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01.
arXiv (CS.CV) 2026-06-18

Sensor Configuration Matters: A Systematic Evaluation of Multimodal SLAM on Quadruped Robots

Autonomous navigation of quadrupedal robots in diverse environments fundamentally relies on resilient Simultaneous Localization and Mapping (SLAM). While visual-inertial SLAM has matured across wheeled, handheld, and aerial platforms, a critical evaluation gap remains regarding how hardware-level sensor configurations affect performance under the aggressive dynamics of legged locomotion. Quadrupeds introduce distinct embodiment-induced sensory challenges, including foot-impact shocks, high-frequency mechanical vibrations, and rapid angular rotations, which degrade standard perception pipelines. To address this gap, we present a systematic evaluation of state-of-the-art visual, visual-inertial, and LiDAR-visual-inertial SLAM methods using the GrandTour dataset recorded on an ANYmal D quadruped. We isolate and quantify the impacts of camera modalities, shutter techniques, and inertial sensor tiers, analyzing their trade-offs across localization accuracy, algorithmic robustness, and computational resource utilization. Our empirical findings demonstrate that hardware selection has substantial influence on system resilience: stereo configurations consistently outperform monocular and RGB-D modalities, global shutter cameras significantly mitigate motion-induced tracking failures compared to rolling shutter cameras, and, crucially, standard inertial integration can degrade the performance of primarily vision-based frameworks under harsh legged locomotion. These insights additionally offer concrete design guidelines for tailoring custom sensor payloads to achieve dependable perception on agile legged systems.

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

Disentangling Perception and Reasoning in Multimodal LLMs via Reward Design

Reinforcement learning with verifiable rewards has driven major gains in LLM reasoning, and it is intuitive to assume this recipe will transfer well to multimodal models. However, multimodal models do two things: first, perceive what is in an image, then reason about what it implies. Because these stages are graded jointly, it is hard to tell how much room reasoning alone has to grow. We study this on algorithmic visual puzzles, where both components are necessary and show that perception, not reasoning, is the binding constraint. Replacing images with simple textual descriptions raises performance by over 20 points on average for Claude models. We then evaluate six reward designs aimed at inducing visual grounding during reasoning without chain-of-thought supervision. Training Qwen-2.5-VL-7B with GRPO, reward design induces long, structured reasoning with self-reflection and visual references, yielding a 5.56-point gain over the base model. These gains are, however, uneven; no single reward improves all categories, and rewards with verifiable accuracy signals trade out-of-domain transfer for in-domain accuracy. These results point to perception-aware reward design as a path forward, so that signals correct perception at its source rather than the reasoning that inherits its errors.

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

Future Dynamic 3D Reconstruction: A 3D World Model with Disentangled Ego-Motion

Forecasting the evolution of dynamic environments is crucial for autonomous agents. While generative world models have recently achieved high photorealism in 2D video synthesis by mixing ego-motion and environmental dynamics within the image plane, they exhibit physical inconsistencies, such as morphing or vanishing objects, especially over long time horizons. In this paper, we propose FR3D, a world model that predicts a persistent 3D latent representation for future dynamic 3D reconstruction. Unlike prior works that treat the world as a sequence of image-based features, FR3D explicitly decouples the 3D evolution of the scene from the agent's trajectory, treating the inferred ego-motion as a latent proxy for action. This disentanglement resolves the ambiguities between self-motion and world-motion, ensuring geometric consistency into the future. Furthermore, we introduce a teacher-student distillation strategy that leverages the spatial "common sense" of off-the-shelf foundation models, leading to robust zero-shot generalization. Extensive experiments demonstrate FR3D's strong performance for future dynamic 3D reconstruction from monocular observations across multiple datasets, even 2 seconds into the future. Project page: https://fr3d-wm.github.io.

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

From Prompts to Tokens: Internalizing Causal Supervision in Vision-Language Model for Multi-Image Causal Reasoning

Visual causal reasoning is essential for understanding and intervening in the physical world, requiring identification of causal variables from visual inputs and reasoning over intervention effects. Despite recent progress, large vision–language models (VLMs) remain brittle at such tasks, especially for interventional and counterfactual queries over multi-image inputs. Most existing explorations inject causal knowledge via textual prompts, leaving causal mechanisms external to model execution and limiting reliable control during inference. To address this problem, we propose BridgeVLM, which internalizes visual causal reasoning by inducing a causal graph from multi-image inputs and converting it into structured Causal Tokens executed by RAMP layers injected into the LLM decoder for causal message passing. We further introduce a unified training interface M3S for fine-grained causal supervision from different granularities (local/global level). BridgeVLM achieves 54.4% accuracy on intervention tasks on CausalVLBench (vs. 33.2% with prompt-level supervision), improves results on Causal3D from 43.6% to 49.0%, and substantially improves causal structure learning on CausalVLBench ($F_1$: 33.4% $\rightarrow$ 75.1%).

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

Know Thy Reasoner: Not All Language Models Explore Alike

arXiv:2604.10827v2 Announce Type: replace Abstract: Compute scaling for LLM reasoning trades off exploring solution approaches (breadth) against refining promising ones (depth), yet why a given trade-off works, and why it often fails to transfer across models, remains unclear. We argue that the optimal strategy depends on the model's diversity profile, the spread of probability mass across solution approaches, and that this must be characterized before any exploration strategy is adopted. We formalize this with a framework decomposing reasoning uncertainty, deriving when depth-based refinement outperforms parallel sampling, and validate it across three model families at both inference and training. Our central finding is that the diversity regime dictates the strategy: low-diversity aligned models benefit from depth-based refinement with lightweight intrinsic signals, whereas high-diversity base models are often harmed by it, and instead need breadth or stronger signals to compensate.

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

Interpretable Sperm Morphology Classification via Attention-Guided Deep Learning

arXiv:2606.20438v1 Announce Type: new Abstract: Male infertility is a major cause of couple infertility, often linked to abnormal sperm morphology. While deep learning models offer automated analysis, most lack interpretability, limiting their clinical adoption. This study proposes an attention-guided deep learning framework for sperm morphology classification. We combine a pretrained EfficientNet-B0 with a Convolutional Block Attention Module (CBAM) to focus on key areas of the sperm head, improving both accuracy and interpretability. Evaluated on the SMIDS and HuSHem public datasets, our model achieves accuracies of 90.2% and 93.9% (macro F1 scores of 0.913 and 0.948), outperforming SimpleCNN and standard EfficientNet-B0. Furthermore, we use Grad-CAM++ visualizations to highlight features influencing the model's decisions. The results demonstrate that this accurate and transparent framework is a practical tool for automated sperm analysis in fertility clinics.

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

Forecasting Bacterial Antimicrobial Resistance Trends Using Machine Learning on WHO GLASS Surveillance Data: A Retrieval-Augmented Generation Approach for Policy Decision Support

arXiv:2602.22673v2 Announce Type: replace Abstract: Background: Antimicrobial resistance (AMR) is a global health threat. While the WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) provides standardized data, population-level machine learning forecasting of resistance trends remains limited. Translating computational forecasts into policy requires transparent interpretation mechanisms. Methods: Surveillance data (2021-2023) comprising 5,909 observations across 44 countries and five WHO regions were processed. A rigorous temporal split prevented data leakage. Six models (Naive, Linear, Ridge, XGBoost, LightGBM, LSTM) were benchmarked to forecast one-year-ahead resistance rates using features including prior-year resistance and antibiotic consumption. Evaluation metrics (MAE, RMSE, sMAPE) were computed, with 95% bootstrap confidence intervals for MAE. A local Retrieval-Augmented Generation (RAG) system utilizing Gemma 4 was implemented to translate forecast findings into policy guidance grounded in retrieved WHO documents. Results: XGBoost achieved the best performance (test MAE = 6.13% [95% CI: 5.83-6.44]), an 85.3% error reduction versus the naive baseline (MAE = 41.79%). SHAP analysis identified prior-year resistance as the dominant predictor (50.5% gain), confirming strong autoregressive behavior. Regional forecast error tracked closely with surveillance coverage, ranging from 3.65% in the European Region to 8.61% in South-East Asia. The RAG pipeline generated accurate, source-attributed policy responses without fabricated citations. Conclusion: Short-term AMR resistance rates exhibit strong temporal autocorrelation that can be accurately forecasted using gradient boosting. Coupling these forecasts with a hallucination-resistant RAG system provides a scalable, evidence-based decision-support framework for AMR governance.

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

Knowledge-Based Zero-Replay Debugging of Multi-Agent LLM Traces

arXiv:2606.14805v1 Announce Type: cross Abstract: Reliable operation of multi-agent large language model (LLM) systems depends on debugging long execution traces, where the few causally decisive events are buried in unstructured logs of messages, routes, memory writes, and tool calls. The standard tool is counterfactual replay (rewind, edit, and re-run the trajectory to measure each event's effect), but its cost grows linearly with the number of candidate events, making exhaustive replay infeasible at scale. We frame trace debugging as a knowledge-based decision-support problem. Each trace is compiled into a structured event knowledge graph over routing, memory, tool-use, uncertainty, and latent evidence, and a calibrated predictor decides where a scarce replay budget should be spent. We do not propose a new replay oracle; we propose a method to predict its results without paying the replay cost. We formulate zero-replay counterfactual-effect prediction: given a trace under a fixed budget, predict which events the oracle would mark high-effect before any replay is performed. BranchPoint-Latent is a lightweight predictor over observable, structural, uncertainty, and latent features of the knowledge graph. Calibrated against a deterministic replay oracle across 37 trace families, a single learning-to-rank gradient-boosted predictor raises per-trace localization (Branch Recall@5) from 0.73 to 0.93 on held-out families at zero oracle-replay cost. Rather than claiming universal dominance, we characterize when cheap graph centrality suffices and when learned evidence is necessary. The result is an auditable, cost-efficient decision-support system for AI-reliability debugging, positioned explicitly on the cost-accuracy frontier with reproducible artifacts.

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

Similarity-based representation factorization for revealing interpretable dimensions in representational data

The study of representations is widespread across fields, including neuroscience, psychology, and artificial intelligence. While representations are often studied and compared through similarities between stimuli, current methods provide only limited access to the dimensions that shape these representations and are often limited in interpretability. To overcome these challenges, here we introduce Similarity-Based Representation Factorization (SRF), a general computational method for recovering low-dimensional, non-negative, interpretable embeddings from similarity matrices derived from measured data. Across simulations and many neural, behavioral, and computational datasets, SRF recovers interpretable dimensions from diverse forms of representational data, even for very sparsely sampled, incomplete data. The dimensions derived from these datasets match those obtained by task-specific models, predict independent behavioral properties, improve exploratory analysis, and offer higher power for confirmatory hypothesis testing than comparing similarity matrices. Together, these results establish SRF as a general-purpose method with broad applications for uncovering, understanding, and using the dimensions underlying representations.

11.
arXiv (CS.CV) 2026-06-16

Geometric Action Model for Robot Policy Learning

Generalist robot policies must follow user instructions while reasoning about how objects, cameras, and robot actions interact in the 3D physical world. Recent vision-language-action models (VLAs) and video world-action models (WAMs) inherit strong semantic or temporal priors from large-scale foundation models, but they still operate primarily on 2D image frames or 2D-derived latent spaces, leaving implicit the 3D geometry required for contact-rich manipulation. We propose the Geometric Action Model (GAM), a language-conditioned manipulation policy that directly repurposes a pretrained geometric foundation model (GFM) as a shared substrate for perception, temporal prediction, and action decoding. GAM splits the GFM at an intermediate layer: the shallow layers serve as an observation encoder, and a causal future predictor inserted at the split layer forecasts future latent tokens conditioned on language, proprioception, and action history. The predicted future tokens are then routed through the remaining GFM blocks for feature propagation and decoding, allowing a single backbone to produce both future geometry and actions. This design equips the GFM with language-conditioned temporal world modeling through minimal architectural modification while preserving its rich geometric priors. Across a broad suite of simulation and real-robot manipulation benchmarks, GAM is more accurate, more robust, faster, and lighter than current foundation-model-scale baselines.

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

Free Energy Heuristics: Fast-And-Frugal Cognition as Active Inference Under Uncertain Precision

Authors:

Chain-of-thought (CoT) improves large language models' performance in math and symbolic reasoning. But on planning, contested ethics, and tasks where the model cannot check itself, more reasoning makes things worse. Both effects are documented; what has been missing is a principled account of which property decides the outcome. We argue it is meta-uncertainty: how unsure the model is about the reliability of its own evidence. When that uncertainty is high, extra reasoning stops adding signal and starts manufacturing false confidence. We prove that the policy minimizing expected free energy under uncertain precision stops integrating cues after a finite number of high-validity ones when the precision prior is heavy-tailed (Theorem 2.6.1), and under a Descending Dominance condition, is sample-wise identical to take-the-best (Theorem 2.7.4). Fast-and-frugal heuristics and active inference are, then, two descriptions of the same computation. The prediction is that on high-meta-uncertainty items, longer CoT should degrade accuracy. We score the regime per item (simulate-and-recover rho > 0.96), build FEH-79, a benchmark of Knightian frames with matched controls, and run a pre-registered study across seven models (five open-weight 3B-32B, two frontier), five CoT lengths, and 7,875 responses. The gate, fixed before any data, required a negative interaction with posterior probability above 0.95 and an accuracy drop of more than 6 points. It held. The high-regime drop is 17.3 points (95% CI [7.7, 25.5]); matched items with definite answers show no cost. The effect is regime-dependent: decisive in capable mid-to-large models, directional in the two frontier systems, absent-to-reversed in the weakest. The framework answers when CoT helps and unifies the Bayesian and fast-and-frugal traditions: less-is-more effects are evidence about the meta-uncertainty regime, not against Bayesian cognition.

13.
arXiv (CS.CV) 2026-06-15

HumP-KD: A Hybrid Uncertainty-Aware Multi-Stage Progressive Knowledge Distillation Framework for Efficient Fire Classification

Real-time fire classification systems require models that are simultaneously accurate, computationally efficient, and deployable on resource-constrained hardware. This work proposes HumP-KD, a Hybrid Uncertainty-aware Multi-stage Progressive Knowledge Distillation framework for efficient fire classification. Two datasets, FlameVision and Dataset-II, containing 8,600 and 31,309 images, are used. Various CNN and transformer baselines are applied under standard preprocessing, online augmentation, Gaussian noise and motion blur robustness conditions. The proposed HumP-KD model distills knowledge from two frozen heterogeneous transformer teachers, Swin-Tiny and ViT-Base, along with their Meta-MLP ensemble, into a lightweight MobileViT-S student via three tightly integrated components. Hierarchical Progressive Knowledge Distillation employs a Hierarchical Feature Builder. It generates a fused spatial attention mask to guide distillation toward discriminative regions selectively. Multi-Stage Knowledge Distillation progressively activates three distillation stages across training. On Dataset-II, HumP-KD achieves a mean F1 score of $0.9876 \pm 0.0063$ across 10 independent trials, significantly outperforming the MobileViT-S baseline trained without distillation ($0.9537 \pm 0.0351$), with statistical significance confirmed by both independent t-test ($p = 0.0195$) and Wilcoxon signed-rank test ($W = 1$, $p = 0.0039$). The proposed method also demonstrates strong generalization across datasets and robustness under degraded visual conditions. The student model retains only 4.94M parameters and 19.01Mb model size, representing a $5.7\times$ parameter reduction over Swin-Tiny and a $17.5\times$ reduction over ViT-Base, while achieving 37.72 CPU FPS, making it suitable for real-time deployment.

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

Something from Nothing: Data Augmentation for Robust Severity Level Estimation of Dysarthric Speech

arXiv:2603.15988v3 Announce Type: replace-cross Abstract: Dysarthric speech quality assessment (DSQA) is critical for clinical diagnostics and inclusive speech technologies. However, subjective evaluation is costly and difficult to scale, and the scarcity of labeled data limits robust objective modeling. To address this, we propose a three-stage framework that leverages unlabeled dysarthric speech and large-scale typical speech datasets to scale training. A teacher model first generates pseudo-labels for unlabeled samples, followed by weakly supervised pretraining using a label-aware contrastive learning strategy that exposes the model to diverse speakers and acoustic conditions. The pretrained model is then fine-tuned for the downstream DSQA task. Experiments on five unseen datasets spanning multiple etiologies and languages demonstrate the robustness of our approach. Our Whisper-based baseline significantly outperforms SOTA DSQA predictors such as SpICE, and the full framework achieves an average SRCC of 0.761 across unseen test datasets.

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

LLMs as ASP Programmers: Self-Correction Enables Task-Agnostic Nonmonotonic Reasoning

arXiv:2604.27960v2 Announce Type: replace Abstract: Recent large language models (LLMs) have achieved impressive reasoning milestones but continue to struggle with high computational costs, logical inconsistencies, and sharp performance degradation on high-complexity problems. While neuro-symbolic methods attempt to mitigate these issues by coupling LLMs with symbolic reasoners, existing approaches typically rely on monotonic logics (e.g., SMT) that cannot represent defeasible reasoning – essential components of human cognition. We present "LLM+ASP," a framework that translates natural language into Answer Set Programming (ASP), a nonmonotonic formalism based on stable model semantics. Unlike prior "LLM+ASP" approaches that require manually authored knowledge modules, domain-specific prompts, or evaluation restricted to single problem classes, our framework operates without any per-task engineering and applies uniformly across diverse reasoning tasks. Our system utilizes an automated self-correction loop where structured feedback from the ASP solver enables iterative refinement. Evaluating across six diverse benchmarks, we demonstrate that: (1) stable model semantics allow LLMs to naturally express default rules and exceptions, outperforming SMT-based alternatives by significant margins on nonmonotonic tasks; (2) iterative self-correction is the primary driver of performance, effectively replacing the need for handcrafted domain knowledge; (3) compact in-context reference guides substantially outperform verbose documentation, revealing a "context rot" phenomenon where excessive context hinders constraint adherence.

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

PersonaDrive: Human-Style Retrieval-Augmented VLA Agents for Closed-Loop Driving Simulation

Closed-loop driving simulators typically populate their environments with non-ego traffic agents that behave largely the same way, produced either by rule-based traffic managers or by learned models trained toward a single behavioral mode. Recent work introduces style variation through post-hoc labels on observational data or LLM-inferred reward weights, but these signals act as proxies for what a style should reward rather than demonstrations of humans explicitly asked to drive in that style. We introduce PersonaDrive, a pipeline that conditions a vision-language-action (VLA) driving agent on retrieved demonstrations from a style-instructed human driving dataset, in which participants drive CARLA leaderboard routes under aggressive, neutral, and conservative instructions on a driver-in-the-loop rig. The pipeline has three stages: (i) offline triplet mining over per-style human driving data using a combined image-text similarity score; (ii) training a lightweight retrieval head that fuses frozen visual features with a small control encoder over per-style databases; and (iii) fine-tuning a single VLA backbone to treat retrieved context points as in-context behavioral demonstrations during waypoint prediction. At inference, the same backbone is conditioned on any style by swapping which per-style database the retrieval head queries, so selecting a style requires no per-style retraining while enabling human-style, style-diverse non-ego agents for closed-loop simulation. On Bench2Drive, PersonaDrive (no style) improves the driving score by 4.6% over SimLingo and 2.5% over HiP-AD, and under style conditioning attains the highest driving score in every style within a roughly 2% band (its weakest style surpassing the strongest baseline, DMW, by 5.4%), while average speed and acceleration rise by 18% and 25% from the conservative to the aggressive instruction.

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

An Empirical Study on Predictive Maintenance for Component X in Heavy-Duty Scania Trucks

arXiv:2606.12486v1 Announce Type: new Abstract: Condition-based Predictive Maintenance (PdM) for truck fleets has gained momentum in recent years. This maintenance strategy aims to minimize unplanned downtimes and reduce costs by monitoring the health status of vehicles and taking proactive action based on their condition. However, the implementation of condition-based PdM systems is challenging due to the large volume of data generated by the trucks, the inherent complexity of detecting failures through sensor data and the difficulties in finding cost-effective trade-offs in the solution's implementation. In this paper, we define and validate a condition-based PdM methodology built on the assumption that the wear-and-tear state of the monitored component can be represented as a monotonically non-decreasing time series. It involves selecting only the most recent observations from the time series and transforming them into a tabular format for classification using machine learning (ML) models designed for tabular data. Our results indicate that the proposed methodology reduces costs on the Scania Component X dataset compared to current state-of-the-art (SOTA) approaches, while also simplifying the modeling process through AutoML.

18.
arXiv (quant-ph) 2026-06-12

Quantum Network Routing based on Surface Code Error Correction

arXiv:2606.12781v1 Announce Type: new Abstract: Quantum networks encounter unavoidable channel noises and erasure errors, presenting a huge obstacle in designing protocols that attain both high reliability and efficiency. Typically, quantum networks fall into two categories: those utilize quantum entanglements for quantum teleportation, and those directly transfer the actual quantum messages. In this paper, we present SurfNet, a quantum network that inherits the main advantages from both categories. It employs surface codes as logical qubits for encoding messages, and utilizes two parallel communication channels to fault-tolerantly transfer each surface code in a modular manner. Our approach of using surface codes can timely correct both operational and photon loss errors within the network, and the integration of the two channels within the network can greatly improve network throughput. For the implementation of SurfNet, we propose a novel network architecture, designed to better integrate surface codes into quantum networks. We also propose a novel error correction decoder, designed to fully utilize the modular characteristic of surface codes within our network. Simulation results demonstrate that SurfNet with its decoder significantly enhances the communication fidelity within quantum networks.

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

SP$^3$: Spherical Priors for Plug-and-Play Restoration

In this paper, we introduce SP$^3$, a novel Plug-and-Play algorithm that accelerates maximum a posteriori image restoration by replacing denoisers with Spherical Encoders (SE) as generative priors. SP$^3$ approximates the intractable proximal prior step by utilizing the SE tightly structured latent space as a robust projection onto the natural image manifold. Alternating this projection with a closed-form data-consistency step, via Half-Quadratic Splitting, achieves stable convergence without requiring gradient computation during inference. This unique formulation unlocks "anytime" restoration capabilities, producing sharp, plausible images from the first iteration. Evaluations across a variety of image restoration tasks demonstrate that SP$^3$ achieves perceptual quality comparable to state-of-the-art zero-shot diffusion and flow methods while being $3$-$630\times$ faster.

20.
bioRxiv (Bioinfo) 2026-06-12

From Proteome Mining to Structural Validation: Phosphopyruvate Hydratase as a Structurally Tractable Drug Target in Kinetoplastid Parasites

Chagas disease, caused by Trypanosoma cruzi, demands novel therapeutic strategies that overcome the toxicity and limited efficacy of current treatments. To address this need, herein we report an integrative, target-centric strategy that combines parasite proteome mining, structural modeling, and experimental validation. Functional enrichment and druggability analyses identified phosphopyruvate hydratase (PPH) as a promising candidate due to its essential metabolic role and limited similarity to human homologs. Notably, proteome mining revealed the presence and conservation of PPH across kinetoplastid parasites, including Leishmania donovani, supporting its evaluation beyond T. cruzi. For the selected PPH sequences, AlphaFold-derived three-dimensional models underwent extensive molecular dynamics refinement, yielding stable conformational ensembles suitable for structure-based studies. Using this validated model, virtual screening of the Latin American Natural Products Database - LANaPDB - identified aptosimon as a top-ranked compound candidate. Molecular dynamics simulations further showed ligand-dependent binding behavior, suggesting alternative binding modes distinct from the canonical substrate configuration. In vitro assays demonstrated consistent antiparasitic activity against intracellular T. cruzi amastigotes (IC50 = 3.52 ug/mL) and Leishmania donovani promastigotes (IC50 = 13.06 ug/mL), supporting the biological relevance of the aptosimon-related lignan chemotype, hinokinin, across two kinetoplastid parasite models. Together, these results support PPH as a structurally tractable and biologically relevant candidate target, while identifying an aptosimon-related lignan chemotype, represented experimentally by hinokinin, as a cross-species antiparasitic scaffold that warrants further biochemical target-validation studies.

21.
bioRxiv (Bioinfo) 2026-06-11

EditorForge: An Active-Site-Aware Framework for Inverse-Folding-Based Protein Redesign

Inverse-folding models can rapidly generate protein sequences compatible with a supplied backbone, but unconstrained redesign is poorly suited to enzyme and genome-editor-associated domains, where catalytic, substrate-proximal, and conserved structural regions must remain protected. In this paper, we present EditorForge, a modular constraint-and-audit suite for editor-domain protein redesign that wraps fixed-backbone inverse folding with explicit design masks, fixed-position enforcement, active-site-proximity auditing, active-site-shielded regeneration, and downstream structural quality control. Using full-length Moloney murine leukemia virus reverse transcriptase structure 4MH8 (MMLV RT 4MH8) as a demonstration target, EditorForge first restricted redesign to a bounded 25-position envelope while fixing 428 residues. An initial audit detected active-site-proximal failure modes despite fixed-position integrity. Later, the Active Site Shield module then removed five unsafe design positions, replaced them with lower-contact alternatives, and regenerated candidates under stricter constraints. Post Shield Audit evaluated 24 regenerated candidates, all of which satisfied the hard sequence/mask and active-site-shield constraints. For the eight candidates that were selected or returned for structure-prediction/refolding quality control. Enhanced RefoldQC found that all 8 evaluated predicted structures passed the computational structure-QC screen. That said, the selected 8 candidates passed the computational structure-QC screen, with global C RMSD values of 1.2061–1.5555~[A], active-site C RMSD values of 0.4098–1.8397~[A], mutation-neighborhood C RMSD values of 1.3155-1.6848~[A], and average pLDDT-like confidence values of 94.87-95.11. In short, EditorForge provides a reproducible triage layer that converts general inverse-folding output into constrained and editor-specific candidate sets for downstream structural and biological review on top of existing structural prediction tools.

22.
arXiv (CS.CL) 2026-06-12

Leveraging Audio-LLMs to Filter Speech-to-Speech Training Data

Large-scale mined corpora provide abundant training data for end-to-end speech-to-speech translation (S2ST) but may contain noise, misalignment, and semantic errors. Filtering noisy data is crucial to maintain robust speech translation performance. We study how to train an audio-language model to make keep/drop decisions on paired speech directly from audio. To obtain reliable supervision without manual labels, we adopt a scalable two-stage Rank-to-Distill strategy. A lightweight ranker generates keep/drop pseudo-labels from noisy speech pairs, then trains an audio large language model to predict keep/drop directly from raw paired speech. The resulting model jointly captures acoustic fidelity and cross-lingual semantic consistency for the selection of speech-conditioned data. Experiments on CVSS-C and SpeechMatrix show consistent improvements over unfiltered training, yielding up to +1.4 ASR-BLEU for end-to-end S2ST.

23.
arXiv (math.PR) 2026-06-17

How long does it take to train an Elephant Random Walk

Authors:

arXiv:2509.15049v2 Announce Type: replace Abstract: We study how conditioning on the first $k$ steps, which we think of as training, affects the long-term behavior of the Elephant Random Walk. When the elephant is conditioned to be at position $k$ at time $k$, the first return time to the origin scales as $k^{(4-4p)/(3-4p)}$ in the diffusive regime, and grows exponentially in the critical regime. We loosely interpret this as a measurement of the rate at which the elephant forgets its training.

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

Decoding Insect Song: A Multitask Semisupervised Orthoptera Bioacoustic Classifier

arXiv:2606.13236v1 Announce Type: cross Abstract: Passive acoustic monitoring holds great promise for ecological inference, yet existing automated tools are typically narrowly trained and non-transferable. We address these limitations with PULSE, a semi-supervised, multi-task framework for Orthoptera bioacoustics, combining weakly-supervised species classification, self-supervised learning on unlabelled field audio, and knowledge distillation from a general-purpose bioacoustic model. Our domain-adapted specialist model outperforms a state-of-the-art general model across all metrics (macro F1: 0.21 vs. 0.07; AUC: 0.74 vs. 0.45; AP: 0.32 vs. 0.19), with active learning further raising F1 to 0.34 and AUC to 0.84. Beyond classification, the learned embeddings encode ecologically meaningful structure, exposed through an interactive visualisation tool for ecological discovery.

25.
arXiv (CS.AI) 2026-06-18

Why SWAVE May Not Be All You Need:A Concept-Evolution Retrospective on Complex-Valued Recurrent Language Models

arXiv:2606.18324v1 Announce Type: cross Abstract: SWave is a complex-valued recurrent language model (169.26M parameters, D=384, L=16, T=2048) trained on FineWeb-Edu using 2xH100 NVL. It was designed around three founding premises: that representing language as complex waves rather than real-valued numbers enables richer information encoding; that a Cayley-parameterised unitary transition provides a mathematical guarantee against state decay or explosion; and that a hidden state which rotates rather than shrinks preserves signal integrity over arbitrarily long contexts. The core of SWave evolved substantially across three development phases. The Resonance Head was found to structurally admit imaginary-channel collapse as a global loss minimum (a failure mode we term cos-domination collapse) and was superseded by an untied head with independent real and imaginary embedding tables from the Phase-Associative Memory (PAM) architecture. This resolved the degenerate minimum and enabled stable 200,000-step training (best-step PPL 22.0 at step 89,861). ComplexNorm and the Wave Propagation Scan proved load-bearing throughout all three phases and were retained to the final architecture. ProtectGatedScan was reframed as a structural prior rather than a learned behaviour. The four multi-scale retention concepts showed no measurable improvement under controlled evaluation and were found non-load-bearing. The ComplexGatedUnit was superseded by a real-valued squared-ReLU channel mixer with fewer parameters. The auxiliary training objectives showed no benefit once structural constraints were resolved. The investigation yields a formal characterisation of cos-domination collapse, a parallel scan with a log-space backward pass for numerical stability, six transferable engineering principles for complex-valued recurrent training, and a plan-to-code traceability methodology for catching structural divergences that conventional test suites miss.