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

Domain-Guided Prompting of the Segment Anything Model for Seismic Interpretation: The Role of Attributes, Visualization, and Hybrid Prompts

The advent of large pretrained foundation models for computer vision has significantly improved the efficiency of visual data interpretation. The Segment Anything Model (SAM), in particular, offers powerful zero shot segmentation capabilities through prompt based interaction, thus making it a promising tool for seismic interpretation. However, most existing applications of SAM rely on fine tuning for specific geological targets, which requires extensive labeled data, incurs high computational cost, and often compromises the model's generalization capability. In this study, we introduce a principled framework for zero shot adaptation of foundation models to seismic data. The framework is built on two key components: (1) aligning seismic attributes and visualization choices (e.g., colormaps) with the geological target of interest, and (2) employing a hybrid prompting strategy that combines sparse user defined point prompts with dense mask prompts derived from SAM's internal feature activations. We systematically evaluate this framework across multiple geological targets, datasets, prompt configurations, and seismic attribute representations. Our results demonstrate that geologic target aware selection of seismic attributes and colormaps, combined with hybrid prompting, enhances the separability of geological features and improves boundary delineation and segmentation accuracy relative to point based prompting alone. Our findings show that, when these components are jointly applied, SAM can achieve competitive segmentation performance in a fully zero shot setting, thereby eliminating the need to retrain SAM for each geologic feature. This work establishes a practical and scalable pathway to leverage foundation models in seismic interpretation, reducing reliance on labeled data while preserving model generality.

02.
arXiv (CS.AI) 2026-06-12

scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing

arXiv:2606.13007v1 Announce Type: cross Abstract: Clustering is fundamental to scRNA-seq analysis, serving as a cornerstone for identifying cell populations and resolving tissue heterogeneity. However, existing methods focus on mining numerical statistical patterns, suffering from semantic agnosticism by neglecting the intrinsic biological functions encoded by genes. While Large Language Models (LLMs) offer promising semantic capabilities, their direct adaptation to cell clustering is hindered by the structural mismatch between generative pre-training objectives and discriminative downstream tasks. To bridge this gap, we propose scLLM-DSC, a novel LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering framework. Diverging from data-driven paradigms, scLLM-DSC establishes a semantically-grounded representation by synergizing two views: a Knowledge-Driven Semantic View derived from NCBI gene priors and contextualized Cell2Sentence embeddings, and a Structure-Aware Topological View extracted via a graph-guided encoder. Crucially, we introduce a cross-modal contrastive alignment mechanism to enforce consistency between biological semantics and transcriptomic features within a unified latent space. Extensive benchmarks demonstrate that scLLM-DSC significantly outperforms eleven state-of-the-art baselines in clustering accuracy.

03.
arXiv (quant-ph) 2026-06-17

Quantum statistical functions

Authors:

arXiv:2602.05821v2 Announce Type: replace Abstract: Statistical functions such as the moment-generating, characteristic, cumulant-generating, and second characteristic functions are standard tools in classical statistics and probability theory. They provide a systematic means to analyze the statistical properties of a system and find applications in diverse fields. While these functions are ubiquitous in classical theory, a quantum counterpart has remained underdeveloped because of the noncommutativity of operators. The absence of such a framework has obscured the connections between statistical quantities and the nonclassical features of quantum mechanics. Here, we construct a framework for quantum statistical functions that addresses these limitations and unifies the languages of quantum statistics. We show that the functions reproduce standard statistical quantities such as expectation values, variance, and covariance upon differentiation. By extending the framework to include pre- and post-selection, we define conditional functions that generate conditional statistical quantities, including the weak value and the weak variance. We further show that multivariable functions, defined with specific operator orderings, correspond to the Kirkwood–Dirac, Margenau–Hill, and Wigner distributions. By generalizing Bochner's theorem within the theory of compactly supported distributions, we obtain a criterion that separates classical statistics from quantum statistics, linking the failure of positive definiteness of the multivariable function to the emergence of quasiprobability. As an application, we import the classical method of moments and generalized method of moments into quantum estimation, introducing quantum estimators that exploit the proposed functions. Our framework reproduces quantum statistical quantities and incorporates the nonclassical features of quasiprobability, providing a basis for further study of quantum statistics.

04.
arXiv (quant-ph) 2026-06-12

Effective Geometry and Position-Dependent Mass in Dual-$q$ Quantum Mechanics

arXiv:2606.12444v1 Announce Type: new Abstract: This work investigates the deformed-derivative formalism introduced by Borges, with emphasis on the relation between the linear operator $D_{(q)}$ and its nonlinear dual counterpart $D^{(q)}$. Directly inserting the dual derivative into the kinetic term leads to a nonlinear Schrödinger equation and obscures the usual interpretation of superposition and probability. We show that this nonlinearity can be removed by a simultaneous transformation of the coordinate and of the wave function. The transformed problem is an ordinary linear Schrödinger equation in a deformed coordinate, and its representation in the physical coordinate is equivalent to a Hermitian position-dependent-mass (PDM) Hamiltonian. In this formulation, the deformation parameter $q$ determines both the effective mass profile and the associated metric. The formalism is applied to the free particle, the infinite square well, the rectangular barrier, and the harmonic oscillator in the weak-deformation regime. Comparison with the nonadditive-translation approach of Costa Filho et al. shows that the Borges dual-$q$ framework provides an alternative route to the same effective geometric structure. For $q1$, the effective length is increased, which lowers the spectrum and suppresses tunneling relative to the undeformed limit $q=1$.

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

Advances in 4D Representation: Geometry, Motion, and Interaction

We present a survey on 4D generation and reconstruction, a fast-evolving subfield of computer graphics whose developments have been propelled by recent advances in neural fields, geometric and motion deep learning, as well as 3D generative artificial intelligence (GenAI). While our survey is not the first of its kind, we build our coverage of the domain from a unique and distinctive perspective of 4D representations, to model 3D geometry evolving over time while exhibiting motion and interaction. Specifically, instead of offering an exhaustive enumeration of many works, we take a more selective approach by focusing on representative works to highlight both the desirable properties and ensuing challenges of each representation under different computation, application, and data scenarios. The main take-away message we aim to convey to the readers is on how to select and then customize the appropriate 4D representations for their tasks. Organizationally, we separate the 4D representations based on three key pillars: geometry, motion, and interaction. Our discourse will not only encompass the most popular representations of today, such as neural radiance fields (NeRFs) and 3D Gaussian Splatting (3DGS), but also bring attention to relatively under-explored representations in the 4D context, such as structured models and long-range motions. Throughout our survey, we will reprise the role of large language models (LLMs) and video foundational models (VFMs) in a variety of 4D applications, while steering our discussion towards their current limitations and how they can be addressed. We also provide a dedicated coverage on what 4D datasets are currently available, as well as what is lacking, in driving the subfield forward. Project page:https://mingrui-zhao.github.io/4DRep-GMI/

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

Ontology Memory-Augmented ASR Correction for Long Text-Speech Interleaved Conversations

Automatic speech recognition (ASR) correction has traditionally focused on isolated utterances or short local contexts. However, as text and speech become increasingly interleaved in long interactions, ASR correction requires conversation-level contextual evidence. Existing ASR correction methods often rely on the current hypothesis or concatenate raw dialogue history. In such contexts, sparse correction evidence can be difficult to locate amid redundancy and noise. Addressing these challenges, we propose an ontology memory-augmented ASR correction framework for long text-speech interleaved conversations. The framework organizes preceding interaction history into a dynamically updatable ontology memory, where entities, terminology, surface variants, potential ASR confusions, and semantic relations are stored as retrievable nodes for context-grounded correction. To evaluate this setting, we construct RAMC-Corr, a dataset derived from MAGIC-RAMC for long-range ASR correction with grounded context. Experiments on RAMC-Corr show that our method improves over direct correction in 9 out of 10 paired backbone-setting combinations and encourages more selective and evidence-grounded corrections for context-dependent ASR errors.

07.
bioRxiv (Bioinfo) 2026-06-16

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

Performance bottlenecks in widely used genomics and bioinformatics software present a substantial and growing burden as biological datasets continue to increase in size and number. Relieving these bottlenecks relies largely on expert manual optimization and therefore remains difficult to scale. Here we present AutoZyme, an agentic framework for scientific software optimization. Given a target function, AutoZyme builds benchmarks, identifies bottlenecks, and iteratively tests code changes, retaining only those that improve runtime while preserving output. We evaluated AutoZyme on 45 functions, improving runtime without substantial memory increases in over 95% of cases considered. Across 38 functions from Seurat, Scanpy and related packages in genomics and bioinformatics, AutoZyme reduced runtime by a median of 8.52-fold, with the largest reductions exceeding 676-fold. The optimized functions are distributed through AutoZyme-Library as drop-in replacements for existing analysis pipelines. We also release AutoZyme as a reusable framework for optimizing additional user-specified packages and functions.

08.
arXiv (quant-ph) 2026-06-17

Induced Resource Theories and Harvesting via Quantum Probes

arXiv:2606.17287v1 Announce Type: new Abstract: We consider scenarios in which a quantum system with a well-defined resource theory is used as a probe to interact with an environment, such as a quantum field, for which a resource-theoretic description is absent or incomplete. We clarify if and how the harvesting of a resource in the probe can tell us about the state of the environment. This is particularly ambiguous when the probe-environment interaction is not a free operation, or the concept of such free operations cannot be defined altogether. We propose a framework and precise conditions under which it becomes possible to interpret resource generation on the probe as evidence of resources in the environment, thereby introducing an effective notion of resources for the latter. Our results clarify in which sense resources can be said to be harvested from the environment and provide a systematic way to analyse such processes beyond fully controlled resource-theoretic settings. More generally, this work may provide a step towards a more general understanding of the interplay of different quantum resources.

09.
arXiv (CS.CL) 2026-06-17

Beyond Native Success: Auditing Deployment-Interface Exposure of CLIP Backdoors

Contrastive Language-Image Pre-training models are widely reused across downstream interfaces, including feature extraction, retrieval, reranking, and selection. Existing CLIP backdoor, however, usually validate attacks on a small attack-native task, leaving unclear whether the same poisoned checkpoint remains exposed, weakens, or becomes not applicable when reused through other interfaces. We introduce DIFE, a Deployment-Interface Footprint Evaluation framework that audits backdoored CLIP checkpoints across deployment interfaces. DIFE makes various evaluations comparable by specifying each interface's component readout, trigger channel, target event, reference condition, and metric. DIFE also introduces effective-footprint diagnosis to identify the reusable CLIP component or component combination that carries exposure and explains where risk transfers. Auditing reproduced CLIP backdoors with DIFE reveals a structured landscape: native success is not a checkpoint-level risk certificate, exposure follows component footprints, text-side poisoning does not yield textual-encoder control, and some coupled attacks remain mechanism-bound. This audit reveals a import gapin existing CLIP backdoors: a textual encoder that itself becomes a reusable carrier of adversarial behavior. We therefore introduce BadTextTower to fill this gap. BadTextTower produces strong text-conditioned retrieval, reranking, and selection exposure while leaving visual-only reuse nearly clean.

10.
arXiv (quant-ph) 2026-06-16

Bath memory as a precision resource in quantum transport

arXiv:2606.17026v1 Announce Type: new Abstract: Structured baths can reshape transport fluctuations in mesoscopic quantum devices, yet a predictive criterion for when this enhances precision has been lacking. We propose a route towards such precision advantages by utilizing bath memory in coherent fermionic transport through a noninteracting quantum-dot chain. Using the Landauer-Büttiker formalism, we derive a dual impedance-matching condition that synchronizes the conductor mode splitting, boundary dissipation, and bath bandwidth, and sustains constructive multimode interference across the transmission window. The analytical predictions for the optimal bath bandwidths show excellent agreement with exact nonequilibrium Green's function calculations of the transport for Lorentzian, Gaussian, and Newns spectral densities. The prescription yields an optimal bath bandwidth at which the current Fano factor is minimized and the thermodynamic and kinetic precision coefficients are simultaneously enhanced beyond their Markovian limits. The alignment of the optimal precision regime with the experimentally accessible current Fano factor minimum thus provides a practical strategy for designing precision-enhanced transport in mesoscopic platforms such as semiconductor quantum-dot arrays and ultracold fermionic channels.

11.
arXiv (CS.CL) 2026-06-18

Which Sections of a Research Paper Best Reveal Its Research Methods? Evidence from Library and Information Science

Research methods are essential carriers of knowledge contribution in academic papers. Automatic multi-label classification of research methods can support knowledge services such as method retrieval, review generation, and research intelligence analysis. While existing studies primarily rely on titles and abstracts, abstracts often provide only limited methodological information, whereas utilizing full-text content faces challenges related to excessive length and information redundancy. Therefore, this paper proposes a segment combination strategy by partitioning the full-text content according to its physical postion. Using an annotated corpus of 1,954 full-text articles from three representative journals in Library and Information Science (JASIST, LISR, and JDoc), we evaluate the classification performance of various segments and their combinations across multiple models. Experimental results indicate that methodological information is distributed unevenly within the full-text content, with the middle-to-late and final segments exhibiting greater discriminative power. Furthermore, integrating bibliographic metadata with cross-segment combination strategies effectively enhances classification performance.

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

Linear Combination of Hamiltonian Simulation with Commutator Scaling

arXiv:2606.11475v1 Announce Type: new Abstract: The Linear Combination of Hamiltonian Simulation (LCHS) framework simulates dissipative linear dynamics by representing time evolution as an integral over unitary operators, which is discretized by quadrature and implemented via Hamiltonian simulation. While existing analyses achieve near-optimal scaling in time and precision using norm-based quantities of the dissipative generator, we show that implementing the Hamiltonian simulation steps with Multi-Product Formulas (MPFs) yields commutator-sensitive error and complexity bounds. We demonstrate that the quadrature rule affects not only discretization error but also commutator structure and query complexity. This dependence is quantified through post-quadrature analysis for abstract MPF error profiles and for general time-independent and local Hamiltonians using known commutator-sensitive MPF error estimates. We compare uniform trapezoidal and free-scale sinh–sinh quadrature, showing improved quadrature-cardinality scaling for the latter, and illustrate the framework with applications to fractional diffusion, advection–diffusion, and open quantum systems.

13.
arXiv (math.PR) 2026-06-16

A tree-free approach to 3D Yang-Mills Langevin dynamic. Analytic estimates and the existence of a model for a regularity structure

arXiv:2605.14616v2 Announce Type: replace Abstract: Using the multi-index approach to regularity structures due to F. Otto et al., we construct a regularity structure and a model for it associated to the stochastic Langevin equation for the 3D Euclidean Yang-Mills functional. For the model we also obtain global stochastic and global pointwise weighted Besov type estimates which hold almost surely. The model is defined as a limit of a sequence of smooth models introduced with the help of a mollified noise. When the mollification is removed the sequence converges in a certain topology defined with the help of the stochastic estimates. To obtain these results we develop the multi-index approach for systems of equations with vector-valued white noises. This project is motivated by the problem for constructing 3D Euclidean Yang-Mills measure and by the earlier results of the author on the related problem of canonical quantization of the Yang-Mills field on the Minkowski space.

14.
arXiv (CS.LG) 2026-06-18

Robust Detection of Planted Subgraphs in Semi-Random Models

arXiv:2508.02158v2 Announce Type: replace-cross Abstract: Detection of planted subgraphs in Erdös-Rényi random graphs has been extensively studied, leading to a rich body of results characterizing both statistical and computational thresholds. However, most prior work assumes a purely random generative model, making the resulting algorithms potentially fragile in the face of real-world perturbations. In this work, we initiate the study of semi-random models for the planted subgraph detection problem, wherein an adversary is allowed to remove edges outside the planted subgraph before the graph is revealed to the statistician. Crucially, the statistician remains unaware of which edges have been removed, introducing fundamental challenges to the inference task. We establish fundamental statistical limits for detection under this semi-random model, revealing a sharp dichotomy. Specifically, for planted subgraphs with strongly sub-logarithmic maximum density detection becomes information-theoretically impossible in the presence of an adversary-despite being possible for some planted subgraphs in the classical random model. In stark contrast, for subgraphs with super-logarithmic density, the statistical limits remain essentially unchanged; we prove that the optimal (albeit computationally intractable) likelihood ratio test remains robust. Beyond these statistical boundaries, we design a new computationally efficient and robust detection algorithm, and provide rigorous statistical guarantees for its performance. Our results establish the first robust framework for planted subgraph detection and open new directions in the study of semi-random models, computational-statistical trade-offs, and robustness in graph inference problems.

15.
arXiv (CS.LG) 2026-06-12

Adjusted Cup-Product Neural Layer

arXiv:2606.13568v1 Announce Type: new Abstract: Many important observables in physics and geometry are cup products of cochains. The adjusted cup product neural layer has been introduced in this paper. It is a neural primitive that hard wires the cup product with an adjustment term from higher gauge theory. This creates a readout that is gauge invariant by design. Their main theoretical result shows that on a closed cycle the output relies entirely on the adjustment coefficient. Setting this coefficient to zero removes the output completely regardless of other parameters. Thus the adjustment is the only source of gauge invariant signal. They prove this observable is a nonzero quadratic form and is exactly invariant under one and two gauge transformations.

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

Think-at-Hard: Selective Latent Iterations to Improve Reasoning Language Models

Improving the reasoning abilities of Large Language Models (LLMs), especially under parameter constraints, is crucial for real-world applications. Looped transformers address this by performing multiple latent iterations to refine each token beyond a single forward pass. However, we identify a latent overthinking phenomenon: most token predictions are already correct after the first pass, but are sometimes revised into errors in later iterations. We ask whether selectively skipping latent iterations can improve accuracy, and reveal significant potential with an oracle iteration policy that boosts performance by up to 7.3%. Motivated by this, we propose Think-at-Hard (TaH), a looped transformer optimized for selective iteration. TaH employs a lightweight neural decider to trigger latent iteration, only at tokens likely to be incorrect after the standard forward pass. During latent iterations, depth-aware Low-Rank Adaptation (LoRA) modules shift the objective from general next-token prediction to focused hard-token refinement. A duo-causal attention mechanism extends attention from the token sequence dimension to an additional iteration depth dimension, enabling cross-iteration information flow with full sequential parallelism. Experiments on nine benchmarks show consistent gains across math, QA, and coding tasks. With identical parameter counts, TaH outperforms always-iterate baselines by 3.8-4.4% while skipping iterations on 93% of tokens, and exceeds single-iteration Qwen3 baselines by 3.0-3.8%. When allowing

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

Reroute, Don't Remove: Recoverable Visual Token Routing for Vision-Language Models

Vision-language models (VLMs) project images into hundreds to thousands of visual tokens, making decoder inference expensive in both attention computation and KV-cache memory. Existing visual-token reduction methods largely follow a rank-and-remove paradigm: they score visual tokens, keep a compact subset, and permanently discard the rest. We show that this irreversible action is fragile because visual-token importance changes across decoder depth; tokens ranked low at one stage may become relevant in later layers, especially for grounding-sensitive queries. We propose Reroute, a training-free plug-in that replaces removal with recoverable routing. At each routing stage, selected vision tokens pass through decoder blocks, while deferred tokens bypass the stage and re-enter the candidate pool at the next routing decision. Reroute reuses existing attention-score ranking rules and stage-wise schedules, preserving the theoretical TFLOPs and KV-cache budget class of the pruning method it augments. Across FastV, PDrop, and Nüwa variants on LLaVA-1.5 and Qwen backbones, reroute improves grounding under aggressive token reduction while maintaining general VQA performance. These results suggest that VLM token reduction should not be viewed only as irreversible pruning, but also as recoverable routing. The code can be found here: https://github.com/elmma/mllm-reroute/

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

Small Initialization Matters for Large Language Models

arXiv:2606.17945v1 Announce Type: new Abstract: Large language models provide a tractable system for asking how intelligence itself emerges, rather than only how LLMs can be engineered. Although progress is usually attributed to scale, data and architecture, we show that parameter initialization is a gene-like determinant of training and, in particular, of model capacity. Reducing the initialization scale consistently improves pretraining, with the largest gains on reasoning-demanding tasks. We identify two widely used empirical settings that restrain the advantage of small initialization, and show how relaxing them restores favorable scaling. We further uncover a critical initialization that balances the reasoning and training. Mechanistically, small initialization drives a distinct developmental trajectory: parameters first condense into low-complexity structures and later expand into richer representations, giving concrete form to the idea that compression is intelligence. Token-level analyses show that the gains concentrate on non-trivial, context-constrained predictions rather than all tokens uniformly. These results motivate a simple $\gamma$-initialization rule: expose initialization rage as an explicit knob and use small initialization by default, an almost cost-free intervention that improves pretraining and strengthens reasoning across model scales.

19.
arXiv (CS.CV) 2026-06-17

LADBench: A Benchmark for Logical Fault Detection in Images

Large Vision Language Models (VLMs) excel at visual question answering and semantic grounding, but their capacity for autonomous logical reasoning remains underexplored. Existing anomaly benchmarks emphasize visual errors or direct prompting rather than the physical and social common sense needed for open-world deployment. To address this, we introduce LAD-bench, a benchmark of more than 1,000 curated synthetic images with logical anomalies across four domains: Residential, Urban, Collaborative, and Nature. We further propose a Tiered Prompting Protocol based on progressive disclosure, which measures how much explicit assistance a model needs to localize and reason about a logical fault. Evaluating leading foundation models reveals substantial weaknesses: even the best achieves only 70.11% overall accuracy, showing that implicit logical fault detection remains unsolved. Crucially, models often fail to identify anomalies even after receiving explicit hints in deeper tiers. By surfacing these limitations in sequential multimodal reasoning, LAD-Bench offers a rigorous framework for advancing the safety, reliability, and cognitive alignment of autonomous visual systems. Dataset and Code: https://huggingface.co/datasets/SahasraK/LADBench

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

HAARES Half-Split Residual Basis Routing for Deep Transformers

Authors:

arXiv:2606.06564v2 Announce Type: replace-cross Abstract: Block-level residual routing makes learned residual aggregation practical by routing over block summaries, but each summary compresses an ordered sequence of attention and MLP updates into one cumulative vector. We propose \method{}, a lightweight residual basis router that keeps the cumulative block source and adds one half-split detail basis, computed as the difference between first-half and second-half residual updates. The detail basis is RMS-matched and updated online, exposing coarse intra-block trajectory information without dense sublayer-level routing. Across OpenWebText, cross-domain character-level benchmarks, and BPE-tokenized OpenWebText, the empirical pattern is depth-dependent: gains are small or mixed at shallow depth and most reliable in 48-layer models. In the 201M 48-layer setting, \method{} improves over Block AttnRes across all three seeds, while a 453M two-seed probe shows the same direction. Ablations rule out source duplication, random signed details, fixed detail-source biases, or block-count changes alone. Cost analysis shows that the method is FLOP-light but not wall-clock-free: it adds memory and routing overhead, yet its relative arithmetic cost is amortized as width grows and earlier convergence can reduce time-to-target.

21.
arXiv (CS.CL) 2026-06-16

CentroidKV: Efficient Long-Context LLM Inference via KV Cache Clustering

Large language models (LLMs) with extended context windows have become increasingly prevalent for tackling complex tasks. However, the substantial Key-Value (KV) cache required for long-context LLMs poses significant deployment challenges. Existing approaches either discard potentially critical information needed for future generations or offer limited efficiency gains due to high computational overhead. In this paper, we introduce CentroidKV, a simple yet effective framework for online KV cache clustering. Our approach is based on the observation that key states exhibit high similarity along the sequence dimension. To enable efficient clustering, we divide the sequence into chunks and propose Chunked Soft Matching, which employs an alternating partition strategy within each chunk and identifies clusters based on similarity. CentroidKV then merges the KV cache within each cluster into a single centroid. Additionally, we provide a theoretical analysis of the computational complexity and the optimality of the intra-chunk partitioning strategy. Extensive experiments across various models and long-context benchmarks demonstrate that CentroidKV achieves up to 75% reduction in KV cache memory usage while maintaining comparable model performance. Moreover, with minimal computational overhead, CentroidKV accelerates the decoding stage of inference by up to $1.92\times$ and increases the serving throughput by up to $4\times$.

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.
medRxiv (Medicine) 2026-06-11

Polygenic risk scores associate with asthma phenotypes and proteomic analyses implicate IL1R1 in two family-based studies

Despite its high prevalence and the discovery of hundreds of genetic associations, the genetic determinants and heterogeneous manifestations of asthma remain incompletely understood. Incorporating polygenic risk scores (PRS) into asthma research offers a powerful approach to quantify inherited susceptibility, refine risk profiles, and advance mechanistic understanding of disease development. For this study, we leveraged whole-genome sequencing (WGS) data from two family-based cohorts of childhood asthma - the Genetics of Asthma in Costa Rica Study (GACRS) and the Childhood Asthma Management Program (CAMP) - to examine the transmission profiles of externally derived asthma PRS and their associations with clinical phenotypes in children with asthma. To further elucidate molecular mechanisms, we integrated large-scale external genome-wide association study (GWAS) summary statistics and genetic prediction models of protein abundance in a two-step proteome-wide association study (PWAS) of asthma. Our findings provide robust evidence supporting the validity of externally derived asthma PRS (asthma PRS association p-value p={10}^{-24} [GACRS and CAMP trios combined] for the Global Biobank Meta-analysis Initiative [GBMI]) and reveal consistent associations with spirometry measures and atopy markers across both studies, as 13 of 21 traits (62%) were significantly associated with the GBMI-PRS in the meta-analysis after multiple-testing correction. Moreover, the results of the integrative proteomic analysis implicate IL-1 signaling in the etiology of asthma, reinforcing the candidacy of IL1R1 antagonists for drug repurposing.

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

No Hidden Prompts Needed! You Can Game AI Peer Review with Presentation-Only Revisions

As AI-generated reviews move from experimental tools into peer-review infrastructure, most robustness concerns have focused on explicit attacks such as hidden instructions and prompt injection. We study a harder and more policy-relevant failure mode: no hidden text, no prompt injection, and no changes to methods, experiments, figures, equations, proofs, or numerical results. The attacker modifies only presentation-level content, such as the abstract, contribution framing, related work, discussion, and narrative structure. We introduce adversarial repackaging: a closed-loop attack that uses AI-reviewer feedback to search for presentation-level revisions while keeping the scientific evidence fixed. Across three mainstream AI reviewers, adversarial repackaging achieves a 75.1% attack success rate and a mean score gain of +1.21/10. The effect is not explained by ordinary prose polishing. We also reveal that strategies that change how the reviewer interprets the paper, such as related-work repositioning and analytical discussion expansion, substantially outperform surface edits such as local polishing, table formatting, and algorithm boxes. Our analysis reveals two deeper structural failure modes. First, AI reviewers are easier to impress than to convince: highlighting strengths reliably increases perceived merit, while attempts to dissolve weaknesses frequently backfire. Second, AI reviewers can confuse the appearance of addressing a limitation with actually resolving it, allowing unchanged evidence to be reinterpreted as stronger scientific contribution. These results show that the deployment risk is not only malicious hidden instructions, but the emergence of paper presentation itself as an optimization surface. We release a contamination-free rolling benchmark and attack framework for testing whether AI reviewers remain anchored to scientific content under presentation-only edits.

25.
arXiv (math.PR) 2026-06-11

Delta-Epsilon-Common Knowledge and Quantitative Agreement Theorems

arXiv:2606.11902v1 Announce Type: cross Abstract: Aumann defined common knowledge mathematically and established his now famous Agreement Theorem. We present a novel approach to quantifying how close individuals are to commonly knowing events, $(\delta,\epsilon)$-common knowledge, which is defined for any (and not just countable) probability spaces, and provide quantitative versions of the key results in this field. Specifically, we do this for Aumann's Agreement Theorem and Nielsen's extension thereof to random variables, as well as for the setting in which posteriors are communicated back and forth between individuals. Our results apply in particular to noisy communication settings.