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

Data Augmentations for Data-Constrained Language Model Pretraining

As AI labs approach a data ceiling where compute capacity outpaces the rate of new high-quality text generation, language model pretraining is shifting toward a data-constrained, compute-abundant regime that demands productive multi-epoch training on fixed corpora. Standard autoregressive (AR) pretraining overfits severely in this setting, reaching its optimum early and then continuously deteriorating. We investigate data augmentation as a regularizer to mitigate this overfitting and enable productive training for hundreds of epochs on the same data. We introduce three orthogonal categories of augmentation for AR pretraining: token-level noise (masking, random replacement), sequence permutations (right-to-left prediction, Fill-in-the-Middle), and target offset prediction ($x_{t+i}$ for $i > 1$). Through systematic ablations, we find that individual augmentations delay overfitting and lower validation loss relative to the baseline, with random token replacement achieving the best minimum loss among individual methods. Combining augmentation categories further lowers the minimum validation loss. Our experiments demonstrate that data augmentations mitigate AR pretraining's data inefficiency and offer a promising solution to the data-constrained regime. All code and data are available at https://github.com/michaelchen-lab/data-augmentations-for-pretraining

02.
arXiv (CS.CL) 2026-06-17

Implicit vs. Explicit Prompting Strategies for LVLMs in Referential Communication

Two recent studies (Jones et al. (2026); Zeng et al. (2026)) reach apparently contradictory conclusions about whether LVLMs can coordinate on efficient referring expressions. We control for task differences between the studies while directly comparing their prompting styles. We replicate the finding that models can coordinate efficient referring expressions when explicitly prompted to do so, suggesting that other task differences are not responsible for divergent results. However, we also find that the same models fail to infer the need for communicative efficiency from a more implicit prompt, highlighting critical differences between how humans and AI systems communicate.

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

"**Important** You should give me full credits!": Exploring Prompt Injection Attacks on LLM-Based Automatic Grading Systems

arXiv:2606.03090v2 Announce Type: replace-cross Abstract: The emergence of large language models (LLMs) has significantly accelerated recent research on LLM-based automatic grading (AG) systems. Benefiting from the strong instruction-following capabilities and broad prior knowledge of LLMs, educators can deploy AG systems across diverse tasks using only natural language rubrics while achieving satisfactory grading performance. Despite these advantages, new security concerns may also arise. In particular, prompt injection (PI) attacks have recently become a major threat to LLM-based applications. In the context of AG, attackers can potentially exploit PI vulnerabilities to manipulate grading systems into assigning artificially high scores regardless of the actual answer quality. Such behavior poses serious risks to the fairness, reliability, and integrity of educational assessment. In this work, we study PI attacks in AG systems, and systematically investigate the effectiveness of such attacks in educational scenarios. We further evaluate the effectiveness of existing defensive strategies against these attacks. Through comprehensive experiments under rubric-based grading settings, we demonstrate that current LLM-based AG systems remain highly vulnerable to PI attacks. We hope that our findings raise awareness of this emerging threat and motivate future research toward secure, robust, and trustworthy LLM-based educational systems.

04.
arXiv (CS.LG) 2026-06-18

Online Distributional Prediction via Latent Cluster Geometry Under Drift and Corruption

arXiv:2606.18778v1 Announce Type: new Abstract: Online learning in non-stationary streams is often formulated as tracking a point estimate, but many applications require predicting the full data-generating distribution. We study online distributional prediction under drift and adversarial corruption. Our approach represents each candidate law through a latent cluster geometry: a variable-size configuration of centers that organizes probability mass and induces a predictive distribution. A Gibbs quasi-posterior over these configurations yields an online predictor by posterior averaging, and the resulting variable-dimensional posterior can be sampled with reversible-jump MCMC. The method therefore avoids specifying a parametric streaming law while retaining a structured latent space for uncertainty, regularization, and comparison. We evaluate performance by cumulative Wasserstein-1 regret against the time-varying true law. The analysis separates two effects: corruption perturbs the loss-based posterior update, whereas drift makes long-horizon posterior memory stale. We address the latter with a restarted variant that temporally localizes the same quasi-Bayesian update. The resulting high-probability bounds decompose into a PAC-Bayesian complexity term, a corruption-sensitive posterior perturbation term, and a dynamic optimal-transport term driven by \(A_T^{\mathrm{OT}}=\sum_{t=2}^T W_2^2(p_{t-1}^*,p_t^*)\). Under bounded support, stable latent geometry, predictive-map regularity, oracle realizability, localized restart windows, sublinear transport action, and sublinear corruption budget, the restarted predictor achieves sublinear cumulative Wasserstein regret. These guarantees require no parametric model for the stream, drift mechanism, or corruption process.

05.
arXiv (CS.CV) 2026-06-11

MLT-Dedup: Efficient Large-Scale Online Video Deduplication via Multi-Level Representations and Spatial-Temporal Matching

The explosive growth of user-generated video content on online platforms is accompanied by the emergence of numerous near-duplicate videos–videos that are identical or highly similar but differ by partial edits. These duplicates degrade user experience and increase storage and bandwidth costs, making large-scale video deduplication a critical task. Existing video deduplication frameworks face a fundamental challenge in retrieving sufficient high-quality candidates under a limited index budget, as well as trade-offs between efficiency and precision. To address these issues, we propose MLT-Dedup, an efficient large-scale online video deduplication framework with Multi-Level representations and spatial-Temporal matching. Our approach employs a Multi-Level Video Encoder (ML-VE) to extract both fine-grained frame-level and sparse clip-level embeddings: sparse embeddings support efficient candidate retrieval, while fine-grained embeddings are loaded for precise pairwise matching. During matching, we introduce DiF-SiM, a Differential Feature-enhanced Similarity Module capable of locating duplicated temporal segments and providing reliable similarity evidence to support policy-driven deduplication decisions. Extensive experiments on a real-world large-scale platform demonstrate that MLT-Dedup reduces online repetition rates by 91% at 90% precision. Furthermore, our sparse retrieval design achieves a 5x increase in indexing capacity, enabling broader candidate coverage in real-world deployment.

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

Electromagnetic Wightman functions and vacuum densities for a brane intersecting the AdS boundary

arXiv:2604.17583v2 Announce Type: replace-cross Abstract: We investigate the combined effects of a brane intersecting the AdS boundary and background gravitational field on the local characteristics of the electromagnetic vacuum. Two types of boundary conditions on the brane are considered, which are higher-dimensional generalizations of the perfect electric (PEC) and perfect magnetic (PMC) boundary conditions in Maxwell's electrodynamics. The brane-induced contributions to the Wightman functions of the vector potential and field tensor are explicitly extracted. Simple expressions in terms of elementary functions are provided. The behavior of the vacuum expectation values (VEVs) is mimicked by a scalar field with a negative effective mass squared determined by the radius of the AdS spacetime. The expectation values of the electric and magnetic fields squares and of the energy-momentum tensor are investigated as local characteristics of the vacuum state. The brane-induced contributions to these VEVs have opposite signs for the PEC and PMC conditions. For the PMC condition, this contribution is negative for the electric field squared and positive for the magnetic field squared. The VEV of the energy-momentum tensor has a nonzero off-diagonal component. The brane-induced vacuum energy density is positive for PMC condition, whereas the normal and parallel stresses change sign as functions of the distance from the brane. Unlike the problem involving a planar boundary in the Minkowski bulk, the vacuum energy-momentum tensor does not vanish in (3+1)-dimensional AdS spacetime.

07.
bioRxiv (Bioinfo) 2026-06-11

A high-quality chromosome-scale reference genome assembly for Asparagus racemosus var. CIM-Shakti (Shatavari), a medicinal plant of Ayurvedic importance

Asparagus racemosus Wild., commonly known as Shatavari, is an important medicinal plant in Ayurveda and is valued for its steroidal saponins, particularly shatavarin compounds, which contribute to its adaptogenic, galactagogue, immunomodulatory, and therapeutic properties. Despite its medicinal and economic importance, genomic resources for this species have remained limited, restricting molecular breeding, pathway discovery, and comparative evolutionary studies within Asparagaceae. Here, we report a high quality chromosome scale reference genome assembly of A. racemosus var. CIM Shakti generated using PacBio HiFi long read sequencing and Omni C chromatin conformation scaffolding. The pseudo haploid assembly spans 817 Mb across 53 scaffolds, with a scaffold N50 of 98.50 Mb, L50 of 5, and a largest scaffold of 113.80 Mb. Ten major chromosome scale pseudomolecules were resolved, corresponding to the haploid chromosome complement of A. racemosus. The assembly showed high gene space completeness, with BUSCO completeness of 99.8% against the Eukaryota dataset and 98.0% against the Embryophyta dataset. BlobToolKit profiling further supported assembly quality, with GC content of approximately 39 to 40% and no major evidence of contamination. EDTA based repeat annotation identified 580.93 Mb of interspersed repetitive elements, accounting for 71.06% of the 817.57 Mb genome assembly. The repeat landscape was dominated by LTR retrotransposons, particularly Gypsy elements, which accounted for 25.01% of the assembly, followed by unclassified LTR elements at 26.58% and Copia elements at 4.84%. Structural and functional annotation identified 29,199 protein coding genes represented by 29,199 transcript models, 138,433 exons, and 125,201 CDS features. The annotation was structurally robust, with an average gene length of 4,605.1 bp, 4.74 exons per transcript, and 97.80% of transcripts containing multiple exons. The CIM Shakti reference genome provides a foundational genomic resource for investigating steroidal saponin biosynthesis, sex chromosome evolution, repeat driven genome expansion, and comparative genomics in Asparagaceae. This assembly will support future studies on medicinal trait improvement, conservation genomics, and genomics assisted breeding of climate resilient Shatavari cultivars.

08.
arXiv (CS.CL) 2026-06-11

Agreement in Representation Space for Open-Ended Self-Consistency

Self-consistency improves LLM reasoning by sampling multiple outputs and selecting the most consistent answer, but existing formulations largely rely on exact matching and therefore remain limited to tasks with categorical outputs. In this work, we study self-consistency in open-ended generation tasks such as code synthesis and text summarization. We hypothesize that consistency can be understood as a geometric property of the generation space, where semantically compatible generations concentrate in similar regions of representation space. To study this hypothesis, we introduce Embedding-Based Agreement (EBA), a simple training-free operationalization that estimates agreement by clustering sampled generations in embedding space. Through experiments on mathematical reasoning, code generation, and summarization, we show that agreement in representation space provides a robust and scalable signal of self-consistency for open-ended tasks. In particular, EBA consistently outperforms random selection and exhibits more stable scaling behavior than recent selection approaches based on LLM evaluation or uncertainty estimation. We further show that these agreement signals remain stable across model families and embedding spaces, even with native hidden representations. Finally, our analysis shows that the geometric location occupied by sampled generations is strongly correlated with generation quality: generations concentrated near central regions of representation space tend to correspond to more reliable outputs, whereas peripheral generations are substantially less accurate. Overall, our findings support viewing self-consistency as a property of the geometric organization of sampled generations rather than exact symbolic overlap.

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

Algorithmic Prompt Generation for Diverse Human-like Teaming and Communication with Large Language Models

Understanding how humans collaborate and communicate in teams is essential for improving human-agent teaming and AI-assisted decision-making. However, relying solely on data from large-scale user studies is impractical due to logistical, ethical, and practical constraints, necessitating synthetic models of multiple diverse human behaviors. Recently, agents powered by Large Language Models (LLMs) have been shown to emulate human-like behavior in social settings. But, obtaining a large set of diverse behaviors requires manual effort in the form of designing prompts. On the other hand, Quality Diversity (QD) optimization has been shown to be capable of generating diverse Reinforcement Learning (RL) agent behavior. In this work, we combine QD optimization with LLM-powered agents to iteratively search for prompts that generate diverse team behavior in a long-horizon, multi-step collaborative environment. We first show, through a human-subjects experiment, that humans exhibit diverse coordination and communication behavior in this domain. We then present a series of experiments showing that our approach captures behaviors that are difficult to observe without large-scale data collection, and a follow-up user study to show that these generated behaviors are human-like. Our findings highlight the combination of QD and LLM-powered agents as an effective tool for studying teaming and communication strategies in multi-agent collaboration.

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

Temporal Preference Optimization for Unsupervised Retrieval

arXiv:2606.17664v1 Announce Type: cross Abstract: Unsupervised dense retrievers offer scalability by learning semantic similarity from unlabeled documents via contrastive learning, but they struggle to capture the temporal relevance, retrieving semantically related but temporally misaligned documents-an important aspect when a document collection spans multiple time periods (e.g., retrieving documents from 2018-2025 for "Who is the president in 2019?" introduces temporal ambiguity). Existing methods rely on supervised training with explicit timestamps, which are not always feasible. We propose TPOUR (Temporal Preference Optimization for Unsupervised Retriever), which uses our novel training method Temporal Retrieval Preference Optimization (TRPO). TRPO reinterprets preference learning in the temporal dimension, guiding the retriever to favor temporally aligned documents. TPOUR further generalizes to unseen time periods via interpolation in a learned time embedding, enabling continuous temporal alignment. Experiments on temporal information retrieval (T-IR), TPOUR outperforms both unsupervised and supervised baselines. Compared to Qwen-Embedding-8B, despite being about 72.7x smaller, TPOUR Contriever improves average nDCG@5 by +4.04 (+12.15%) on explicit and +4.98 (+15.21%) on implicit queries. We provide our code at https://github.com/agwaBom/TPOUR.

11.
Nature (Science) 2026-06-17

Navigating a crowded developing brain leaves neurons with broken DNA

As neurons migrate to their final destinations in the forming brain, their DNA gets damaged. The brain has evolved a fix, but there can be lasting consequences if repair fails. As neurons migrate to their final destinations in the forming brain, their DNA gets damaged. The brain has evolved a fix, but there can be lasting consequences if repair fails.

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

Open-SWE-Traces: Advancing Dual-Mode Multilingual Distillation for Software Engineering Agents

arXiv:2606.16038v1 Announce Type: cross Abstract: The path toward autonomous software engineering is currently bottlenecked by a severe deficit of diverse, large-scale trajectory data. We address this by introducing \ourdataset, an expansive dataset of 207,489 agentic trajectories spanning nine programming languages (Python, Go, TS, JS, Rust, Java, PHP, C, C++). Sourced from 20,000 real-world PRs via OpenHands and SWE-agent harnesses, the dataset utilizes a hybrid-reasoning synthesis: Minimax-M2.5 generates trajectories with explicit "thinking" processes, while Qwen3.5-122B provides high-quality "non-thinking" traces. Filtered for permissive licenses (MIT, Apache, BSD) from SWE-rebench-V2, this data facilitates the training of models capable of long-horizon reasoning. We validate the dataset by fine-tuning the Qwen3-30B-A3B series (Thinking, Instruct, and Coder). The best performing model achieves resolve rates of 61.7% on SWE-bench Verified, 57.1% on SWE-bench Multilingual, and 36.8% on SWE-bench Pro. These results establish Open-SWE-Traces as a premier resource for distilling human-level software engineering capabilities into efficient, open-source agentic LLMs.

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

SCC-Loc: A Unified Semantic Cascade Consensus Framework for UAV Thermal Geo-Localization

Cross-modal Thermal Geo-localization (TG) provides a robust, all-weather solution for Unmanned Aerial Vehicles (UAVs) in Global Navigation Satellite System (GNSS)-denied environments. However, profound thermal-visible modality gaps introduce severe feature ambiguity, systematically corrupting conventional coarse-to-fine registration. To dismantle this bottleneck, we propose SCC-Loc, a unified Semantic-Cascade-Consensus localization framework. By sharing a single DINOv2 backbone across global retrieval and MINIMA$_{RoMa}$ matching, it minimizes memory footprint and achieves zero-shot, highly accurate absolute position estimation. Specifically, we tackle modality ambiguity by introducing three cohesive components. First, we design the Semantic-Guided Viewport Alignment (SGVA) module to adaptively optimize satellite crop regions, effectively correcting initial spatial deviations. Second, we develop the Cascaded Spatial-Adaptive Texture-Structure Filtering (C-SATSF) mechanism to explicitly enforce geometric consistency, thereby eradicating dense cross-modal outliers. Finally, we propose the Consensus-Driven Reliability-Aware Position Selection (CD-RAPS) strategy to derive the optimal solution through a synergy of physically constrained pose optimization. To address data scarcity, we construct Thermal-UAV, a comprehensive dataset providing 11,890 diverse thermal queries referenced against a large-scale satellite ortho-photo and corresponding spatially aligned Digital Surface Model (DSM). Extensive experiments demonstrate that SCC-Loc establishes a new state-of-the-art, suppressing the mean localization error to 9.37 m and providing a 7.6-fold accuracy improvement within a strict 5-m threshold over the strongest baseline. Code and dataset are available at https://github.com/FloralHercules/SCC-Loc.

14.
arXiv (CS.AI) 2026-06-15

A Fixed-Point Neural Operator for Size- and Functional-Transferable Hamiltonian Prediction

arXiv:2606.14498v1 Announce Type: cross Abstract: Predicting the Kohn-Sham Hamiltonian with machine learning can accelerate density functional theory while retaining access to molecular orbitals, energy levels, and electronic-structure observables that energy-only surrogates cannot resolve. Yet element-wise agreement with the converged Hamiltonian, an implicit fixed point of the self-consistent field iteration, does not determine the occupied subspace that governs orbital energies and densities. Here we present HamEvo, a neural operator that learns the single-step self-consistent update and returns the converged Hamiltonian as its fixed point. HamEvo is pre-trained on intermediate self-consistent trajectories and calibrated at equilibrium with density-matrix supervision. Across benchmarks from MD17 to drug-like QMugs, HamEvo lowers Hamiltonian errors by 35-49% over direct-regression and deep-equilibrium baselines, and predicts QMugs HOMO and LUMO energies with mean absolute errors of 0.036 and 0.053 eV, near the 1 kcal/mol chemical-accuracy scale. Few-shot fine-tuning with only 20 reference conformations extends HamEvo to molecules of up to 122 atoms, well beyond the size range covered by pre-training. With thermal molecular-dynamics sampling, HamEvo captures temperature-dependent HOMO-LUMO gap renormalization beyond the harmonic approximation. Inference is up to 242 times faster than conventional DFT.

15.
arXiv (quant-ph) 2026-06-17

Tensor network compression using fluid dynamics as a testbed: Analytical foundations in one dimension

arXiv:2606.17064v1 Announce Type: cross Abstract: High performance computers produce extreme-scale data sets that require sampling or compression if they are to be used to their full potential. Existing data compression techniques typically exploit features such as sparsity in the data, homogeneity in the data, or {\it a priori} knowledge of what subsets of data are of most interest. Fluid dynamics data in general do not exhibit these features and so are attractive test beds for generic compression techniques that are objective, robust, and tuneable with respect to information lost due to compression. Presented here is a method based on tensor networks, specifically matrix product states or tensor trains, that meets these requirements. The method is demonstrated for compression in one-dimension and is extensible to higher dimensionality. Lossless compression is demonstrated for random Fourier series for sufficiently high bond dimension of the tensor network, with the memory required to store the tensor network scaling directly proportional to the bond dimension. The lossy compression exhibited at lower bond dimension can be well within the relative error of many fluid simulations. The compression algorithm is tested for the time evolution of Burger's equation with excellent results. We additionally demonstrate the capability to perform computations in the compressed form through a tensor network periodic convolution that can be orders of magnitude faster than using fast Fourier transforms and the convolution theorem. In addition to being an attractive method for working with data sets generated by existing computers, the tensor network methods utilised are directly translatable to the emerging paradigm of quantum computing.

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

Gaussian Light Field Splatting: A Physical Prior-Driven Vision Transformer for Unsupervised Low-Light Image Enhancement

Existing unsupervised low-light image enhancement methods often encounter local exposure imbalance and color distortion under complex non-uniform illumination. In addition, most Vision Transformers lack an explicit mechanism for modeling the physical priors of illumination degradation. To address these limitations, we propose GLFS, a Gaussian light field splatting-based Vision Transformer that integrates continuous physical illumination modeling from Gaussian splatting into the Transformer architecture. In GLFS, scene illumination is represented by a superposition of anisotropic Gaussian basis functions. Physics-guided biases are introduced into self-attention to adaptively infer a spatial gain field, enabling accurate and uniform restoration under complex illumination. To reduce color bias and structural degradation during enhancement, a color-vector angular loss and a luminance-edge loss are further developed. These losses enforce hue consistency and improve the structural fidelity of local details. Extensive ablation studies and quantitative evaluations show that GLFS provides clear advantages in illumination correction and detail preservation. It achieves state-of-the-art performance and offers a new representation paradigm for low-light image enhancement.

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

AVIS: Adaptive Test-Time Scaling for Vision-Language Models

Modern Vision-Language Models (VLMs) benefit from chain-of-thought prompting and test-time scaling, but these gains often come with prohibitive inference cost due to large visual contexts and long decoding chains. We view this cost through two coupled axes: Visual Context Scaling (VCS), which controls how much visual evidence is passed to the language model, and Visual Reasoning Scaling (VRS), which controls how much inference-time reasoning search is performed. Existing methods typically optimize one axis at a time, leaving the joint allocation of compute across these axes underexplored. We introduce Adaptive Visual Inference Scaling (AVIS), a lightweight policy that adapts both VCS and VRS per query. AVIS realizes VCS through Key Diversity Visual (KDV) pruning, a training-free $O(N)$ key-based rule for removing redundant visual tokens before prefilling, and realizes VRS through adaptive self-consistency, using a learned difficulty predictor to select the number of reasoning rollouts. AVIS is deployment-friendly and compatible with shared-prefill inference, where all rollouts reuse a single prefilling pass and KV cache. Across diverse image and video reasoning benchmarks, AVIS improves the accuracy–compute trade-off relative to VCS-only and VRS-only baselines, and remains effective on top of RL post-trained VLMs while keeping compute and latency low.

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

Scalable Deep Unfolding of Conic Optimizers

arXiv:2606.13825v1 Announce Type: cross Abstract: Deep unfolding (DU) accelerates iterative optimizers by introducing learnable components and training them through unrolled iterations, but extending DU to the large-scale semidefinite programs (SDPs) common in robotics has remained limited. Unrolling a full-update conic solver such as COSMO exposes two obstacles that prior work on learned conic solvers has not: backpropagating through the per-iteration linear-system solve incurs memory quadratic in the problem size once the coefficient matrix is formed explicitly, and backpropagating through the positive semidefinite (PSD) cone projection becomes numerically unstable when eigenvalues coincide. We address the first obstacle with a matrix-free implicit differentiation rule that operates entirely through matrix-vector products, reducing memory from $O(n^2)$ to $O(n)$ and enabling backpropagation at scales where direct factorization runs out of memory. We address the second with a backward rule based on the Dalečkii–Krein representation of the Fréchet derivative, which remains well-defined under repeated eigenvalues. Together these make it possible to learn lightweight hyperparameter policies and warm-starts for a full-update conic solver. We evaluate on nonlinear covariance steering problems solved via sequential convex programming (SCP), as well as standalone SDPs and second-order cone programs ranging from max-cut and Lovász $\vartheta$ SDPs to robust estimation and control problems. The learned policies outperform state-of-the-art solvers across all problems, and can provide up to a 50$\times$ speedup depending on the class. When used as a subroutine in SCP, the learned approach delivers over a 30$\times$ speedup compared to COSMO.

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

ScoutVLA: UAV-Centric Active Perception via a Dual-Expert VLA Model for Open-World Embodied Question Answering

Aerial Embodied Question Answering (EQA) requires Unmanned Aerial Vehicles (UAVs) to actively perceive the environment and answer natural language questions. Existing outdoor EQA systems usually stop once the target enters the UAV's field of view, leaving the fine-grained viewpoint adjustment needed for evidence-seeking questions largely unresolved. To address this issue, we introduce FG-EQA, a fine-grained active perception EQA benchmark with more than 40K simulated trajectories and 1K real-world trajectories. Drawing inspiration from the ``waggle dance'' of scout bees, which iteratively adjust their flight paths to verify target information, we propose ScoutVLA, an evidence-driven Vision-Language-Action model for outdoor EQA. To emulate this active exploration behavior, ScoutVLA features a decoupled dual-expert architecture: a vision-language expert infers the semantic intent to identify missing evidence, while an independent action expert employs high-DoF flow matching to generate continuous viewpoint-refinement trajectories. To balance the competing demands of continuous control and semantic reasoning, we devise a decoupled training strategy with a knowledge insulation mechanism that prevents the action gradients from erasing the model's multimodal reasoning ability. Extensive simulated experiments and a qualitative real-world field study both verify the superiority of ScoutVLA over the state-of-the-art baselines, demonstrating a 10.48$\boldsymbol{\times}$ higher average strict success rate and a 7.72$\boldsymbol{\times}$ higher average QA correctness.

20.
arXiv (CS.LG) 2026-06-16

Hidden Degradation Costs in Energy-Cost-Only HEMS Optimisation: Study on Battery and PV Sensitivity

arXiv:2606.16051v1 Announce Type: cross Abstract: Residential battery energy storage systems (BESS) are increasingly deployed alongside photovoltaic (PV) generation to reduce household energy costs under volatile time-of-use (TOU) tariffs. Model predictive control (MPC) is a widely adopted optimisation strategy for home energy management systems (HEMS), typically formulated to minimise net energy cost, subject to physical and operational constraints. However, battery degradation is rarely embedded in the optimisation objective, meaning its cost is unquantified and aggressive; high-cycle-count strategies could incur significant losses once deployed to physical systems. This paper presents a receding-horizon mixed-integer linear programming (MILP) baseline for a UK residential HEMS, using demand data from the REFIT dataset. A 3 by 3 sensitivity study is conducted across three battery sizes and three PV array sizes, with post-hoc degradation cost estimated using the Naumann stress model and rainflow cycle counting. Results show that degradation remains constant for each battery size and can exceed energy cost savings by up to 1,060 %. These results demonstrate that energy-cost-only optimisation systematically underestimates the true system cost, motivating a degradation-aware control formulation.

21.
arXiv (CS.CL) 2026-06-12

RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery

Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and challenging. Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have supported Target ID; however, no benchmark currently exists for identifying the biological impacts of PPIs. To bridge this gap, we introduce the RAG Benchmark for PPIs (RAGPPI), a factual question-answer benchmark of 4,420 question-answer pairs that focus on the potential biological impacts of PPIs. Through interviews with experts, we identified criteria for a benchmark dataset, such as a type of QA and source. We built a gold-standard dataset (500 QA pairs) through expert-driven data annotation. We developed an ensemble auto-evaluation LLM that incorporates expert labeling characteristics, average fact-abstract similarity (F1), and low-similarity fact counts (F2), enabling the construction of a silver-standard dataset (3,720 QA pairs). We are committed to maintaining RAGPPI as a resource to support the research community in advancing RAG systems for drug discovery QA solutions.

22.
bioRxiv (Bioinfo) 2026-06-21

SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning

Genome assembly is a computational pipeline designed to reconstruct chromosomes from small sequencing reads. Following their assembly, contiguous sequences (contigs) are arranged into chromosome-long sequences during scaffolding. Hi-C, a long-range linkage information between regions of the genome widely used in recent large sequencing projects, is often required to correctly order contigs. Several tools have been developed to automate this task following either statistical or deep-learning approaches. Statistical approaches summarise 2D Hi-C matrices into contact densities across sequences, thus ignoring informative visual patterns. The sole existing deep-learning tool uses a transformer-based computer vision model to correct the assembly. It has been trained on several species and uses Hi-C matrices directly. Yet it comes as a supplementary step in the scaffolding process, introducing extra computation time, and has been trained on a dataset that might contain labelling errors, which could provide sub-optimal results. We propose SPA-C, an hybrid pipeline combining the strengths of both approaches. Linkage prediction is handled with a frugal CNN-based model and a graph-solving algorithm is used to generate the scaffolds. Through our input's design, the model is able to both correct errors within assemblies and link contigs, leveraging small, local Hi-C contact matrices. We handled low-complexity regions that might induce erroneous predictions using an external tool, improving the overall accuracy of generated assemblies. On a benchmark of six various genomes and four standard metrics, SPA-C outperformed four out of four state-of-the-art methods while achieving comparable start-to-end computation time.Python and Bash scripts are available on GitHub (https://github.com/SPA-C/SPA-C.git) and Zenodo (https://doi.org/10.5281/zenodo.19000361).

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

Benchmarking Counterfactual Prediction in Epidemic Time Series with Time-Varying Interventions

arXiv:2606.05692v2 Announce Type: replace-cross Abstract: Deep learning has enabled significant advances in time-series causal inference, yet progress remains constrained by the lack of realistic benchmarks with observable counterfactual outcomes. Existing datasets either rely on real-world observations without ground-truth counterfactuals or on simplified simulations that fail to capture complex causal dynamics. To address this gap, we develop a large-scale benchmark for counterfactual prediction in epidemic time series under dynamic interventions. Unlike existing benchmarks, it supports static and time-varying treatments, as well as both single-policy and multi-policy intervention settings, enabling evaluation of causal inference methods across a broad range of causal inference scenarios. Leveraging a calibrated agent-based model grounded in real-world demographic, mobility, epidemiological, and policy data, we generate realistic counterfactual trajectories across more than 150 U.S. counties. Using this benchmark, we evaluate widely used and state-of-the-art causal inference methods, revealing substantial performance differences and highlighting the challenges of realistic time-series causal reasoning.

25.
arXiv (CS.CV) 2026-06-17

TaFD: Threat-Aware Frequency Decoupling for Adversarial Robustness against Heterogeneous Attacks

Multi-threat robustness remains a fundamental challenge in deep learning. Although joint adversarial training (JAT) is widely adopted, it suffers from negative transfer under heterogeneous threats, particularly between $\ell_p$-bounded and semantic attacks. Through first-order gradient analysis, we formalize this as gradient incompatibility and theoretically establish the necessity of decoupled optimization. We further reveal that these conflicting threats exhibit separable spectral characteristics in the frequency domain. Motivated by this observation, we propose Threat-aware Frequency Decoupling (TaFD), a two-stage defense framework that reformulates JAT as a frequency-domain divide-and-conquer paradigm. TaFD first discovers latent threat domains via unsupervised clustering of attack spectral prototypes and trains a lightweight classifier for inference-time threat domain identification. Conditioned on the prediction, TaFD employs a Frequency-Conditional Convolution that learns threat-domain-specific spectral masks and routes each sample to the corresponding expert, enforcing structural parameter separation and alleviating optimization conflicts. We validate TaFD on three representative image-classification benchmarks (CIFAR-10, CIFAR-100, and Tiny-ImageNet) and on two representative architectures (the convolutional ResNet and the hybrid-transformer MobileViT). Extensive results demonstrate that TaFD achieves more balanced robustness against heterogeneous attacks than existing JAT and frequency-domain baselines, improving average robust accuracy by approximately 11\% over the strongest baseline while maintaining leading clean accuracy.