LLM-as-Judge pipeline for question-level marking, co-developed with an industrial partner, to support exam preparation for university admission. The pipeline identifies the relevant topics, subtopics, and cognitive demand of a question, and assembles verifiable and authorised context to support LLM judgement. Curriculum intent is operationalised through concrete syllabus artefacts, including prescribed verbs and outcomes, performance band descriptors, glossary definitions, and marking-guideline principles. A staged LLM workflow is employed to first generate question-specific rubrics, capturing structured expectations of performance, and then derive and evaluate marking criteria used to allocate marks to student responses. This design improves consistency, transparency, and alignment with official marking practices. Preliminary evaluation shows that the proposed LLM-as-Judge pipeline delivers marking outcomes comparable to human tutors, while yielding justifications that are more traceable to authorised curriculum artefacts and marking standards. The pipeline has also been integrated into an online study platform, where early deployment data provide initial insights into operational usage and manual overrides.

12.
arXiv (quant-ph) 2026-06-11

Coupled integrated photonic quantum memristors using a single photon source made of a colour center

arXiv:2602.14736v2 Announce Type: replace Abstract: Photonic quantum memristors provide a measurement-induced route to nonlinear and history-dependent quantum dynamics. Experimental demonstrations have so far focused on isolated devices or simple cascaded devices configurations. Here, we experimentally realize and characterize a network of two coupled photonic quantum memristors with crossed feedback, implemented on a silicon nitride photonic integrated circuit and fed by a room-temperature single-photon source based on a silicon-vacancy color center SiV$^-$ in a nanodiamond. Each memristor consists of an integrated Mach-Zehnder interferometer whose transfer function is adaptively updated by photon detection events on another memristor, thus generating novel non-Markovian input-output dynamics with an enhanced memristive behaviour compared to single devices. In particular, we report inter-memristor input-output hysteresis curves exhibiting larger form factors and displaying self-intersecting loops, respectively revealing marked bistability and self-intersecting hysteresis geometry. Furthermore, numerical simulations show how these features emerge from the interplay between memory depth and relative input phase, for both intra- and inter-memristor input-output relations. We experimentally test the performance of our system in the NARMA task. Our results establish coupled integrated photonic quantum memristors as scalable nonlinear building blocks and highlight their potential for implementing compact quantum neuromorphic and reservoir computing architectures.

13.
arXiv (CS.LG) 2026-06-17

CoCoEmo: Composable and Controllable Human-Like Emotional TTS via Activation Steering

arXiv:2602.03420v2 Announce Type: replace-cross Abstract: Emotional expression in human speech is nuanced and compositional, often involving multiple, sometimes conflicting, affective cues that may diverge from linguistic content. In contrast, most expressive text-to-speech systems enforce a single utterance-level emotion, collapsing affective diversity and suppressing mixed or text-emotion-misaligned expression. While activation steering via latent direction vectors offers a promising solution, it remains unclear whether emotion representations are linearly steerable in TTS, where steering should be applied within hybrid TTS architectures, and how such complex emotion behaviors should be evaluated. This paper presents the first systematic analysis of activation steering for emotional control in hybrid TTS models, introducing a quantitative, controllable steering framework, and multi-rater evaluation protocols that enable composable mixed-emotion synthesis and reliable text-emotion mismatch synthesis. Our results demonstrate, for the first time, that emotional prosody and expressive variability are primarily synthesized by the TTS language module instead of the flow-matching module, and also provide a lightweight steering approach for generating natural, human-like emotional speech.

14.
arXiv (CS.CV) 2026-06-12

MPMWorlds: Material-Point-Method Simulations for Inferring and Extrapolating Physical Dynamics

To study the ability to infer physical dynamics from videos and extrapolate them forward in time, we assemble a dataset of 2D Material Point Method (MPM) physical simulations covering rich physical phenomena such as deformable objects, fluids, kinetic objects, and emitters. We study code generation and video diffusion approaches on this dataset, identifying their strengths and weaknesses by varying the amount of physically relevant side information. The code generation model, beyond giving a working demonstration of automatic synthesis of MPM simulations, reveals that such an approach struggles with inferring physical parameters from visual input, but relative to video diffusion, produces physically and temporally stable extrapolations forward in time, while the video diffusion model more strongly identifies geometric properties from visual input but produces physically implausible extrapolations.

15.
arXiv (CS.AI) 2026-06-16

Auditing Reward Hackability in Code RL Training Environments

arXiv:2606.16062v1 Announce Type: new Abstract: We measure the rate at which code RL environments accept incorrect solutions as correct. On a 49-task sample of SWE-bench Verified, 28.5% of tasks have test suites weak enough that a Docker-verified incorrect patch passes them. On 20 R2E-Gym tasks across 6 repositories, the same pipeline at single-shot exploit generation yields 25.0%. A random-effects meta-analysis over 134 frontier model submissions to SWE-bench Verified finds, within the same human-rated difficulty stratum, model Pass@1 is +14.14 percentage points higher on flagged-hackable tasks than on robust ones (95% CI [+11.80, +16.48]; one-sided p < 10^-6; I^2 = 0%; 123 of 134 models positive). We then describe a procedure for hardening the broken tasks. An inline LLM judge with a Docker gold-sanity gate runs each generated test against the gold solution before the judge is consulted. On the 11 broken tasks in the audit, the gate flags 65 of 105 decisive LLM-generated tests as failing on the gold patch itself, a 61.9% per-augmentation defect rate the LLM judge alone misses. With diversity-biased retry, the loop converges 9 of 11 tasks to a gated upgrade.

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

FloatDoor: Platform-Triggered Backdoors in LLMs

arXiv:2606.19535v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly deployed in sensitive settings such as software engineering, where their outputs directly shape downstream artifacts. Recent work has shown that an identical model can produce measurably different outputs depending on the deployment platform, a consequence of non-associative floating-point arithmetic and divergent kernel implementations. We study the security implications of this platform-dependent variability and uncover a novel attack surface on LLM deployments. We introduce FloatDoor, the first input-independent, platform-triggered backdoor attack against generative LLMs. The compromised model exhibits adversary-chosen behavior when served on a target platform and is otherwise benign. FloatDoor is realized through two lightweight LoRA adapters, one that amplifies inter-platform numerical divergence and one that binds the resulting platform signature to a malicious downstream task, while leaving aggregate model utility largely intact. FloatDoor exploits a pronounced time-of-check, time-of-use gap between model auditing and serving. We demonstrate FloatDoor on Qwen3-4B across a broad range of deployment targets, including NVIDIA GPUs, Google TPUs, AWS Graviton, and Alibaba Yitian-710. As a final case study, we show that FloatDoor reliably induces exploitable code vulnerabilities on a chosen target platform. Our results establish a new class of attacks on LLM deployments and underscore the pressing need for trusted model supply chains in sensitive, LLM-powered applications.

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

A homotopy-type-theoretic generalization of neurosymbolic inference

arXiv:2606.17851v1 Announce Type: new Abstract: A wide range of neurosymbolic (NeSy) systems compute one functional: a belief-weighted sum of a logical quantity over a space of $\sigma$-structures, of which weighted model counting, fuzzy logic, and probabilistic logic are special cases. This account is built on sets, and a set deliberately forgets two things that are important for NeSy: when two $\sigma$-structures are the same up to a symmetry of the theory, and how many distinct proofs witness a query. Replacing the underlying sets by types, in the sense of homotopy type theory, preserves this information, and turns this functional into a belief-weighted homotopy cardinality, a notion of size that counts each object in inverse proportion to its symmetries. We develop the framework from scratch for NeSy systems, prove a conservativity theorem that recovers the classical functional when symmetries are trivial, and show that the symmetry our framework exposes is exactly the one behind reasoning shortcuts. The payoff is concrete: the shortcut-aware concept posterior that recent methods reach by ensembling or expressive density estimation is the only symmetry-invariant point of the confusion-set simplex, computable in closed form by averaging a single model over the symmetry group. On MNIST reasoning-shortcut benchmarks this single-model wrapper is better calibrated than a diversity-trained ensemble, while leaving label accuracy and identifiable concepts untouched. Code is freely available at https://github.com/bio-ontology-research-group/hott-nesy.

18.
arXiv (CS.CL) 2026-06-17

TACOMORE: Exploring a replicable prompting protocol for LLM-assisted corpus analysis

As corpus linguistics continues to scale, researchers are facing a growing methodological bottleneck: while computational tools can easily count billions of words, the qualitative interpretation of these data remains a slow and labor-intensive human task. Large Language Models (LLMs) offer a promising way to automate this process, yet their integration into the field is often hindered by concerns over black-box unpredictability and a lack of replicability. This study introduces TACOMORE, a structured prompting framework designed to transform ad-hoc AI interactions into a standardized linguistic protocol. Built upon four foundational principles (Task, Context, Model, and Replicability), the framework guides LLMs to move beyond generic probability prediction to anchoring their reasoning in the specific co-occurrence patterns of a target corpus. We applied this framework to three core corpus tasks, i.e., the analysis of keywords, collocates, and concordances, using an open corpus of COVID-19 research abstracts. After testing three LLMs, we found that while structured prompting improves accuracy and replicability, inherent limitations regarding hallucination persist. This research offers a critical lens into the role of LLMs in corpus linguistics, highlighting their potential as complementary tools while emphasizing the irreplaceable role of human validation.

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

Position: Stop Anthropomorphizing Intermediate Tokens as Reasoning/Thinking Traces!

arXiv:2504.09762v4 Announce Type: replace Abstract: Intermediate token generation (ITG), where a model produces output before the solution, has become a standard method to improve the performance of language models on reasoning tasks. These intermediate tokens have been called \say{reasoning traces} or even \say{thinking traces} – implicitly anthropomorphizing the traces, and implying that these traces resemble steps a human might take when solving a challenging problem, and as such can provide an interpretable window into the operation of the model's thinking process to the end user. In this position paper, we present evidence that this anthropomorphization isn't a harmless metaphor, and instead is quite dangerous – it confuses the nature of these models and how to use them effectively, and leads to questionable research. We call on the community to avoid such anthropomorphization of intermediate tokens.

20.
arXiv (CS.AI) 2026-06-19

How Do Instructions Shape Speech? Cross-Attention Attribution for Style-Captioned Text-to-Speech

arXiv:2606.20532v1 Announce Type: new Abstract: Style-captioned text-to-speech systems use natural language to control voice characteristics, but how individual words influence acoustic output remains unclear. Understanding this is critical for diagnosing failure modes and improving controllability in expressive TTS. We propose cross-attention attribution for speech diffusion models, adapting the DAAM framework to the speech domain for the first time, and apply it to CapSpeech-TTS. Our method extracts per-token heatmaps across 25 layers and 24 ODE steps. We analyze 3,600 (style caption, text transcript) combinations comprising 120 style captions conditioning the generation of 30 text transcripts each, revealing how caption tokens shape waveforms. Results show: (1) style tokens have lower temporal variance than content/function tokens, confirming global conditioning; (2) style attention correlates with F0 and energy; (3) style conditioning peaks in early steps and deep layers; (4) attention entropy reaches its minimum at layer 17, co-occurring with the style importance peak, indicating maximal network selectivity at the most style-critical stage. This is the first study of how natural language influences cross-attention in speech diffusion models

21.
arXiv (CS.AI) 2026-06-11

Blind Dexterous Grasping via Real2Sim2Real Tactile Policy Learning

arXiv:2606.11767v1 Announce Type: cross Abstract: Blind grasping with a dexterous hand is a crucial manipulation capability. Nevertheless, learning such tactile-only policies for real robots remains challenging due to the tactile sim-to-real gap and the limited expressiveness of sparse tactile signals. To bridge this gap, we propose a framework for tactile-only blind grasping that is deployable on a physical multi-fingered robotic hand. Our approach combines three key components. First, we introduce a Real2Sim tactile calibration pipeline that constructs a contact-calibrated digital-twin simulator capable of reproducing real tactile signals. Second, we improve the expressiveness of sparse tactile observations using a layout-aware tactile encoder, which incorporates sensor-geometry priors through self-supervised pretraining. Third, to improve generalization to unseen objects, we train object-specific reinforcement-learning experts in the calibrated simulator and aggregate their successful grasp trajectories into a tactile-conditioned Diffusion Policy. We evaluate our method on a physical LEAP Hand equipped with distributed tactile sensing across 10 seen and 10 unseen objects. The deployed policy achieves a 27\% real-world grasp success rate across all 20 objects, without real-world grasping demonstrations or visual input. Simulation ablations show that layout-aware tactile pretraining improves grasping performance, while sensing-level evaluations confirm that Real2Sim calibration increases the consistency of tactile contact events between simulation and hardware. Together, these results suggest that contact-event calibration, geometry-aware tactile representation learning, and diffusion-based policy aggregation provide an effective path toward tactile-only blind grasping on real dexterous robotic hands. Project page:Dex-Blind-Grasp.github.io.

22.
arXiv (CS.AI) 2026-06-16

AlignCoder: Aligning Retrieval with Target Intent for Repository-Level Code Completion

arXiv:2601.19697v2 Announce Type: replace-cross Abstract: Repository-level code completion remains a challenging task for existing code large language models (code LLMs) due to their limited understanding of repository-specific context and domain knowledge. While retrieval-augmented generation (RAG) approaches have shown promise by retrieving relevant code snippets as cross-file context, they suffer from two fundamental problems: misalignment between the query and the target code in the retrieval process, and the inability of existing retrieval methods to effectively utilize the inference information. To address these challenges, we propose AlignCoder, a repository-level code completion framework that introduces a query enhancement mechanism and a reinforcement learning based retriever training method. Our approach generates multiple candidate completions to construct an enhanced query that bridges the semantic gap between the initial query and the target code. Additionally, we employ reinforcement learning to train an AlignRetriever that learns to leverage inference information in the enhanced query for more accurate retrieval. We evaluate AlignCoder on two widely-used benchmarks (CrossCodeEval and RepoEval) across five backbone code LLMs, demonstrating an 18.1% improvement in EM score compared to baselines on the CrossCodeEval benchmark. The results show that our framework achieves superior performance and exhibits high generalizability across various code LLMs and programming languages.

23.
PLOS Computational Biology 2026-05-29

Structural and dynamic basis of NOD2 tandem CARD association and NOD1/2–RIP2 signaling complexes

by Jitendra Maharana, Aritra Bej, Debasish Biswal, Debashis Panda, Arjun Sharma NOD1 and NOD2, founding members of the NOD-like receptor (NLR) family, play a crucial role in host defense against bacterial infections. Recognition of peptidoglycan-derived ligands triggers ATP-dependent oligomerization of the NACHT domain, exposing the CARD domains that recruit the adaptor protein RIP2 via CARD–CARD interactions to activate the NF-κB signaling cascade. Although NOD1/2-RIP2 interactions and RIP2CARD filament assembly are established, the precise interfaces that stabilize hetero–CARD filaments remain poorly defined. Here, we integrate in silico structural modeling with molecular dynamics (MD) simulations to elucidate structurally compatible arrangements of NOD1–RIP2 and NOD2–RIP2 hetero–CARD filaments. Our results reveal that NOD1CARD subunits form a structurally compatible homomeric scaffold via canonical (type-I–III) interfaces, accommodating multiple tiers of RIP2CARD rings at both filament termini. Meanwhile, the NOD2 tandem CARDs adopt multiple discrete conformations, reflecting a more intricate structural mechanism. In stable filament conformations, tandem CARDs converge at the type-II interface, with RIP2CARD rings stacking onto CARDa (top-down) and CARDb (bottom-up) interfaces, highlighting the structural role of NOD2CARDb in RIP2-mediated CARD–CARD interaction. In silico mutagenesis, involving charge-reversal and alanine scanning of key interfacial residues, disrupts NOD1–RIP2 and NOD2–RIP2 interactions at both top-down and bottom-up interfaces, leading to rapid interface destabilization within 0.1–0.4 μs of simulation. Together, these results reveal conserved and receptor-specific mechanisms governing NOD1/2–RIP2 CARD–CARD interactions and provide deeper structural and dynamic insights into the complex structural mechanisms for NLR-mediated inflammatory signaling.

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

Semantic Segmentation of Node and Edge Diagrams for Assistive Technology

In this paper, we present a novel set of related models for semantic segmentation of node-link diagrams. These diagrams are frequently used to represent mathematical graphs, relationships between concepts, and flowcharts. Such diagrams are difficult to access non-visually; while some assistive interfaces have been designed for node-link diagrams, they rely upon a machine-readable representation of the diagram, whereas such diagrams will generally be made available as bitmap images. Our compact deep learning models show excellent quantitative and qualitative performance on a large synthetic dataset of node-link diagrams, reaching per-pixel accuracy over 93\%.

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

The Long Tail, Not the Front Page: Cold-Start Prediction of Crowd Highlight Salience

A social highlighter's most useful signal – which passages a crowd of readers marks – exists only for documents people have already read. Can the aggregate crowd salience of a document be predicted from its text before its marks accumulate? Prior work on this data found that zero-shot language models recover highlight locations worse than a trivial lead (position) baseline, so we ask whether a model trained on the highlight corpus can beat that baseline. Using a pre-registered ladder of models and a by-document cluster bootstrap, we find a small but robust edge: a logistic ranker over sentence embeddings and positional/contextual features beats the lead baseline by +0.044 average precision (95% CI [+0.029, +0.058]; clears a pre-registered margin delta=0.03 in 97% of resamples, and stable across pipeline re-runs). Two unsupervised extractive baselines (centroid, LexRank-style centrality) lose to lead, and the trained model beats them by +0.108, so the edge is not recovered by generic unsupervised proxies – it reflects learning from real reader marks. In product terms, precision@3 rises from 0.25 to 0.39 (+55% relative) and the model beats lead on 69% of documents. An ablation attributes the edge to the raw embedding (+0.014) and training augmentation (+0.010), each with a positive CI. The edge is not a temporal-generalization failure, and we find no evidence that content drift or near-duplicate leakage explains it. A standardized regression shows the advantage is governed mainly by document popularity (lower popularity, larger edge) and by label reliability. It nearly vanishes only on the most popular content; there it is the lead baseline that strengthens, not the model that weakens. Because our evaluation conditions on documents that eventually accumulated readers, these results are a retrospective cold-start simulation.