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

PROBE: Probabilistic Occupancy BEV Encoding with Analytical Translation Robustness for 3D Place Recognition

We present PROBE (PRobabilistic Occupancy BEV Encoding), a learning-free LiDAR place recognition descriptor that models each BEV cell's occupancy as a Bernoulli random variable. Rather than relying on discrete point-cloud perturbations, PROBE analytically marginalizes over continuous Cartesian translations via the polar Jacobian, yielding a distance-adaptive angular uncertainty $\sigma_\theta = \sigma_t / r$ in $\mathcal{O}(R{\cdot}S)$ time. The primary parameter $\sigma_t$ represents the expected translational uncertainty in meters, a sensor-independent physical quantity that enhances cross-sensor generalization while reducing the need for extensive per-dataset tuning. Pairwise similarity combines a Bernoulli-KL Jaccard with exponential uncertainty gating and FFT-based height cosine similarity for rotation alignment. Evaluated on four datasets spanning four diverse LiDAR types, PROBE achieves the highest accuracy among handcrafted descriptors in multi-session evaluation and competitive single-session performance relative to both handcrafted and supervised baselines. The source code and supplementary materials are available at https://sites.google.com/view/probe-pr.

02.
arXiv (CS.LG) 2026-06-11

Enhancing Spectral Embedding through Robust and Flexible Knowledge Transfer in Electronic Health Records

arXiv:2606.11570v1 Announce Type: cross Abstract: We propose a spectral-based, unsupervised representation learning framework to derive low-dimensional embeddings for clinical concepts and patients in rare disease cohorts from electronic health records, where data are high-dimensional but sample sizes are limited. To overcome this challenge, we incorporate a knowledge matrix extracted from a broader population that shares a partially overlapping subspace with the rare-disease cohort. Our method departs from existing approaches by relaxing restrictive one-to-one signal-alignment assumptions between the latent data matrix and knowledge matrix, allowing more flexible and realistic forms of structured sharing. We introduce a novel two-step spectral embedding procedure: first, we identify and remove irrelevant components from the knowledge matrix; then, we apply a projection-based method to separately recover shared and heterogeneous components. Simulations and an analysis of a real-world multiple sclerosis cohort show that the proposed method outperforms competing approaches, particularly in challenging scenarios where shared signals are weak and only partially aligned, as is common in rare-disease data.

03.
arXiv (quant-ph) 2026-06-19

Strain- and Electric-Field-Tunable Valley Polarization in Mo0.75V0.25Te2(Mo3VTe8) for Valleytronic Application

arXiv:2606.19954v1 Announce Type: cross Abstract: Valley polarization in 2D TMDs is promising for low-power valleytronic and spin-valley information processing, but time-reversal symmetry in pristine nonmagnetic TMDs keeps the K+ and K- valleys degenerate, limiting device applications. In this work, we investigated the structural stability, electronic properties, and tunable valley polarization of V-alloyed MoTe2 monolayer, Mo0.75V0.25Te2, using first-principles density functional theory (DFT) calculations. Substitutional alloying of MoTe2 with V introduced magnetic exchange interaction, which, together with spin-orbit coupling (SOC), lifted the valley degeneracy at the unequal valleys. The alloyed structure was found to be energetically and dynamically stable due to the absence of imaginary phonon modes. In pristine MoTe2, SOC produced spin splittings of 34.0 meV and 218.9 meV in the conduction bands and valence bands, respectively, but no valley polarization was observed. In contrast, Mo0.75V0.25Te2 exhibited spontaneous valley polarization of 37.3 meV in the conduction band and 78.2 meV in the valence band. The valley polarization was further enhanced by external electric fields and biaxial strain. A transverse electric field along the crystal c axis produced the maximum valley splitting of 132.8 meV in the valence band, whereas biaxial tensile strain increased the valence band valley splitting up to 160.8 meV. The maximum conduction band valley splitting reached 54.4 meV under 2% biaxial compressive strain. These results demonstrated that V alloying, combined with electric-field and strain engineering, provides an effective strategy for achieving large and tunable valley polarization in MoTe2. Thus, Mo0.75V0.25Te2 can be considered a promising 2D platform for tunable valleytronic device applications, such as transistors and sensors.

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

Improving Cross-Format Robustness in Language Models with Multi-Format Training

Large language models often remain sensitive to answer format: a question solved correctly in one form may fail in another semantically equivalent form. To study this gap, we define cross-format robustness as the extent to which a model answers the same underlying question consistently across formats. We then compare full-format training with FormatMix, which expands only a subset of training items into multiple equivalent formats using either random or targeted selection. Across GLM4 and Llama-3.1, multi-format supervision consistently improves both task performance and cross-format robustness, whereas Multiple-choice question (MCQ)-only supervision alone brings little benefit and can even reduce robustness. We further find that expanding only about 30% of the training set into multiple formats often recovers most of the gain from full-format training, and this effect appears across the model families and sizes we study. These results suggest that format diversity, rather than additional supervision alone, is the key driver of robustness. That lightweight multi-format augmentation is a practical way to make LLMs less sensitive to answer format without changing the base model.

05.
arXiv (CS.LG) 2026-06-16

Surrogate-Assisted Framework for SI-Compliant Interconnect Design Optimization Using the Earth Mover's Distance

arXiv:2606.15234v1 Announce Type: cross Abstract: This work presents a deterministic, machine-assisted framework for SI-compliant PCB design based on the Earth Mover's Distance (EMD). In contrast to conventional surrogate-based optimization methods that rely on iterative black-box search procedures, the proposed approach follows an interpretable, sequential evaluation strategy. Neural surrogate models are first used to efficiently predict waveform describing features from topology-dependent design parameters. A decision tree then acts as a physically motivated quality gate that identifies SI-compliant waveforms according to predefined SI criteria. Within the resulting valid solution space, the Earth Mover's Distance is employed as a similarity metric to rank candidate designs according to their proximity to an ideal reference signal. This enables not only the deterministic identification of admissible parameter regions but also a transparent prioritization of physically superior solutions without inverse modeling or stochastic search procedures. The methodology is demonstrated using a large-scale set of simulated DDR3 fly-by waveforms. By combining surrogate prediction, interpretable classification, and EMD-based waveform evaluation, the framework provides an explainable and computationally efficient alternative to conventional optimization strategies for supporting PCB development with AI-based methods.

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

Looped World Models

Current world models face a fundamental tension: faithful long-horizon simulation demands deep computation, but deeper models are expensive to deploy and prone to compounding errors. We resolve this by introducing Looped World Models (LoopWM), which are the first looped architectures for world modelling. Our method iteratively refines latent environment states through a parameter-shared transformer block. This yield up to 100x parameter efficiency over conventional approaches with adaptive computation that automatically scales depth to match the complexity of each prediction step. Orthogonal to scaling model size and training data, LoopWM establishes iterative latent depth as a new scaling axis for world simulation, which might significantly push the community forward.

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

Dual-branch Prompting for Multimodal Machine Translation

Multimodal Machine Translation (MMT) typically enhances text-only translation by incorporating aligned visual features. Despite the remarkable progress, state-of-the-art MMT approaches often rely on paired image-text inputs at inference and are sensitive to irrelevant visual noise, which limits their robustness and practical applicability. To address these issues, we propose D2P-MMT, a diffusion-based dual-branch prompting framework for robust vision-guided translation. Specifically, D2P-MMT requires only the source text and a reconstructed image generated by a pre-trained diffusion model, which naturally filters out distracting visual details while preserving semantic cues. During training, the model jointly learns from both authentic and reconstructed images using a dual-branch prompting strategy, encouraging rich cross-modal interactions. To bridge the modality gap and mitigate training-inference discrepancies, we introduce a distributional alignment loss that enforces consistency between the output distributions of the two branches. Extensive experiments on the Multi30K dataset demonstrate that D2P-MMT achieves superior translation performance compared to existing state-of-the-art approaches. Our code is publicly available at https://github.com/MentaY/DDP.

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

When Cars Have Stereotypes: Auditing Demographic Bias in Objects from Text-to-Image Models

While prior research on text-to-image generation has predominantly focused on biases in human depictions, demographic bias in generated objects remains relatively underexplored. We introduce SODA (Stereotyped Object Diagnostic Audit), a novel framework for systematically measuring these biases through automated attribute discovery and three standardized metrics: Base vs. Demographic Divergence (BDS), Cross-Demographic Disparity (CDS), and Visual Attribute Concentration (VAC). Applying SODA to 8,000 images across five state-of-the-art models and eight object categories (e.g., cars), we find that "neutral" prompts produce outputs most visually similar to middle-aged and White people, suggesting these groups are implicitly over-represented in model defaults. Furthermore, demographic cues trigger highly skewed stereotypical outputs: 26.6% of object-model-demographic combinations produce results where all 20 generated images share the exact same attribute value (e.g., rose gold laptops for women). Finally, prompt-level debiasing reduces inter-group disparity but paradoxically collapses within-group diversity, replacing one stereotype with another. SODA offers a practical pipeline for making these implicit associations measurable, serving as a step toward more responsible AI development.

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

CoffeeBench: Benchmarking Long-Horizon LLM Agents in Heterogeneous Multi-Agent Economies

arXiv:2606.16613v1 Announce Type: new Abstract: As LLM agents become capable of increasingly long-horizon tasks, evaluating their performance in economic systems is becoming increasingly important. Unlike existing benchmarks that primarily evaluate a single agent interacting with a passive environment, economic systems are inherently multi-agent, requiring autonomous agents to communicate, negotiate, and transact while pursuing their own objectives over extended periods. We introduce CoffeeBench, a benchmark for evaluating LLM agents in a long-horizon multi-agent economy composed of heterogeneous firms. In CoffeeBench, two farmers, two roasters, and two retailers autonomously operate their businesses over a 90-day simulation, each seeking to maximize cumulative net income through communication and transactions while managing cash, inventory, and pricing. The evaluated model controls one coffee roaster, while the remaining firms are controlled by fixed reference agents. Across several recent open-weight and proprietary LLMs, all models outperform a passive baseline that takes no actions, with most achieving positive net income. Analysis of agent behavior reveals substantial differences in long-horizon economic interaction: higher-performing models communicate more actively with other firms, whereas Claude~Haiku~4.5 exhibits an idle-drift failure mode, repeatedly choosing inaction despite producing coherent assessments and plans. We release our code and agent trajectories to support future research.

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

DataEvolver: Automatic Data Preparation for Large Language Models through Multi-Level Self-Evolving

arXiv:2606.07001v2 Announce Type: replace-cross Abstract: High-quality training data is essential to large language models (LLMs) and typically requires extensive and costly manual curation. Existing automatic data preparation methods rely on predefined pipelines or customized human instructions, which limits their adaptability to diverse data distributions and lacks principled guidance from high-quality examples. In this paper, we introduce DataEvolver, the first self-evolving data preparation system that automatically constructs pipelines to transform raw data into high-quality data. DataEvolver employs a multi-level mechanism to ensure both pipeline executability and effectiveness. At the operator level, it incrementally expands the operator set to construct a logical plan while resolving dependency conflicts. At the pipeline level, it instantiates logical plans into executable code and iteratively refines pipeline orchestration through a feedback loop that reduces the distribution gap between prepared data and high-quality examples. Experiments on seven benchmarks show that DataEvolver substantially improves data quality and achieves an average 10\% gain in downstream LLM performance compared with training on original data, highlighting new opportunities for the iterative co-evolution of LLMs and data.

11.
arXiv (quant-ph) 2026-06-16

Lattice surgery for near-term experimental logical qubit entanglement creation in planar architectures

arXiv:2606.15190v1 Announce Type: new Abstract: In the era of early fault-tolerant quantum computing, basic demonstrations of entanglement operations between a few logical qubits are at the frontier of recent developments in quantum computing. In this work, we describe in detail, at both the logical and physical qubit levels, a logical teleportation protocol between two surface code logical qubits based on lattice surgery. We address several aspects of the teleportation protocol pertinent to superconducting qubit architectures. We explore the modularity constraints in the number and location of stabilizer readouts and compare variants of the teleportation protocol in this regard. Additionally, we investigate potential performance improvements related to in-sequence decision logic and the optimal size of the interface region between two surface code patches on a superconducting chip. Based on our simulations, we show possible near-term improvements in lattice surgery protocols that facilitate fault-tolerant quantum computing in superconducting circuit architectures.

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

Generalizing Beyond Suboptimality: Offline Reinforcement Learning Learns Effective Scheduling through Random Solutions

arXiv:2509.10303v2 Announce Type: replace-cross Abstract: Online reinforcement learning (RL) approaches have demonstrated strong performance on Job Shop Scheduling (JSP) and Flexible JSP (FJSP) problems by learning scheduling policies through direct interaction with simulated environments. However, these methods often require extensive training interactions, limiting their sample efficiency and practical applicability. Motivated by this challenge, we introduce Conservative Discrete Quantile Actor-Critic (CDQAC), an offline RL algorithm that learns effective scheduling policies directly from static, suboptimal datasets. CDQAC couples a quantile-based critic with delayed policy updates to estimate the return distribution of machine-operation pairs. Extensive experiments on JSP and FJSP benchmarks demonstrate that CDQAC consistently outperforms the data-generating heuristics, surpasses state-of-the-art offline and online RL baselines, and is highly sample efficient, requiring only 1 to 5% of the original dataset to learn high-quality policies. Our analysis suggests that, in scheduling, offline RL performance is governed mainly by state-action coverage rather than the quality of individual trajectories. Scheduling couples a dense reward aligned with the makespan objective with equal-length trajectories across heuristics, enabling effective learning from a broad range of behaviors. Consistent with this observation, datasets generated by a simple random heuristic with broader coverage let it outperform policies trained on datasets produced by stronger heuristics such as Genetic Algorithms.

13.
arXiv (CS.AI) 2026-06-18

DeepInflation: an AI agent for research and model discovery of inflation

arXiv:2601.14288v2 Announce Type: replace-cross Abstract: We present DeepInflation, an AI agent designed for research and model discovery in inflationary cosmology. Built upon a multi-agent architecture, DeepInflation integrates Large Language Models (LLMs) with a symbolic regression (SR) engine and a retrieval-augmented generation (RAG) knowledge base. This framework enables the agent to automatically explore and verify the vast landscape of inflationary potentials while grounding its outputs in established theoretical literature. We demonstrate that DeepInflation can successfully discover simple and viable single-field slow-roll inflationary potentials consistent with the latest observations (with the ACT DR6 results taken as an example) or any given $n_s$ and $r$, and provide accurate theoretical context for obscure inflationary scenarios. DeepInflation serves as a prototype for a new generation of autonomous scientific discovery engines in cosmology, which enables researchers and non-experts alike to explore the inflationary landscape using natural language. This agent is available at https://github.com/pengzy-cosmo/DeepInflation.

14.
medRxiv (Medicine) 2026-06-23

Multivariate Echocardiographic Phenotyping of Hypertensive Heart Failure Using Unsupervised Machine Learning: A Pilot Study

Background Heart failure in hypertensive patients is heterogeneous and poorly captured by traditional left ventricular ejection fraction (LVEF) based classification. Multivariate echocardiographic data combined with unsupervised machine learning may provide a more precise phenotypic characterization. This pilot study evaluated the feasibility of unsupervised clustering of routine transthoracic echocardiographic data to identify phenotypic subgroups of hypertensive heart failure. Methods This retrospective pilot study analyzed transthoracic echocardiography reports from hypertensive patients with clinical heart failure. After data cleaning and exclusion of incomplete records, 102 patients with 11 echocardiographic variables were included. Variables describing left ventricular geometry, systolic function, and diastolic performance were standardized and subjected to K-means clustering. Optimal cluster number was determined using the elbow method and silhouette analysis. Cluster characteristics were assessed using descriptive statistics and Kruskal Wallis testing. Concordance with LVEF based heart failure categories was evaluated. Results Three distinct echocardiographic phenotypes were identified. Cluster 0 (n = 50) demonstrated preserved LVEF with concentric remodeling, consistent with heart failure with preserved ejection fraction (HFpEF) phenotype. Cluster 1 (n = 37) showed marked ventricular dilation and reduced systolic function, consistent with heart failure with reduced ejection fraction (HFrEF). Cluster 2 (n = 15) exhibited concentric hypertrophy with intermediate LVEF, consistent with heart failure with mildly reduced ejection fraction (HFmrEF) like phenotype. All echocardiographic variables differed significantly across clusters (p < 0.001). While Cluster 0 showed strong concordance with HFpEF (96%), Clusters 1 and 2 demonstrated substantial overlap across LVEF categories, indicating partial discordance between structural phenotypes and LVEF based classification. Conclusion Application of unsupervised machine learning to routine echocardiographic data identifies distinct heart failure phenotypes in hypertensive patients. These phenotypes demonstrate significant structural heterogeneity beyond LVEF based classification, supporting the utility of data-driven approaches for refined cardiac phenotyping. This pilot study provides a foundation for larger prospective studies.

15.
arXiv (quant-ph) 2026-06-16

Optimizing resource bounds in direct fidelity estimation

arXiv:2606.16336v1 Announce Type: new Abstract: Direct fidelity estimation provides a way to estimate the fidelity between an experimentally prepared state and a desired pure target state without performing full tomography. Two influential formulations were introduced in 2011 by Flammia and Liu and by da Silva, Landon-Cardinal, and Poulin. In these protocols, the total estimation error is controlled through two distinct probabilistic steps: first, the fidelity is approximated using randomly sampled Pauli observables; second, each sampled expectation value is estimated from finitely many measurement outcomes. In this work we show that additional structural information about the noise can substantially sharpen the corresponding resource bounds. In particular, for some canonical channels the effective number of sampled Pauli settings can be reduced, leading to lower measurement cost both in the general pure-state setting and in the case of a stabilizer state. These results illustrate a broader point: worst-case confidence bounds in direct fidelity estimation can be significantly conservative when experimentally relevant structure is ignored. As a technical ingredient, we also revisit the allocation of the total accuracy and confidence budgets between the two probabilistic steps. Reformulating the analysis in terms of separate error parameters yields a constrained optimization problem whose solution lowers the average number of measurements in the general pure-state setting. Numerical simulations based on quantum circuits implemented in Qiskit illustrate both the improvement obtained under structured-noise assumptions and the conservativeness of the original worst-case bounds.

16.
arXiv (CS.AI) 2026-06-18

ASTRA: A Scalable Next-Generation ATCO Training Simulator with Autonomous Simpilots

arXiv:2606.18319v1 Announce Type: cross Abstract: Air Traffic Control Operators (ATCOs) are vital in ensuring the safe, orderly, and efficient flow of air traffic, yet training capacity is constrained by reliance on specialized human trainers known as simpilots, who must role-play both pilots and ATCOs in a simulated airspace. Existing automated solutions rely on Western-centric speech models that perform poorly in Singaporean operational contexts, with off-the-shelf systems exhibiting Word Error Rates (WER) of up to 107.80% on Singaporean-accented aviation speech. We introduce ASTRA, an end-to-end training simulator that automates these simpilot roles through a pipeline that transcribes ATCO speech, interprets instructions, and generates appropriate pilot and ATCO responses using locally adapted voice models. Our fine-tuned Automatic Speech Recognition (ASR) pipeline reduces WER to 23.45%, substantially outperforming existing approaches in this domain. Beyond traffic simulation, ASTRA incorporates an AI-assisted performance evaluation framework that assesses trainee radiotelephony communications across accuracy, brevity, and completeness, achieving post-optimization scores of 91.7%, 88.2%, and 86.9%, respectively. Built on open-source foundations such as DSPy and Unsloth, this approach enables scalable, standardized ATCO assessment while reducing instructor workload.

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

Quantized Stochastic Primal-Dual Methods for Distributed Optimization under Relaxed Global Geometry

arXiv:2606.11339v1 Announce Type: cross Abstract: We study distributed optimization with stochastic gradients and finite-bit communication modeled by random (unbiased) quantization. We propose q-PDGD, a quantized stochastic primal-dual method, and analyze it under relaxed global geometry. Under restricted secant inequality (RSI), a constant step-size yields linear contraction to an explicit neighborhood determined by gradient noise, quantization distortion, and network connectivity, while a diminishing step-size achieves O(1/k) convergence without shared-minimizer assumptions. Under Polyak-Lojasiewicz (PL) inequality, we obtain linear-to-neighborhood convergence in the same stochastic quantized setting. Our results match the best-known centralized stochastic rates in oracle complexity, and are supported by experiments demonstrating the predicted tradeoffs between quantization level, step-size choice, and graph structure.

18.
arXiv (CS.AI) 2026-06-16

Adaptive $k$NN graph model

arXiv:2601.16509v2 Announce Type: replace-cross Abstract: The $k$-nearest neighbors ($k$NN) algorithm is a cornerstone of non-parametric classification in artificial intelligence, yet its deployment in large-scale applications is persistently constrained by the computational trade-off between inference speed and accuracy. Existing approximate nearest neighbor solutions accelerate retrieval but often degrade classification precision and lack adaptability in selecting the optimal neighborhood size ($k$). Here, we present an adaptive graph model that decouples inference latency from computational complexity. By integrating a Hierarchical Navigable Small World (HNSW) graph with a pre-computed voting mechanism, our framework completely transfers the computational burden of neighbor selection and weighting to the training phase. Within this topological structure, higher graph layers enable rapid navigation, while lower layers encode precise, node-specific decision boundaries with adaptive neighbor counts. Benchmarking against eight state-of-the-art baselines across six diverse datasets, we demonstrate that this architecture significantly accelerates inference speeds, achieving real-time performance, without compromising classification accuracy. These findings offer a scalable, robust solution to the inherent inference bottleneck of $k$NN, laying an adaptive structural foundation for graph-based nonparametric learning.

19.
arXiv (CS.AI) 2026-06-15

ANSR-DT: A Neuro-Symbolic Framework for Adaptive and Explainable Digital Twins

arXiv:2501.08561v4 Announce Type: replace Abstract: Digital twins are increasingly used to monitor and optimize industrial systems, yet many existing frameworks remain difficult to interpret, slow to adapt, and limited in their ability to incorporate explicit domain knowledge. This paper presents ANSR-DT, an adaptive neuro-symbolic framework that unifies temporal anomaly detection, symbolic reasoning, and reinforcement-learning-based decision support within a single digital twin pipeline. ANSR-DT combines a CNN-LSTM model for multivariate pattern recognition with Prolog-based reasoning that converts learned signals into explicit rules, enabling transparent diagnoses and traceable decision paths. A PPO-based adaptation layer further refines operational responses under changing conditions while preserving interpretability. Experiments against 8 baselines show that ANSR-DT delivers competitive predictive performance together with stable rule extraction, scalable symbolic reasoning, and actionable explanations. Additional validation on the Skoltech Anomaly Benchmark (SKAB) further indicates that the framework transfers beyond synthetic settings. These findings position ANSR-DT as a practical foundation for trustworthy, adaptive, and explainable industrial digital twins.

20.
arXiv (quant-ph) 2026-06-17

A Quantum Approach to Stochastic Optimization in Insurance Underwriting

arXiv:2605.01169v2 Announce Type: replace Abstract: The presence of stochastic elements in combinatorial optimization problems makes them particularly challenging, as such problems quickly become intractable for classical computers even at relatively small sizes. In this work, we propose a novel quantum-classical hybrid scheme for solving a class of stochastic optimization problems known as chance-constrained knapsack problems, in which item weights follow probability distributions and constraints may be violated within a specified risk tolerance. Our method employs knapsack-specific QAOA-based circuits to generate samples which, when combined with a new self-consistent classical recovery scheme introduced in this work, produce high-quality solutions. Experiments carried out on IBM Heron processors, using circuits with depths up to 177 and comprising 3443 gates acting on as many as 150 qubits, yield solutions that indicate performance comparable to classical optimization schemes. The proposed quantum-classical scheme paves the way to tackling such problems, with the potential to outperform approaches that rely solely on classical computation.

21.
arXiv (CS.CL) 2026-06-11

CRANE: Constrained Reasoning Injection for Code Agents via Nullspace Editing

Code agents must both reason over long-horizon repository state and obey strict tool-use protocols. In paired Instruct/Thinking checkpoints, these capabilities are complementary but misaligned. The Instruct model is concise and tool-disciplined, whereas the Thinking model offers stronger planning and recovery behavior but often over-deliberates and degrades agent performance. We present CRANE (Constrained Reasoning Injection for Code Agents via Nullspace Editing), a training-free parameter-editing method that treats the Thinking-Instruct delta as a directional pool of candidate reasoning edits for the Instruct backbone. CRANE combines magnitude thresholding to denoise the delta, a Conservative Taylor Gate to retain edits that are jointly beneficial for reasoning transfer and tool-use preservation, and Graduated Sigmoidal Projection to suppress format-critical update directions. By merging paired Instruct and Thinking checkpoints, CRANE delivers strong gains over either individual model while preserving Instruct-level efficiency: on Roo-Eval it achieves pass1 of 66.2% (+19.5%) for Qwen3-30B-A3B and 81.5% (+8.7%) for Qwen3-Next-80B-A3B; on SWE-bench-Verified it resolves up to 14 additional instances at both scales (122/500 and 180/500); and on Terminal-Bench v2 it improves pass1/pass5 by up to 2.3%/7.8%, reaching 7.6%/17.9% and 14.8%/30.3%, respectively, consistently outperforming alternative merging strategies across all three benchmarks.

22.
bioRxiv (Bioinfo) 2026-06-15

DAQplugin: Deep Learning based Real-time Model Evaluation Plugin for ChimeraX

Although an increasing number of protein structures are determined by cryogenic electron microscopy (cryo-EM), protein structure modeling frequently suffers from residue misassignments and sequence register shifts, particularly in regions with ambiguous density. Here, we present DAQplugin, a ChimeraX plugin that performs real-time evaluation of protein models against cryo-EM density maps using the deep-learning-based residue-wise model quality (DAQ) score. Unlike existing validation tools that are typically applied after model construction, DAQplugin enables real-time deep-learning-based validation during model building and refinement. To our knowledge, DAQplugin is the first tool that provides real-time deep-learning based validation of protein models for cryo-EM map within an interactive modeling environment. In addition to identifying potential modeling errors, DAQplugin also provides guidance for correcting sequence register shifts by suggesting alternative residue placements along the backbone. The computation in this plugin is designed to run efficiently on general CPUs without requiring GPU hardware. Using DAQplugin, users can perform deep-learning-based validation on standard laptops during interactive model building, model-map fitting, and refinement. DAQplugin is able to facilitate more accurate interpretation of cryo-EM density maps and improve the reliability assessment of protein structure models.

23.
bioRxiv (Bioinfo) 2026-06-19

Accurate detection of tumor clonality and ongoing expansion mode from genomic data

Recent evidence shows that despite considerable effort, currently available algorithms for estimating intra-tumor heterogeneity (ITH) remain limited. We developed DECODE (Deciphering Cancer Origin from DNA Evolution), a novel mutation clustering method that incorporates the impact of sample-specific sequencing coverage and mutation calling biases. On synthetic data, DECODE outperformed existing methods across multiple clonality metrics and accurately detected and characterized the neutral tail in the site frequency spectrum (SFS), which encodes the tumor's ongoing expansion mode. In acute myeloid leukemia, accounting for the neutral tail enabled DECODE to yield more parsimonious clonal decompositions that align more closely with known subclonal dynamics that drive relapse. Applied to data from The Cancer Genome Atlas, DECODE not only detected a neutral SFS tail in most samples across tumor types but also uncovered a clinically meaningful link between ITH and survival in low-grade glioma. By jointly inferring clonality and expansion mode, DECODE provides two complementary and prognostically relevant readouts of tumor evolution from single tumor genomic samples.

24.
arXiv (quant-ph) 2026-06-15

Tamed Feynman-Kac diffusion processes: Killing-branching intertwine

arXiv:2605.07824v2 Announce Type: replace-cross Abstract: Relaxation to equilibrium of a drifted Brownian motion is quantified by a transition probability density function, whose main (multiplicative) entry is an inferred Feynman-Kac kernel of the Schr\"{o}dinger semigroup operator. Although seemingly devoid of a natural probabilistic significance (except for its explicit path integral definition), the pertinent kernel relaxes to equilibrium as well. The implicit Feynman-Kac potential ${\cal{V}}(x)$, continuous, confining and bounded from below, may take negative values. If positive, ${\cal{V}}(x)$ can be interpreted as the killing rate of the decaying diffusion process. In case of relaxing F-K kernels the killing effects are tamed (often overcompensated). The taming inavoidably appears in conjunction with the existence of the negativity subdomains of ${\cal{V}}(x)$ in $R$. If locally ${\cal{V}}(x) < 0$, its sign inversion $- {\cal{V}}(x)$ can be interpreted as the branching (cloning, alternatively bifurcation) rate in the course of the other wise free random motion. The arising killed diffusion processes with branching, we interpret as the possible path-wise background of tamed (relaxing) Feynman-Kac diffusions. We present acomputer-assisted path-wise arguments, towards a consistency of the killing/branching taming scenario, for a number of nonlinear model systems in one space dimension. Special attention is paid to Feynman-Kac potential shapes in the double well form, where an analytic access to eigenvalues and eigenfunctions is scarce. Throughout the paper the dynamics refers to the positive real time. Since the Newton-type equations of motion for admissible classical trajectories have a Euclidean form (due to the sign inverted force term), we give a brief resume of a couple of their explicit solutions, without recourse to the Euclidean time intuitions, and the instanton lore of related quantum model systems.

25.
arXiv (CS.CV) 2026-06-12

DiskChunGS: Large-Scale 3D Gaussian SLAM Through Chunk-Based Memory Management

Recent advances in 3D Gaussian Splatting (3DGS) have demonstrated impressive results for novel view synthesis with real-time rendering capabilities. However, integrating 3DGS with SLAM systems faces a fundamental scalability limitation: methods are constrained by GPU memory capacity, restricting reconstruction to small-scale environments. We present DiskChunGS, a scalable 3DGS SLAM system that overcomes this bottleneck through an out-of-core approach that partitions scenes into spatial chunks and maintains only active regions in GPU memory while storing inactive areas on disk. Our architecture integrates seamlessly with existing SLAM frameworks for pose estimation and loop closure, enabling globally consistent reconstruction at scale. We validate DiskChunGS on indoor scenes (Replica, TUM-RGBD), urban driving scenarios (KITTI), and resource-constrained Nvidia Jetson platforms. Our method uniquely completes all 11 KITTI sequences without memory failures while achieving superior visual quality, demonstrating that algorithmic innovation can overcome the memory constraints that have limited previous 3DGS SLAM methods.