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01.
arXiv (CS.CL) 2026-06-11

Where Do Backdoors Live? A Component-Level Analysis of Backdoor Propagation in Speech Language Models

Speech language models (SLMs) are systems of systems: independent components that unite to achieve a common goal. Despite their heterogeneous nature, SLMs are often studied end-to-end; how information flows through the pipeline remains obscure. We investigate this question through the lens of backdoor attacks. We first establish that backdoors can propagate through the SLM, leaving all tasks highly vulnerable. From this, we design a component analysis to discover the role each component takes in backdoor learning. We find that backdoor persistence or erasure is highly dependent on the targeted component. Beyond propagation, we examine how backdoors are encoded in shared multitask embeddings, showing that poisoned samples are not directly separable from benign ones, challenging a common separability assumption used in filtering defenses. Our findings emphasize the need to treat multimodal pipelines as intricate systems with unique vulnerabilities, not solely extensions of unimodal ones.

02.
Nature (Science) 2026-06-10

Efficient and accurate neural-field reconstruction using resistive memory

作者:

Applications such as medical imaging, augmented and virtual reality, and embodied artificial intelligence (AI) depend on the ability to reconstruct complex signals from sparse observations. These applications are characterized by incomplete measurements and limited computational resources. Traditional approaches to digital hardware face the following challenges: explicit signal representations require heavy sampling and storage, data movement across the von Neumann bottleneck dominates energy and latency, and CMOS (complementary metal–oxide–semiconductor)-based circuits offer limited parallel efficiency. Here we present a software–hardware co-optimization framework for sparse-input signal reconstruction. At the software level, we use neural fields1 to implicitly represent signals using neural networks, which are further compressed by low-rank decomposition and structured pruning. At the hardware level, we design a resistive-memory-based computing-in-memory platform, featuring a Gaussian encoder and a multi-layer perceptron processing engine. The Gaussian encoder leverages the intrinsic stochasticity of resistive memory for efficient encoding, whereas the processing engine enables precise weight mapping through a hardware-aware quantization circuit. On a 40-nm 256 Kb resistive-memory macro, the system delivers 23.5×, 21.0× and 32.3× gains in projected energy efficiency, together with 10.8×, 38.8× and 6.2× gains in projected parallelism, for three-dimensional computed tomography sparse reconstruction, novel view synthesis and dynamic-scene novel view synthesis, without compromising on reconstruction quality. This work advances AI-driven signal reconstruction technology and paves the way for future efficient and robust medical AI and three-dimensional vision applications. A co-optimized AI hardware–software system using resistive-memory computing improves energy efficiency and parallelism for sparse signal reconstruction in imaging and three-dimensional vision applications.

03.
arXiv (CS.CV) 2026-06-18

Geometry-Aware Dataset Condensation for Diffusion Model Training

Dataset condensation aims to construct compact datasets from real data via synthesis or selection. However, existing approaches are ill-suited for diffusion model training: synthetic data generation often yields low-fidelity samples unsuitable for authentic modeling, while real subset selection typically fails to preserve the distributional geometry required by diffusion likelihood objectives. To address this, we propose to reformulate real subset selection as a geometry-aware distribution alignment problem. By incorporating one-sided partial optimal transport, our method selectively aligns a compact subset with the full data distribution while allowing unmatched mass in low-density regions, ensuring the preserved geometric structure necessary for effective diffusion model training. To further ensure distributional fidelity, we complement geometric alignment with lightweight feature-statistics and semantic consistency regularization. An efficient two-stage discrete optimization strategy is proposed to achieve this alignment objective. Extensive experiments across diffusion variants, subset sizes, image resolutions, and training rounds show that our method achieves superior fidelity and distributional coverage in diffusion model training. Codes are available at https://github.com/2018cx/GADC.

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

Robust and Interpretable Adaptation of Equivariant Materials Foundation Models via Sparsity-promoting Fine-tuning

arXiv:2606.18691v1 Announce Type: new Abstract: Pre-trained materials foundation models, or machine learning interatomic potentials, leverage general physicochemical knowledge to effectively approximate potential energy surfaces. However, they often require domain-specific calibration due to physicochemical diversity as well as mismatches between practical computational settings and those used in constructing the pre-training data. To address this, we propose a sparsity-promoting fine-tuning method that selectively updates model parameters by exploiting the structural properties of E(3)-equivariant materials foundation models. On energy and force prediction tasks across molecular and crystalline benchmarks, our method matches or surpasses full fine-tuning and equivariant low-rank adaptation while updating only $\sim$3~\% of parameters, and in some cases as little as $\sim$0.5~\%. Beyond energy and force calibration, we further demonstrate task generalizability by applying our method to magnetic moment prediction and magnetism-aware total energy modeling. Finally, analysis of sparsity patterns reveals physically interpretable signatures, such as enhanced $d$-orbital contributions in transition metal systems. Overall, our results establish sparsity-promoting fine-tuning as a flexible and interpretable method for domain specialization of equivariant materials foundation models.

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

Embedded Machine Learning for Microcontroller-Class Edge Devices: Data, Feature, Evaluation, and Deployment Pipelines

arXiv:2606.18122v1 Announce Type: cross Abstract: Embedded machine learning moves inference from cloud services to resource-constrained devices that must acquire data, preprocess signals, run a model, and act within tight limits on memory, energy, and latency. This paper presents a systems-oriented synthesis of an embedded machine-learning workflow for microcontroller-class platforms. The emphasis is placed on engineering decisions that are often hidden in generic machine-learning introductions: sampling and buffering, feature extraction as dimensionality reduction, validation under class imbalance, model/runtime co-design, and streaming deployment. Two representative signal families are used throughout the paper. The first is inertial motion recognition, where a two-second, three-axis accelerometer window is transformed from raw samples into root-mean-square and spectral features before classification. The second is keyword spotting, where audio is sampled, anti-aliased, transformed into mel-frequency cepstral coefficients, and processed by a compact one-dimensional convolutional network. The paper concludes with practical design rules for robust on-device inference, including data curation, quantization, thresholding, scheduling, and field monitoring.

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

Benchmarking Large Vision-Language Models on Fine-Grained Image Tasks: From Evaluation to Diagnosis

Recent advancements in Large Vision-Language Models (LVLMs) have demonstrated remarkable multimodal perception and reasoning capabilities. While numerous benchmarks have evaluated LVLMs from holistic or task-specific perspectives, their capabilities on fine-grained image tasks-fundamental to computer vision-remain insufficiently understood. To address this gap, we introduce FG-BMK, a comprehensive fine-grained evaluation benchmark containing 1.01 million questions and 0.28 million images, covering diverse scenarios from common object-centric domains to specialized domains. FG-BMK jointly evaluates dialogue-level fine-grained semantic recognition and feature-level visual discriminability through human-oriented and machine-oriented paradigms, enabling diagnostic analysis of whether LVLM failures arise from insufficient visual representations, weak visual-to-semantic grounding, or limited fine-grained knowledge. Through extensive experiments on a diverse set of representative LVLMs/VLMs, we find that current LVLMs remain inadequate fine-grained recognizers, with failures arising from intertwined bottlenecks in visual representations, semantic grounding, modality alignment, and category-level knowledge. We further analyze training design factors for improving fine-grained capabilities and examine how visual and linguistic perturbations affect LVLM predictions. These findings provide diagnostic insights into the limitations of current LVLMs and offer guidance for future data construction and model design in developing more reliable LVLMs for fine-grained visual tasks. Our code is open-source and available at https://fg-bmk.github.io/.

07.
arXiv (CS.CL) 2026-06-16

Benchmarking LLM Agents on Meta-Analysis Articles from Nature Portfolio

Meta-analysis is a demanding form of evidence synthesis that combines literature retrieval, PI/ECO-guided study selection, and statistical aggregation. Its structured, verifiable workflow makes it an ideal substrate for evaluating systematic scientific reasoning, yet existing benchmarks lack ground truth across the full retrieval-screening-synthesis pipeline. We introduce MetaSyn, a dataset of 442 expert-curated meta-analyses from Nature Portfolio journals. Each entry pairs a research question with PI/ECO criteria, a retrieval corpus of 140k PubMed articles, verified positive studies, hard negatives that are topically similar but PI/ECO-ineligible, and complete search strategies and date bounds. Benchmarking twelve pipeline configurations (nine RAG variants and a protocol-driven agent) reveals a critical screening bottleneck: despite a retrieval ceiling of 90.9% recall at K=200, no system recovers more than 52.7% of ground-truth included literature. Current LLMs fail to reliably separate eligible studies from PI/ECO-failing distractors in pools of comparable topical relevance. Stage-attributed metrics capture where systems succeed and fail; a single end-to-end score does not.

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

Information-Theoretic Measures in AI: A Practical Decision Guide

arXiv:2604.23716v2 Announce Type: replace Abstract: Information-theoretic (IT) measures are ubiquitous in artificial intelligence: entropy drives decision-tree splits and uncertainty quantification, cross-entropy is the default classification loss, mutual information underpins representation learning and feature selection, and transfer entropy reveals directed influence in dynamical systems. A second, less consolidated family of measures, integrated information (Phi), effective information (EI), and autonomy, has emerged for characterizing agent complexity. Despite wide adoption, measure selection is often decoupled from estimator assumptions, failure modes, and safe inferential claims. This paper provides a practical decision framework for all seven measures, organized around three prescriptive questions for each: (i) what question does the measure answer and in which AI context; (ii) which estimator is appropriate for the data type and dimensionality; and (iii) what is the most dangerous misuse. The framework is operationalized in two complementary artifacts: a measure-selection flowchart and a master decision table. We cover both AI/ML and decision-making agent application domains per measure, with standardized Bridge Boxes linking IT quantities to cognitive constructs. Three worked examples illustrate the framework on concrete practitioner scenarios spanning representation learning, temporal influence analysis, and evolved agent complexity.

09.
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.

10.
arXiv (CS.LG) 2026-06-11

PAWS: Preference Learning with Advantage-Weighted Segments

arXiv:2606.11982v1 Announce Type: new Abstract: Preference-based reinforcement learning (PbRL) learns policies from human trajectory-level comparisons, avoiding explicit reward design and expert demonstrations. Existing methods typically train utility functions on trajectory or segment-level preferences while relying on per-step utility estimates during policy optimization. This training and inference mismatch induces a distribution shift that severely degrades temporal credit assignment and limits policy learning. We analyze this issue and propose PAWS, a segment-based preference learning method that performs policy updates directly using segment-level advantage functions. By aligning utility training with policy optimization, PAWS preserves trajectory-level preference information and avoids unreliable per-step learning signals. Experiments on simulated robotic manipulation and locomotion tasks demonstrate that PAWS consistently outperforms existing PbRL approaches, highlighting the importance of distribution-consistent preference learning.

11.
arXiv (CS.CV) 2026-06-12

YOLO-AMC: An Improved YOLO Architecture with Attention Mechanisms for Building Crack Detection

Crack detection plays an important role in infrastructure inspection and Structural Health Monitoring (SHM). However, cracks typically appear as thin, low-contrast structures and are easily affected by background noise, posing challenges for existing object detection models. This study proposes an improved YOLO-based architecture with integrated attention mechanisms, termed YOLO-AMC (YOLO with Attention Mechanisms for Crack Detection), to enhance automated crack detection performance. Based on YOLOv11, the original C2PSA module is removed, and multiple attention mechanisms, including Global Attention Mechanism (GAM), Residual Convolutional Block Attention Module (Res-CBAM), and Shuffle Attention (SA), are introduced into the multi-scale feature fusion layers of the Neck to strengthen cross-scale feature integration. Experimental results demonstrate that YOLO-AMC consistently outperforms baseline models YOLOv11n and YOLOv8n across multiple evaluation metrics. Among the evaluated attention modules, GAM achieves the best detection performance, obtaining mAP@0.5 = 0.9917 and mAP@0.5:0.95 = 0.9506 on the test dataset, which are higher than those of YOLOv11 (0.9833 / 0.9112) and YOLOv8 (0.9707 / 0.8921). Furthermore, while maintaining a computational complexity of 7.6 GFLOPs, the proposed model achieves 110.95 FPS on an NVIDIA RTX 4090 platform and approximately 5 FPS on a Raspberry Pi 5 edge device, demonstrating a favorable trade-off between accuracy and deployment efficiency. The implementation code for this study is available on GitHub at https://github.com/CY-Tsai24/YOLO-AMC.

12.
arXiv (CS.LG) 2026-06-11

Integral Formulation of QENDy for Robust Nonlinear System Identification

arXiv:2606.11629v1 Announce Type: cross Abstract: This manuscript proposes an integral formulation of the newly defined quadratic embedding method for identifying nonlinear systems (QENDy). In the original algorithm, trajectory data points along with their time derivatives are used. Methods for calculating time derivatives make the algorithm sensitive to noise. Our integral formulation does not use the time derivatives. This results in a more robust method to learn the dynamics.

13.
arXiv (CS.CV) 2026-06-12

Triangle Splatting SLAM

We present a dense RGB-D SLAM system using differentiable triangles as the 3D map representation. While 3D Gaussian Splatting has emerged as the leading method for novel-view synthesis, triangles remain the standard primitive for traditional rendering hardware, game engines, and downstream tasks requiring explicit geometry such as simulation, collision, and editing. Recent offline methods have demonstrated that an unstructured 'triangle soup' can be optimised into a photorealistic mesh via Delaunay triangulation across a set of posed images. Building upon this insight, we present the first dense SLAM system to employ Triangle Splatting to perform both tracking and mapping through online differentiable rendering of a triangle soup. The map can be converted into a connected mesh on-the-fly via restricted Delaunay triangulation, enabling new online capabilities such as mesh deformation and collision checking. On Replica and TUM-RGBD, our system outperforms baselines on 3D geometry, matches the camera-tracking accuracy, and enables online mesh-based scene editing.

14.
arXiv (CS.AI) 2026-06-16

Visual-Seeker: Towards Visual-Native Multimodal Agentic Search via Active Visual Reasoning

arXiv:2606.15231v1 Announce Type: new Abstract: Multimodal large language models (MLLMs) have demonstrated impressive capabilities in many visual tasks, but they often struggle with factual grounding when confronted with complex, open-world scenarios. While recent multimodal deep search agents attempt to address this issue by utilizing external tools, the visual-native search paradigm remains underexplored. Existing methods primarily rely on simple images with explicit semantics and text-only evidence trajectories, limiting the agent's ability to perform multi-hop, cross-modal reasoning and search. To address these limitations, we propose Visual-Seeker, a visual-native multimodal deep search agent via active visual reasoning. Rather than treating vision as a static input, our agent actively attends to fine-grained visual details, dynamically harvests visual evidence throughout the search process. To unlock its visual-native potential, we design an active visual reasoning data pipeline and synthesize 5K high-quality multimodal trajectories for model training. Extensive experiments demonstrate the state-of-the-art performance across five challenging multimodal search benchmarks, even surpassing several proprietary models, validating robust visual-native reasoning and search in real-world web environments. The code and data can be accessed at: https://github.com/ZhengboZhang/Visual-Seeker.

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

VisualClaw: A Real-Time, Personalized Agent for the Physical World

Vision language models are serving as general-purpose interfaces for complex multimodal tasks. However, deployment still faces three gaps: VLMs typically incur high latency and cost when processing dense video frames and long prompts, the agent scaffold remains static after deployment, and standard video-QA benchmarks do not test whether agents can use visual evidence inside tool-using workspaces. We present VisualClaw, a self-evolving multimodal agent built around two principles. First, hybrid encoding reduces deployment cost by filtering less informative streaming frames with a cascaded gate and compressing the text skill bank through hot/cold top-k injection. Second, skill evolution lets the agent learn from failures: retrieved memories condition an evolver as direct concatenated context or as guided evidence, producing skill-bank updates that help future questions. Across 4 video-QA benchmarks with 2 VLMs, VisualClaw cuts per-question API cost by an average -98% versus full-frame upload and by -25.9% over the offline uniform 8 frame baseline, while boosting accuracy in most settings, e.g., an average +3.85% and a peak +15.80% on EgoSchema with Gemini 3 Flash. To address the gap, we curate VisualClawArena, a 200-scenario multimodal agentic benchmark built through a strict five-stage pipeline; models must use video evidence, documents, dynamic updates, and executable checks inside a workspace. On VisualClawArena, the same framework with computer-use agent backends improves macro accuracy by +2.9% for Codex (GPT-5.5) and +3.2% for Claude Code (Sonnet 4.6) over no-evolution baselines, with a -9.5% cost reduction compared to the uniform-sampled baseline. These properties make VisualClaw a natural fit for edge applications, where the cascade reduces a 1-hour streaming session from ~3,600 API uploads down to only 5-20 calls and the self-evolution makes it a perfect personalized assistant.

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

OBCache: Optimal Brain KV Cache Pruning for Efficient Long-Context LLM Inference

Large language models (LLMs) with extended context windows enable powerful applications but impose significant memory overhead, as caching all key-value (KV) states scales linearly with sequence length and batch size. Existing cache eviction methods address this by exploiting attention sparsity, yet they typically rank tokens heuristically using accumulated attention weights without considering their true impact on attention outputs. We propose Optimal Brain Cache (OBCache), a principled framework that formulates cache eviction as a layer-wise structured pruning problem. Building upon the Optimal Brain Damage (OBD) theory, OBCache quantifies token saliency by measuring the perturbation in attention outputs induced by pruning tokens, with closed-form scores derived for isolated keys, isolated values, and joint key-value pairs. Our scores account not only for attention weights but also for information from value states and attention outputs, thereby enhancing existing eviction strategies with output-aware signals. Experiments on LLaMA and Qwen models demonstrate that replacing the heuristic scores in existing works, which estimate token saliency across different query positions, with OBCache's output-aware scores consistently improves long-context accuracy. Code is available at https://github.com/DreamSoul-AI/OBCache.

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

MADAR: An Address-Free Processor

arXiv:2606.15535v1 Announce Type: cross Abstract: In a modern processor, computing is the cheap part. Most of its area and energy go to addressing – moving operands to and from a register file and cache, and running the tags, ports, miss queues, and bypass networks that find a value where it was left. MADAR deletes that machinery by abolishing the address. All state circulates in rings of slots that advance one position per clock; instructions and data ride in the same slots; a value is named by its place in an orbit – a \rp{} coordinate – not by an address; a fixed station computes when a circulating instruction sweeps past its operands, on a schedule set at compile time; and a hierarchy of rings of increasing period replaces the cache hierarchy, movement between them scheduled rather than triggered by a miss. No prior circulating-store, dataflow, or statically scheduled machine combines all four of these. We define the execution model, validate it in a cycle-accurate register-transfer-level implementation, show it compilable – a constructive scheduler emits programs cross-checked against the implementation – and price it with a first-order energy model. The payoff is clearest for AI acceleration: the multiply-accumulate at the heart of every matmul and convolution compiles to a streaming form whose energy per operation stays flat as the reduction grows, and the operand reuse that makes matrix multiplication efficient is carried by the ring-period hierarchy – the memory hierarchy doing by rotation what a cache does by tags. MADAR is a new design point for any computation whose data movement is known before the program runs.

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

Structure-Oriented Randomized Neural Networks for Poisson-Nernst-Planck and Poisson-Nernst-Planck-Navier-Stokes Systems

arXiv:2606.19912v1 Announce Type: cross Abstract: We develop a structure-oriented randomized neural network framework, termed SO-RaNN, for the Poisson-Nernst-Planck (PNP) system and the Poisson-Nernst-Planck-Navier-Stokes (PNP-NS) system. The decoupled linearized subproblems are solved iteratively by randomized neural networks in a space-time framework. For the concentration variables, a pointwise cut-off is used to enforce positivity at the value level, and discrete mass-scaling factors are computed at selected correction instants and interpolated in time, so as to ensure exact mass matching at those instants and to promote approximate mass preservation between them. To introduce an auxiliary discrete dissipation mechanism, we further employ an SAV-type post-processing correction, which yields monotonicity of the SAV auxiliary variable under the ideal SAV update. For the PNP-NS system, a structure-preserving randomized neural network (SP-RaNN) is used for the velocity field, so that the velocity approximation satisfies the incompressibility constraint pointwise by construction. On the theoretical side, we derive residual-based estimates for the raw, uncorrected RaNN solvers of the linearized subproblems, formulate a conditional local-in-time convergence result for the raw outer Picard iteration of the PNP system, and analyze the value-level positivity correction together with the mass-correction and SAV post-processing steps. For the PNP-NS system, we establish an approximation result for the SP-RaNN space and provide a conditional error statement for the corresponding linearized Oseen-type problem. Numerical experiments demonstrate approximation accuracy in the source-driven manufactured tests and illustrate the intended value-level positivity correction, selected-time mass matching, computed free-energy curves based on the final gauge-fixed potential, and divergence-free approximation in benchmark tests.

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

Discrete optimal transport is a strong audio adversarial attack

arXiv:2509.14959v3 Announce Type: replace-cross Abstract: In this paper, we investigate discrete optimal transport (DOT) as a black-box attack against modern automatic speaker verification (ASV) and anti-spoofing countermeasure (CM) systems. Our attack operates as a post-processing distribution-alignment step. Frame-level WavLM embeddings of generated speech (or another person speech) are aligned to an unpaired bona fide speech pool using entropic optimal transport and a top-k barycentric projection, followed by neural vocoding. Unlike gradient-based attacks, the proposed method requires no access to model parameters, gradients, or training data. Experiments on ASVspoof2019 and ASVspoof5 demonstrate that DOT attack substantially increases CM EER and substantially degrades ASV performance across multiple spoofing attacks. The attack transfers across datasets and remains effective after CM fine-tuning. Analysis using speaker similarity, Fréchet Audio Distance, and visualization of embedding distributions suggests that DOT succeeds by shifting source speech toward bona fide regions of the representation space rather than by maximizing speaker similarity. These results indicate that optimal-transport-based distribution alignment represents a previously underexplored attack vector for contemporary ASV and anti-spoofing systems.

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

Descriptor: Certus Caliber Classification Gunshot Dataset (C3GD)

arXiv:2606.18135v1 Announce Type: cross Abstract: In this work, we introduce the Certus Caliber Classification Gunshot Dataset (C3GD), a publicly accessible data set developed for the analysis of firearm muzzle blast sounds. The dataset aims to provide a wide variety of firearms, calibers, cartridges, microphones, and microphone locations with metadata detailed beyond what is currently otherwise available. It comprises more than 8000 field-collected data points from 28 firearms across 16 calibers. Because data collection in the field is costly, much of the existing research has been done using gunshot audio collected from the internet, which increases the risk of low-quality data and label noise. This dataset is primarily focused on caliber classification, but can also be used for gunshot detection, audio separation, and audio signal processing, providing a diversified and real-world reference. The dataset aims to provide enough diversity to be able to generalize to more real-world applications while also providing enough metadata for detailed academic analysis.

22.
bioRxiv (Bioinfo) 2026-06-16

Better data, better trees: GenBank-GISAID deduplication and source-specific artifact masking in viral genomics

GenBank and GISAID are the primary repositories for viral genomic data, but integrating records across them remains a challenge. The same sequence could be made available in both databases without any cross-reference linking the two entries. Consequently, there is no systematic way to identify this redundancy, which compromises the compilation of representative, non-redundant large-scale datasets. In parallel, the growth of viral genomic data has increased the risk of systematic technical artifacts introduced during sequencing or assembly. These artifacts can inflate substitution rate estimates and degrade temporal signal, biasing evolutionary rate estimates. To address both challenges, here we present a formal, reproducible workflow integrating two newly developed complementary tools: G2G matcher for cross-repository harmonization and Lab-Specific Bias FILTer (LSBFILT) for masking of laboratory-specific artifacts. Using the Eastern/Central/South African (ECSA) chikungunya virus lineage as a proof-of-concept, we demonstrate that our integrated workflow restores temporal signal and provides a robust, curated dataset for downstream phylodynamic analyses. Critically, restricting masking of homoplastic sites to specific sequences reduces the substitution rate estimate from an inflated 8.517 x 10e-4; to 5.078 x 10e-4; substitutions/site/year and increases the coefficient of determination (R2) of the root-to-tip regression analysis from 0.353 to 0.677. By enabling systematic cross-repository harmonization and source-specific artifact masking, we provide the molecular epidemiological community with scalable tools to reconcile fragmented genomic data and reduce technical biases, fostering more accurate and reproducible phylogenetic analysis. G2G matcher is available at https://github.com/andrezaleite/G2G-Matcher, and LSBFILT at https://github.com/khourious/LSBFILT.

23.
arXiv (CS.AI) 2026-06-16

The Model Knows, the Decoder Finds: Future Value Guided Particle Power Sampling

arXiv:2605.02427v3 Announce Type: replace Abstract: A recurring pattern in "reasoning without training" is that base LLMs already assign non-trivial probability mass to correct multi-step solutions; the bottleneck is locating these modes efficiently at inference time. Power sampling provides a principled way to bias decoding toward such modes by targeting p_theta(x)^alpha with alpha > 1, but practical approximations must account for future-dependent correction factors that determine which prefixes remain promising. We introduce Auxiliary Particle Power Sampling (APPS), a blockwise particle algorithm for approximating the sequence-level power target with a bounded population of partial solutions. APPS propagates hypotheses in parallel using proposal-corrected power reweighting and refines their survival through future-value-guided selection at resampling boundaries. This redistributes finite compute across competing prefixes rather than committing to a single unfolding path, while providing a direct scaling knob in the particle count and predictable peak memory. We instantiate the future-value signal with short-horizon rollouts and also study an amortized variant that replaces rollouts with a lightweight learned selection head. AMore broadly, APPS improves the accuracy–runtime trade-off of training-free decoding, further supporting the view that inference-time power approximation can recover gains often attributed to post-training.

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

Neural Network-Based Parametric Model Reduction for Predicting Turbulent Flow for Different Vehicle Geometries

arXiv:2606.24265v1 Announce Type: cross Abstract: Numerical simulations in industrial applications often require performing numerous high-precision computations parameterized by specific experimental conditions. For instance, in vehicle body design, aerodynamic simulations are essential for evaluating the aerodynamic characteristics of various proposed body geometries. However, computational resource constraints often become a bottleneck. Therefore, achieving the desired accuracy while minimizing computational cost is crucial. To address this challenge, model reduction methods have been developed to decrease the degrees of freedom by constraining the possible states of a physical system to a lower-dimensional subspace. In particular, reduction techniques that project the system onto a nonlinear subspace using neural networks have been actively studied. Our previous research developed a reduced-order model that integrates neural-network-based model reduction with a time-evolution method, implemented as a distributed parallel training framework to process high-resolution flow field data efficiently. In this study, we extend this reduction approach by incorporating a variational autoencoder to assess its robustness in high-Reynolds-number flows around multiple vehicle bodies with varying geometries. Specifically, we evaluate the reconstruction accuracy of vortex generation across different spatial and temporal scales using a compact latent representation, with a particular focus on the flow behavior near the rear end of the vehicle body.

25.
bioRxiv (Bioinfo) 2026-06-14

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

Intrinsically disordered regions (IDRs) are central contributors to protein function, evolution and human disease, yet the evolutionary routes that seed new disordered segments within pre-existing proteins are still poorly understood. Sequence insertions provide a powerful mechanism for disorder expansion, but the genomic donors of inserted IDR and its long-term conformational fate remain largely unknown. Transposable elements (TEs), abundant mobile genetic elements with distinctive compositional biases, represent compelling candidates for generating disorder within proteins. Here, we systematically mapped TE-derived segments across human proteins and isoforms, and we found that these insertions are strongly enriched in intrinsic disorder. The structural consequences of their insertion are shaped by TE class and family, reflecting the sequence biases of the elements from which they originate. Recent, Primate specific insertions preferentially generate disordered segments, whereas older insertions more frequently occupy ordered structural contexts, revealing an age-dependent transition in the conformational state of TE-derived sequences. TE-containing isoforms are expressed at lower levels than TE-free isoforms, particularly when insertions are young and disorder-rich, suggesting that intrinsic disorder may constrain the cellular tolerance of newly exonized sequences. These findings identify TEs as a major evolutionary mechanism linking genome mobility to the emergence of new disordered conformational ensembles in the human proteome.