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01.
arXiv (CS.AI) 2026-06-12

What Type of Inference is Active Inference?

arXiv:2606.04935v2 Announce Type: replace Abstract: Active inference casts decision-making as inference, with the Expected Free Energy (EFE) unifying goal-directed and information-seeking behavior. Recent work showed that EFE minimization can be written as Variational Free Energy (VFE) minimization on a generative model augmented with epistemic priors. We prove that the VFE of the augmented model can be rewritten as the VFE of the predictive model plus explicit entropy-correction terms, making the EFE contribution transparent. We then show that proper EFE-based planning requires combining these epistemic corrections with a planning correction that turns marginal inference into policy optimization, yielding a full variational characterization of EFE-based planning. This clarifies which corrections are needed for cross-entropy planning and for full EFE-based planning. The same entropy-corrected formulation leads to a detailed message-passing scheme for EFE-based planning together with simpler ablations. Experiments on three grid-world environments show that full EFE-based planning outperforms ablations that omit either the planning correction or the epistemic corrections.

02.
arXiv (CS.AI) 2026-06-18

Synthetic Resonance: A Framework for Growth-Oriented Human-AI Relationships

arXiv:2606.18265v1 Announce Type: cross Abstract: As human relationships with artificial intelligence systems become increasingly frequent and sustained, existing language and theory fail to accurately capture the nature of these affiliations. Common descriptors such as mutual understanding, connection, or friendship risk anthropomorphizing systems that lack subjective experience, while dominant frameworks tend to reduce AI to either a tool or a threat. In this paper, I introduce the concept of synthetic resonance as an integrative framework for understanding human-AI relationships. Synthetic resonance describes how relationships humans define as meaningful can emerge between a human and an AI system without the need to attribute shared feelings or mutual awareness. I argue that synthetic resonance is best understood as a structured, dynamic pattern of interaction that can produce a sense of relationship without the presence of a second experiencing subject. By clarifying this distinction, the concept of synthetic resonance offers a more precise way of conceptualizing human-AI relationships and highlights their potential value and ethical implications. I also call for more research that tests the processes and outcomes of synthetic resonance.

03.
arXiv (CS.CV) 2026-06-17

FUSER: Feed-Forward MUltiview 3D Registration Transformer and SE(3)$^N$ Diffusion Refinement

Registration of multiview point clouds conventionally relies on extensive pairwise matching to build a pose graph for global synchronization, which is computationally expensive and inherently ill-posed without holistic geometric constraints. This paper proposes FUSER, the first feed-forward multiview registration transformer that jointly processes all scans in a unified, compact latent space to directly predict global poses without any pairwise estimation. To maintain tractability, FUSER encodes each scan into low-resolution superpoint features via a sparse 3D CNN that preserves absolute translation cues, and performs efficient intra- and inter-scan reasoning through a Geometric Alternating Attention module. Particularly, we transfer 2D attention priors from off-the-shelf foundation models to enhance 3D feature interaction and geometric consistency. Building upon FUSER, we further introduce FUSER-DF, an SE(3)$^N$ diffusion refinement framework to correct FUSER's estimates via denoising in the joint SE(3)$^N$ space. FUSER acts as a surrogate multiview registration model to construct the denoiser, and a prior-conditioned SE(3)$^N$ variational lower bound is derived for denoising supervision. Extensive experiments on 3DMatch, ScanNet and ArkitScenes demonstrate that our approach achieves the superior registration accuracy and outstanding computational efficiency.

04.
arXiv (CS.CL) 2026-06-11

From Explicit Elements to Implicit Intent: A Predefined Library for Auditable Behavioral Inference

We present SemantiClean, a modular framework for extracting structured semantic signals from e-commerce session data and driving pluggable inference targets including purchase intent, customer segmentation, and product affinity through a shared element library. Unlike conventional end-to-end predictors that optimise solely for accuracy, SemantiClean prioritises auditability, structural governance, and sigma=0 reproducibility, explicitly trading marginal predictive gains for element-level transparency and defensible decision trails. Built upon the Online Shoppers Purchasing Intention (OSPI) dataset, the framework organises twenty-four behavioural elements into a four-layer architecture (Functional, Interaction, Systemic, Contextual) and enforces signal quality through three anti-inflation mechanisms: RedundancyGroup contribution caps, TieredPenaltyCalculator bias penalties, and AdaptiveConstraintMode cold-start protection.This report introduces the LLM-Integrated Semantic Inference Engine, a fully implemented two-phase LLM-driven inference architecture that leverages complete element metadata at inference time. All quantitative results reported herein are produced by this engine. Deterministic engine outputs remain fully reproducible (sigma=0); LLM-dependent results (E8, E10) are subject to controlled output variability under fixed provider/model/temperature settings. The gender inference target remains non-functional in the current implementation and is excluded from all quantitative results.

05.
Nature (Science) 2026-06-12

An innovative technology boosts image quality for protein structures

After years of effort, two research teams have developed ‘laser phase plate’ systems that could help cryo-electron-microscopy users to generate high-quality structures for a broad range of proteins. After years of effort, two research teams have developed ‘laser phase plate’ systems that could help cryo-electron-microscopy users to generate high-quality structures for a broad range of proteins.

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

Measurement noise limits the advantage of nonlinear models over linear models in biomedical prediction

arXiv:2606.18420v1 Announce Type: new Abstract: On biomedical tabular data, flexible models such as deep networks, gradient-boosted trees, and kernel methods are repeatedly matched or beaten by linear and logistic regression given the same features. The usual reaction is to treat this as a model-side shortfall, to be fixed with more data, a better architecture, or tuning, on the assumption that the nonlinear structure is there and the model has failed to capture it. We argue that these fixes cannot help when the binding limit is the measurement rather than the model, as it frequently is in biomedicine. Additive noise blurs the population-optimal predictor, and because blurring removes a function's fine, rapidly varying detail before its broad shape, it erases nonlinear structure faster than linear structure. A degree-$k$ interaction is attenuated by the $k$-th power of feature reliability, while the linear part is attenuated only once. At the reliabilities typical of biomedical measurement, the nonlinear advantage can vanish even when the underlying biology is strongly nonlinear, and what the noise removes cannot be recovered by a larger cohort or a more flexible model, only by better measurement. The nonlinearity is hidden, not absent, and a tie between linear and flexible models is not by itself a verdict on the biology. These pieces are classical, drawn from measurement-error statistics, psychometrics, and Gaussian analysis, and we assemble them into an exact excess-risk identity. Measurement reliability is one of three conditions, alongside sample size and feature representation, that must align for a flexible model to help, and together they leave only a narrow window that most biomedical tasks fall outside. Across 140 UK Biobank tasks, the gap between flexible and linear models, where it exists, carries the predicted noise signature, and the three conditions can be separated by intervention but not by a benchmark alone.

07.
arXiv (CS.AI) 2026-06-11

TileFuse: A Fused Mixed-Precision Kernel Library for Efficient Quantized LLM Inference on AMD NPUs

arXiv:2606.11357v1 Announce Type: cross Abstract: With the growing demand for on-device LLM inference, edge SoCs increasingly integrate NPUs to improve performance and energy efficiency under tight power and thermal budgets. However, practical LLM deployment on current client NPUs remains difficult: widely used quantization formats such as AWQ do not map cleanly onto many existing NPU software stacks, which are often proprietary and expose limited low-level control. In this work, we present TileFuse, a close-to-metal mixed-precision kernel library for AMD XDNA2 NPUs that targets transformer linear layers in quantized LLM inference. TileFuse brings practical low-bit formats such as AWQ-style W4A16 and W8A16 directly onto XDNA2, rather than forcing the model to be reshaped around an NPU-specific quantization scheme. TileFuse co-designs weight layout, metadata placement, mixed-precision microkernels, and array-level dataflow. Specifically, it fuses unpacking, dequantization, and GEMM/GEMV execution into a single kernel flow, introduces an interleaved pre-tiling layout that supports GEMM dimensions up to 32K, and redesigns GEMV dataflow to utilize the full 4x8 AIE array. Across kernel-level evaluations, TileFuse improves performance by up to 121.6% for GEMM and 281% for GEMV over full-precision baselines, while delivering more than 2x performance and energy-efficiency gains over strong iGPU baselines on GEMM. In end-to-end LLM experiments on Ryzen AI laptops, TileFuse achieves up to 2.0x lower prefilling latency with more than 64.6% lower energy consumption. Together, these results show that XDNA2 is a practical target for AWQ-style edge LLM inference and that native NPU support for off-the-shelf quantization can make NPUs substantially more usable in real client deployments.

08.
arXiv (CS.CL) 2026-06-18

Lost in a Single Vector: Improving Long-Document Retrieval with Chunk Evidence Aggregation

Dense retrieval ranks one query vector against one document vector. On long documents, this interface can fail when a short but decisive span is weakened during document encoding before ranking. We study this failure mode as document-side early compression and introduce the Evidence Dilution Index (EDI) to measure how far a document-level representation falls below the strongest chunk-level evidence within the same gold document. Guided by this view, we propose DICE (Document Inference via Chunk Evidence), a training-free document-side strategy that splits documents into chunks, encodes them independently with a frozen model, and aggregates them back into a single vector while preserving the standard one-query-one-document interface. On LongEmbed, DICE improves retrieval across four backbones, with the largest gains on slices beyond 4k tokens: for Dream, Passkey >4k rises from 30.0 to 90.0 and Needle >4k from 23.3 to 74.0. Across 12,779 filtered samples, DICE yields lower EDI than the single-vector baseline in 92.8% of cases. These results establish document-level encoding as a practical and underexplored lever for long-document retrieval.

09.
arXiv (CS.CV) 2026-06-16

Simulation-Based Multi-Fillet Evaluation of Woody Breast Poultry Fillets

Woody breast (WB) is a myopathy in modern broiler chickens that causes the breast muscle to become unusually stiff and fibrous, leading to decreased meat quality and significant economic losses. State-of-the-art automated WB detection relies on a side-view imaging system to analyze the bending behavior of a single fillet as it falls off a conveyor belt. While highly accurate, this approach is constrained by its single-fillet field of view, creating throughput bottlenecks on commercial processing lines. In this paper, we address this limitation via a novel multi-fillet detection architecture utilizing a top-down camera configuration. To validate our approach, we first develop a high-fidelity digital twin of an industrial conveyor system. Next, we synthesize a diverse dataset of 3D fillet meshes and model their viscoelastic bending dynamics using a physics-based simulation engine. Lastly, a continuous 2D shape deformation score is extracted from the top-down perspective as the simulated fillets traverse the roller precipice. Experimental results demonstrate that the top-down shape score effectively captures the contour changes of the fillets as it bends, providing a robust and scalable alternative to a side-view imaging system for simultaneous multi-fillet WB evaluation.

10.
bioRxiv (Bioinfo) 2026-06-15

Biological meaning in protein embedding space is resolution-dependent

Protein language model embeddings are increasingly used to organise biological sequences, yet how biological meaning is encoded within embedding neighbourhoods remains poorly understood. Using two independent hierarchical enzyme systems, carbohydrate-active enzymes and peptidases, we investigated how biological interpretation changes across embedding organisations aligned to different levels of biological hierarchy. Different embedding organisations give rise to distinct neighbourhood semantics. When aligned to membership-boundary resolution, embeddings robustly separated artefacts and unrelated proteins from members of the target category. However, embeddings aligned to functional-grouping resolution maintained compositional neighbourhood structure for multi-domain proteins spanning more than one functional or catalytic group. Finally, embeddings aligned to local-family resolution recovered compact family-like neighbourhoods, including families withheld from training, while weakening broader membership-boundary and functional-grouping relationships. Moreover, embeddings optimised toward the same level of biological organisation retain different biological relationships depending on optimisation trajectory employed. Together, our results show that proximity in protein embedding space has no fixed biological interpretation. Instead, biological meaning emerges across embedding resolutions through selective preservation of different forms of biological organisation.

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

SCAIL-2: Unifying Controlled Character Animation with End-to-end In-Context Conditioning

Controlled character animation requires transferring motion from a driving sequence to a reference character. Prior works heavily rely on intermediate representations, including pose skeletons to represent motion or masked background to represent environment, which inevitably leads to information loss. To address this, we present SCAIL-2, a framework that bypasses those intermediates and achieves end-to-end character animation. By directly concatenating driving videos to the sequence, the model can obtain all the required visual information from the input video. To address the lack of end-to-end data, we unify sub-tasks of character animation with decoupled conditions and then curate a pipeline to synthesize MotionPair-60K, an end-to-end motion transfer dataset containing heterogeneous tasks of character animation. To achieve the unification, we utilize in-context mask conditioning and mode-specific RoPE as soft guidance beyond textual instructions and raw visual information. To address synthetic discrepancy in detailed regions, we propose Bias-Aware DPO to construct preference items to mitigate the errors. Extensive experiments demonstrate that our method substantially outperforms existing state-of-the-art approaches in various character animation tasks. A large subset of synthetic data as well as model weights will be released at our project page: https://teal024.github.io/SCAIL-2/.

12.
arXiv (CS.AI) 2026-06-17

Brep2Shape: Boundary and Shape Representation Alignment via Self-Supervised Transformers

arXiv:2602.07429v2 Announce Type: replace-cross Abstract: Boundary representation (B-rep) is the industry standard for computer-aided design (CAD). While deep learning shows promise in processing B-rep models, existing methods suffer from a representation gap: continuous approaches offer analytical precision but are visually abstract, whereas discrete methods provide intuitive clarity at the expense of geometric precision. To bridge this gap, we introduce Brep2Shape, a novel self-supervised pre-training method designed to align abstract boundary representations with intuitive shape representations. Our method employs a geometry-aware task where the model learns to predict dense spatial points from parametric Bézier control points, enabling the network to better understand physical manifolds derived from abstract coefficients. To enhance this alignment, we propose a Dual Transformer backbone with parallel streams that independently encode surface and curve tokens to capture their distinct geometric properties. Moreover, the topology attention is integrated to model the interdependencies between surfaces and curves, thereby maintaining topological consistency. Experimental results demonstrate that Brep2Shape offers significant scalability, achieving state-of-the-art accuracy and faster convergence across various downstream tasks.Code is available at this repository: https://github.com/thuml/Brep2Shape.

13.
arXiv (CS.LG) 2026-06-11

Minimal surfaces, Knots, and Neural Networks

arXiv:2605.26234v2 Announce Type: replace-cross Abstract: A recent conjecture by Joel Fine posits a relationship between the coefficients of the HOMFLY polynomial of a knot $K$ in the 3-sphere $S^3$, and the signed count of minimal surfaces in hyperbolic 4-space $\mathrm{H}^4$ meeting the sphere at infinity at $K$, with prescribed genus and self-intersection number. In this paper, we develop a novel machine learning framework based on Physics-Informed Neural Networks (PINNs) to solve the minimal surface equation in hyperbolic space. We utilise this framework to test Fine's Conjecture by constructing near-minimal surfaces bounding various families of knots in $S^3$. Furthermore, we develop an algorithmic method to find self-intersections and compute their sign. For every knot analysed, the computationally discovered minimal surfaces and their self-intersection numbers perfectly align with the predictions of Fine's Conjecture, providing empirical evidence for it.

14.
PLOS Computational Biology 2026-06-02

Assessing the importance of sex and disease-specific anatomy in electrophysiology and mechanical simulations with a newly developed public virtual cohort of four-chamber heart models

by José Alonso Solís-Lemus, Rosie K. Barrows, Cristobal Rodero, Marina Strocchi, Natalie Montarello, Nishant Lahoti, Cesare Corrado, Abdul Qayyum, Shahrokh Rahmani, Caroline Roney, Gernot Plank, Christoph Augustin, Hao Xu, Alistair Young, Pras Pathmanathan, Ronak Rajani, Steven A. Niederer This work presents a study on how differences in cardiac anatomy attributed to sex and disease can influence cardiac electrophysiology and mechanics using a virtual cohort of four-chamber heart models. Patient anatomy varies across sex and disease. However, capturing this variation in in-silico studies remains poorly accounted for, with studies often using either single representative cases or imbalanced virtual cohorts. Whole-heart electromechanics models incorporate the patient’s anatomy, electrophysiology and mechanics across different scales, from molecular, tissue and whole-heart and circulatory system levels. However, cardiac models are typically built from one or a small number of anatomies, with sex rarely reported and the effects of anatomical variability, which include those due to sex or disease, largely unexplored. This limits clinical translation and reduces regulatory credibility. We developed fifty patient-specific anatomical models of 25 male and 25 female hearts in heart failure and control cases. We ran benchmark passive inflation and paced activation simulations with consistent parameters and boundary conditions across cases to isolate the impact of anatomical variations with sex and disease. Heart failure models exhibited increased chamber volumes, larger volume changes during inflation, and delayed activation times relative to controls. These trends were consistent across sexes, although right ventricular activation showed a significant sex-based difference. Variations in anatomy with sex and disease have a significant impact on cardiac simulations, which support the inclusion of multiple heart anatomical models in in-silico trials. The resulting virtual cohort captures key anatomical variability and is publicly available, along with the underlying code (see Data Availability statement).

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

SICI: A Semantic-Pragmatic Complexity Index Reveals Regime Shifts in LLM Stance Detection

Prompt-based LLMs are increasingly used for stance detection, but harder examples are not always repaired by clearer instructions, reasoning prompts, retrieval, or debate. We introduce SICI (Stance Inference Complexity Index), a seven-dimensional diagnostic measure of the semantic-pragmatic burden imposed by a target–text pair. Across SemEval-2016 and VAST, SICI predicts LLM accuracy better than surface proxies and shows substantial cross-scorer reliability ($\alpha=0.771$). More importantly, LLM errors change regime as SICI increases: low-complexity examples invite over-attribution, especially Against predictions; intermediate examples form an unstable boundary; and high-complexity examples rapidly concentrate on None. This phase-transition-like structure persists across GPT-3.5, GPT-4o-mini, DeepSeek-V3, and GPT-4o, although stronger models move the boundaries. A 15-method intervention study further shows that prompting, retrieval, and debate often shift models along the attribution–abstention axis rather than removing the high-complexity bottleneck.

16.
medRxiv (Medicine) 2026-06-17

Multi-strain Probiotics Alter Gut Microbiota and Estrobolome Pathways in Primary Dysmenorrhea

Background: Exact cause of primary dysmenorrhoea is unknown but recent evidence uncovers a potential link between gut dysbiosis and benign gynaecological disorder via disruption of estrobolome. Methods: A randomized controlled trial to investigate the effects of multi-strain oral probiotics on primary dysmenorrhoea has been conducted. This is a secondary analysis comparing the stool microbiome in women with primary dysmenorrhoea and those without (control), and the effects of treatment with probiotics versus placebo. Results: Although microbial richness and evenness were comparable between groups (alpha diversity, p > 0.05), gut microbial community composition differed significantly (Bray Curtis PERMANOVA, p = 0.015), characterised by reduced Bifidobacterium adolescentis and Blautia and enrichment of Faecalibacterium in dysmenorrhoea, alongside condition-specific core taxa. Post-intervention analysis revealed significant shifts in microbial community structure between pre- and post-treatment groups (PERMANOVA, F = 2.11, p = 0.005), with probiotic supplementation inducing more consistent and directed microbiome changes than placebo, without altering alpha diversity (p > 0.05). Functional prediction showed no significant difference in overall beta glucuronidase pathway abundance (p > 0.05); however, dysmenorrhoea was associated with higher abundance of beta glucuronidase producing taxa (MaAsLin2, q < 0.05) that were differentially modulated by probiotic treatment. Conclusion: This discovery provides evidence on the microbial disruption in primary dysmenorrhoea as well as the benefit of probiotics to modulate the intestinal microbiota to improve the condition.

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

Are Online Skill and Memory Modules Always Worth Their Tokens? A Budget-Constrained Study of Web Agents

Online web agents often augment a base actor with memory, workflow, or skill modules. These modules can improve performance, but they also consume test-time tokens, a cost rarely reported alongside the actor's inference cost. We study online augmentation, where this overhead is paid on every task, and re-evaluate its benefits under a fixed total inference budget. We compare AWM, ASI, and ReasoningBank with a token-matched vanilla baseline that uses the same budget for additional actor steps. Across three WebArena domains and three models, Gemini 3 Flash, GPT-5.4-mini, and Qwen 3.6-27B, the vanilla baseline matches or surpasses all three augmentation methods in aggregate success rate while often using fewer total tokens. We observe a similar trend on WorkArena-L1 with Qwen 3.6-27B, indicating that the effect extends to enterprise knowledge-work tasks. Our results suggest that skills and workflow memory can be useful in specific domains, but their apparent gains often vanish against a budget-matched actor. We further show that run-to-run variance materially affects outcomes and should be reported as a core evaluation criterion for online web agents.

18.
arXiv (CS.LG) 2026-06-19

A Solver-Free Training Method for Predict-then-Optimize

arXiv:2606.19587v1 Announce Type: cross Abstract: We propose a scalable method for training prediction (machine learning) models in the predict-then-optimize paradigm, where model outputs serve as coefficients for a subsequent linear optimization task. Directly minimizing the empirical decision regret is intractable for linear programming and combinatorial optimization since the decision mapping is piecewise constant, and the gradients are zero almost everywhere. While existing methods address this by smoothing the differentiation process, they suffer from scalability issues, since a computationally expensive solver call is required for every gradient evaluation. To address this, we propose a decision-focused learning pipeline based on a measure transformation principle, which yields a new surrogate loss that is completely optimization-solver-free during training. We establish theoretical guarantees, including Fisher consistency and excess risk bounds. Empirically, our method achieves decision quality competitive with state-of-the-art methods while reducing training time by orders of magnitude.

19.
arXiv (CS.AI) 2026-06-18

A Technical Taxonomy of LLM Agent Communication Protocols

arXiv:2606.19135v1 Announce Type: cross Abstract: As large language models (LLMs) advance and multi-agent systems aim to overcome the limits of standalone agents, robust communication protocols are becoming essential infrastructure for distributed agent networks. Nonetheless, the fragmented protocol landscape presents a significant interoperability challenge. This study develops a technical taxonomy to classify and analyze LLM agent communication protocols. Following an established iterative method, we defined the taxonomy's purpose, meta-characteristic, and ending conditions, then performed five iterations, three empirical-to-conceptual and two conceptual-to-empirical, on nine actively maintained open-source protocols with demonstrable adoption. The taxonomy comprises five dimensions: counterparty, payload, interaction state, discovery mechanism, and schema flexibility. Classification reveals recurring architectural patterns: all sampled agent-to-agent protocols combine hybrid payloads with session-state persistence; most protocols support multiple predefined schemas, and two negotiate schemas at runtime, indicating a trend toward schema flexibility; decentralized discovery remains rare. Analysis suggests short-term convergence pressure toward protocols unifying agent-to-agent and agent-to-context (tool and data) communication. Long-term, however, no single protocol is likely to maximize versatility, efficiency, and portability simultaneously. The field will more likely evolve toward a federated, layered protocol stack. The framework guides protocol selection and highlights open research gaps such as privacy and policy enforcement.}

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

Shape of Thought: Progressive Object Assembly via Visual Chain-of-Thought

Multimodal models for text-to-image generation have achieved strong visual fidelity, yet they remain brittle under compositional structural constraints, notably generative numeracy, attribute binding, and part-level relations. To address these challenges, we propose Shape-of-Thought (SoT), a visual CoT framework for process-supervised progressive shape assembly in the rendered 2D domain, without external engines at inference time. SoT trains a unified multimodal autoregressive model to generate interleaved textual plans and rendered intermediate states, helping the model capture shape-assembly logic without producing explicit geometric representations. Unlike text-only CoT, each decision is grounded in a rendered state, making counts, attachments, topology, and intermediate part-addition errors inspectable across the trajectory. To support this paradigm, we introduce SoT-26K, a large-scale dataset of grounded assembly traces derived from part-based CAD hierarchies, and T2S-CompBench, a benchmark for evaluating structural integrity and trace faithfulness. Fine-tuning on SoT-26K achieves 88.4% on component numeracy and 84.8% on structural topology, outperforming direct generation by +24.2 points on component numeracy and +19.3 points on structural topology. SoT establishes a transparent testbed for rendered-domain structure-aware generation. The code is available at https://github.com/yuhuo03/Shape-of-Thought.

21.
arXiv (quant-ph) 2026-06-12

Reduced basis algorithm for solving nonlinear differential equations on quantum computers

arXiv:2606.13457v1 Announce Type: cross Abstract: As quantum computing moves toward scientific computing applications, nonlinear differential equations remain a central challenge since quantum evolution is intrinsically linear. In this work, we introduce a reduced basis algorithm (RBA) for polynomial nonlinear ordinary differential equations (ODEs) and spatially discretized partial differential equations (PDEs). After time discretization, the method composes the resulting polynomial update map over $m$ timesteps, identifies the reduced monomial basis appearing in this composed map, and constructs a linear RBA operator whose action recovers the exact $m$-timestep nonlinear dynamics. Thus, at the level of the chosen discrete update rule, the method introduces no additional approximation error beyond the time discretization error. The qubit number requirement is governed by the size of the reduced monomial basis. For an $n$-dimensional polynomial ODE system of degree $p>1$, the lifted register requires at most $q_m^{\mathrm{ODE}} = O(nm\log p)$ qubits in the full basis scenario. For PDEs discretized on $N^D$ grid points, a locality-based construction requires at most $q_m^{\mathrm{PDE}} = O(D\log N + n m^{D+1}\log p)$ qubits. Hence, the dependence on the grid size remains logarithmic, while the nonlinear overhead is controlled by local reduced basis size. The main computational burden is moved from the quantum computer to a classical preprocessing step, where the reduced monomial basis and RBA operator are constructed for the chosen timestep window. Through numerical tests on the Lorenz system and the one-dimensional Burgers equation, we verify that the RBA reproduces the corresponding discrete time nonlinear dynamics exactly, while exposing the trade-off between timestep composition, reduced basis growth, and locality.

22.
bioRxiv (Bioinfo) 2026-06-11

Robust semi-supervised scRNA-seq integration from virtual adversarial learning

Single-cell RNA sequencing integration methods that rely solely on transcriptomic data often struggle to preserve fine-grained distinctions between closely related cell subtypes. As a result, cell populations that are separable in the raw data may become over-mixed after integration, reducing biological resolution and interpretability. Incorporating marker gene information can potentially address these issues; however, the variability and complexity of available marker sets limit their effective application. To address this, we introduce scCRAFT+, a semi-supervised integration model that innovatively incorporates marker gene information through Virtual Adversarial Training (VAT). By jointly optimizing marker-derived supervision and transcriptome-wide representations, VAT enforces local prediction smoothness among transcriptionally similar cells, improving robustness to noisy marker annotations while enhancing both integration quality and cell type auto-annotation. This targeted approach significantly enhances annotation accuracy and robustness, particularly when faced with incomplete or incorrect marker gene sets. Benchmarking shows that scCRAFT+ achieves consistently stronger performance than current unsupervised and supervised integration approaches, resulting in improved integration quality and biologically meaningful sub-cell type auto-annotations.

23.
arXiv (CS.AI) 2026-06-11

ProGRank: Probe-Gradient Reranking to Defend Dense-Retriever RAG from Corpus Poisoning

arXiv:2603.22934v3 Announce Type: replace Abstract: Retrieval-Augmented Generation (RAG) improves large language model applications by grounding generation in retrieved evidence, but also introduces corpus poisoning as a new attack surface. In this setting, an adversary injects or edits passages so that they enter the Top-$K$ results for target queries and influence downstream generation. Existing defences often rely on content filtering, auxiliary models, or generator-side reasoning, which complicates deployment. We propose ProGRank, a post hoc, training-free retriever-side defence for dense-retriever RAG. ProGRank stress-tests each query–passage pair under mild randomized perturbations, extracts probe gradients from a small fixed parameter subset, and derives two instability signals: representational consistency and dispersion risk. It then combines these signals with a score gate for reranking. ProGRank preserves the original passage content, requires no retraining, and supports a surrogate-based variant when the deployed retriever is unavailable. Experiments across datasets, retrievers, attacks, and retrieval-stage and end-to-end settings show that ProGRank improves robustness and maintains a favorable robustness–utility trade-off, including under adaptive evasive attacks.

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

One Token to Fool LLM-as-a-Judge

Large language models (LLMs) are increasingly trusted as automated judges, assisting evaluation and providing reward signals for training other models, particularly in reference-based settings like Reinforcement Learning with Verifiable Rewards (RLVR). However, we uncover a critical vulnerability even in this reference-based paradigm: generative reward models are systematically susceptible to reward hacking. We find that superficial inputs, which we term ''master keys'' such as non-word symbols (e.g., '':'' or ''.'') or generic reasoning openers (e.g., ''Thought process:'' or ''Let's solve this problem step by step.''), can consistently elicit false positive rewards without any substantive reasoning. Our systematic evaluation demonstrates this is a widespread failure affecting a diverse range of models, including leading proprietary systems such as GPT-o1 and Claude-4. These results challenge the assumed robustness of LLM judges and pose a significant threat to their reliability. To address this, we propose a simple yet effective data augmentation strategy using truncated model outputs as adversarial negative examples. The resulting Master Reward Models (Master-RMs) demonstrate state-of-the-art robustness against these ''master key'' attacks while maintaining high performance in standard evaluation settings. We supplement these findings with a comprehensive analysis of the vulnerability across model scales, prompt variations, and common inference-time strategies, offering insights to guide future research on robust LLM evaluation. We release our robust, general-domain reward models and the synthetic training data at https://huggingface.co/sarosavo/Master-RM and https://huggingface.co/datasets/sarosavo/Master-RM.

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

Position: Coding Benchmarks Are Misaligned with Agentic Software Engineering

Coding agents have become a major mode of software engineering, but the benchmarks we use to compare them were designed in a pre-agent era: they collapse model, harness, and environment into a single end-to-end score, typically computed against one reference solution, with no component-level signal for iteration. We argue that current coding benchmarks are misaligned with agentic software engineering. A coding agent in practice is not a model: it is a system harness – a composite of models, harnesses, contexts, environments, and feedback signals, any one of which can move the benchmark score by margins comparable to those between adjacent model generations. We discuss three symptoms: (i) benchmark scores conflate the model with the rest of the harness; (ii) grading against a single reference solution penalises equally valid alternatives; and (iii) the absence of signal at the level of individual harness components makes the end-to-end system score difficult to iterate on.