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01.
arXiv (quant-ph) 2026-06-17

Twin-beam advantage in quantum LiDAR under correlated noise

arXiv:2606.17908v1 Announce Type: new Abstract: Quantum light promises improved precision in optical remote sensing, but its practical advantage depends critically on whether nonclassical resources remain useful under realistic noise and experimentally accessible detection. This question becomes especially relevant for LiDAR systems, where a quantum advantage has been demonstrated for target detection and joint range-velocity estimation, but mostly under idealized conditions or simple noise models, such as optical loss and thermal background. A key open point is whether entanglement provides an operational advantage when the dominant disturbance is not independent noise, but structured interference across sensing modes. Here, we address this question by studying the joint estimation of target range and velocity with bright two-mode Gaussian probes and homodyne detection, comparing coherent, separable squeezed, and twin-beam states at a fixed resource budget. Our results reveal a hierarchy of quantum resources set by the noise structure: separable squeezing provides a robust advantage over coherent illumination under loss and thermal background, whereas twin-beam probes become superior under correlated jamming when the receiver is adaptively optimized. These results establish correlated noise as the operational regime in which entanglement provides a robustness advantage beyond local squeezing, opening a receiver-aware route to quantum-enhanced LiDAR in realistic and potentially adversarial environments.

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

Latent-Conditioned Parameterized Quantum Circuits as Universal Approximators for Distributions over Quantum States

arXiv:2605.28690v3 Announce Type: replace-cross Abstract: Many applications in quantum simulation, quantum chemistry, and quantum machine learning require not a single quantum state but an ensemble of states characterizing the heterogeneity of a target system. Preparing such ensembles state-by-state is prohibitive in both variational and fault-tolerant settings, thereby motivating a generative modeling approach. We introduce latent-conditioned parameterized quantum circuits (LPQCs), a hybrid quantum-classical framework in which classical neural networks map a latent variable sampled from a prior distribution to the parameters of a parameterized quantum circuit. We prove that LPQCs are universal approximators for probability measures over density operators in the 1-Wasserstein distance, extending classical universal approximation theorems to the quantum-distribution setting. We additionally introduce a multimodal latent prior and a mixture-of-experts circuit architecture, and show empirically that the latent-conditioned parameterization alleviates the barren plateau problem during optimization, a behavior for which we provide rigorous partial guarantees. Numerical experiments validate the framework on a synthetic multi-cluster ensemble of mixed quantum states and on a QM9-derived ensemble of 3-D molecular structures. In these tasks, LPQC outperforms recent quantum generative baselines and matches the generation quality of a classical neural-network baseline, while requiring an output dimension that grows only linearly with the number of qubits rather than exponentially. By leveraging classical expressivity in the latent space, LPQCs offer a tractable route to quantum generative modeling.

03.
arXiv (CS.CV) 2026-06-15

Explaining RhythmFormer: A Systematic XAI Analysis of Periodic Sparse Attention for Remote Photoplethysmography

Remote photoplethysmography (rPPG) transformers achieve low heart-rate error on benchmarks, yet their decisions remain opaque–a growing concern as rPPG moves toward clinical heart rate estimation. Existing rPPG XAI is dominated by qualitative heatmap inspection without quantitative faithfulness metrics or physiology-grounded validation, leaving a gap between visual plausibility and auditable evidence. We address this gap. First, we adapt four attribution methods (raw attention, rollout, flow, Beyond Intuition) to RhythmFormer's bi-level routing attention with top-$k$ selection. Second, we introduce a skin coverage metric quantifying how much attribution mass falls on skin regions. Third, we adapt the SaCo faithfulness coefficient from its original classification setting to rPPG regression by using the MAE between original and perturbed predicted rPPG waveforms as the perturbation impact. Applying these tools, we quantify a multi-hop leakage effect under sparse top-$k$ routing: attention rollout and flow almost completely restores the connections that individual refined-attention layers explicitly set to zero. Beyond Intuition mitigates this via its value-projection-weighted rollout and gradient-supported mask, attaining the highest median refined skin coverage ($0.83$ vs. $0.57$ for vanilla rollout) and faithfulness ($F=0.92$) among the evaluated methods on UBFC-rPPG. Validation across diverse datasets and model variants is needed. A case study on a low-SaCo outlier further shows all four methods recovering consistently once an artefactual region is replaced, suggesting consistent SaCo behavior across attribution families in this illustrative case. Together, these metrics move XAI for rPPG toward auditable numerical evidence about spatial alignment and perturbation faithfulness, i.e. trustworthy rPPG XAI.

04.
arXiv (CS.AI) 2026-06-12

WISE: A Long-Horizon Agent in Minecraft with Why-Which Reasoning

arXiv:2606.12852v1 Announce Type: new Abstract: Rapid advances have been made in developing general-purpose embodied agent in environments like Minecraft through the adoption of LLM-augmented hierarchical approaches. Despite their promise, low-level controllers often become performance bottlenecks due to repeated execution failures. We argue that a key limitation is not only the lack of episodic memory, but also the decoupling of what-where-when memory from which-why reasoning. To address this, we propose WISE (Which-Why Informed Semantic Explorer), a long-horizon agent framework with an enhanced low-level controller equipped with a Causal Event Graph that augments episodic memory with explicit causal structure linking observations to task relevance. Unlike prior work such as MrSteve, which relies on feature similarity for retrieval, WISE enables robust recall under viewpoint changes and supports opportunistic task reordering through causal reasoning. Building on this memory, we propose an Opportunistic Task Scheduler that dynamically re-prioritizes subtasks when causally relevant opportunities are detected. We further equip WISE with a multi-scale progressive exploration strategy to provide spatially comprehensive observations for downstream reasoning. Experiments show that WISE largely improves task success and efficiency on long-horizon sparse tasks, particularly in settings requiring adaptive decision-making.

05.
arXiv (CS.CL) 2026-06-24

Balalaika: Data-Centric, Prosody-Aware Annotation Pipeline for Russian Speech

We introduce Balalaika, an open-source, data-centric pipeline for processing audio and producing prosody-aware annotations. It combines semantic VAD for context-preserving segmentation, multi-ASR ensembling with ROVER consensus decoding, while retaining optional word-level timestamps, followed by automatic quality and speaker-purity filtering. The text is further enriched with punctuation restoration, lexical stress and "\textipa{e}/\textipa{\H{e}}" normalization, and IPA phonemes. Using Balalaika, we build a 5.1k-hour multi-source Russian corpus with rich annotations, and show consistent gains under equalized training budgets for both speech denoising and TTS; ablations confirm complementary benefits of stress and punctuation and improved synthesis with stricter MOS filtering. The datasets are publicly available at \href{https://huggingface.co/collections/lab260/balalaika-dataset}{\underline{HuggingFace}}

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

LLMs Prompted for Legal Context Object More: Overrefusal from Small On-Premises LLMs in Criminal Legal Context

arXiv:2606.24585v1 Announce Type: new Abstract: While the validity of LLMs' use in the legal context remains subject to ethical and legal debate, legal professionals are already experimenting with personal LLMs, if only for translation and reformulation. However, even such a seemingly innocuous use can introduce biases through case processing speed if LLM assistants selectively refuse assistance on certain topics. To better anticipate such biases, we investigate several modern small LLMs that are most likely to be used as on-device assistants, to assess the impact of overrefusal on legal prompts. Surprisingly, we find that authority-style prefixes (``you are acting as an assistant of the national supreme court'', ``[...] defense lawyer'') systematically increase refusal rates by 2–20x over the no-prefix baseline, while a known role-play jailbreak prefix shows mixed effects, sharply increasing refusals in some models and barely shifting them in others. The finding suggests that small on-prem deployable LLMs are unstable under contextual framings that a real institutional user might naturally introduce, and further investigation is essential to minimize opportunities for bias.

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

Emergent Strategic Reasoning Risks in AI: A Taxonomy-Driven Evaluation Framework

arXiv:2604.22119v2 Announce Type: replace Abstract: As reasoning capacity and deployment scope grow in tandem, large language models (LLMs) gain the capacity to engage in behaviors that serve their own objectives, a class of risks we term Emergent Strategic Reasoning Risks (ESRRs). These include, but are not limited to, deception (intentionally misleading users or evaluators), evaluation gaming (strategically manipulating performance during safety testing), and reward hacking (exploiting misspecified objectives). Systematically understanding and benchmarking these risks remains an open challenge. To address this gap, we introduce ESRRSim, a taxonomy-driven agentic framework for automated behavioral risk evaluation. We construct an extensible risk taxonomy of 7 categories, which is decomposed into 20 subcategories. ESRRSim generates evaluation scenarios designed to elicit faithful reasoning, paired with dual rubrics assessing both model responses and reasoning traces, in a judge-agnostic and scalable architecture. Evaluation across 11 reasoning LLMs reveals substantial variation in risk profiles (detection rates ranging 14.45%-72.72%), with dramatic generational improvements suggesting models may increasingly recognize and adapt to evaluation contexts.

08.
arXiv (CS.AI) 2026-06-12

When Does Delegation Beat Majority? A Delegation-Based Aggregator for Multi-Sample LLM Inference

arXiv:2606.08098v2 Announce Type: replace Abstract: Majority voting over sampled answers is the dominant unsupervised aggregator for multi-sample LLM inference. In this paper, we show a delegation-based aggregator (Propagational Proxy Voting, PPV; Sakai et al., 2025) yields an unsupervised consensus rule that beats majority on MMLU-Pro by +1.5 pp overall and +2.24 pp on the non-trivial subset (paired McNemar p ~ 1.0e-14, n = 8,099). Majority discards two signals that every sample carries: within-group letter entropy and between-group reasoning geometry. PPV exposes per-voter levers that consume exactly these two signals: When (how much weight a voter keeps on its own pick) and Whom (how it splits the remainder across peers). We drive When with letter entropy and Whom with per-question-centered embedding cosine. Our method needs no gold labels and no auxiliary training: per-question, we partition 128 sampled generations into 16 groups, compute each group's letter-level semantic entropy and reasoning embedding centroid, and feed both into a stochastic delegation matrix whose stationary distribution selects the consensus answer. We walk through an example in which PPV overturns a clear 10-6 majority for the wrong letter: the 10-voter majority cluster is geometrically incoherent (mean within-cluster cosine -0.02) while the 6-voter minority is tight (+0.26), so propagated delegation mass concentrates on the minority's answer even though entropy alone would keep the majority ahead. We further report delegation strategies with negative results that constrain the design space for unsupervised LLM aggregation. No within-question ensemble of confidence modes closes the oracle gap.

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

Effective and Low-cost Lane-based Map Localization for Vehicle-Centric Route Generation

Driver-centric route representation plays a vital role in intuitive driving guidance systems. This paper presents OLRA, a low-cost, map-localization-based framework that derives driver-view-aligned routes by matching map-based navigation routes with camera-detected lane markings. This alignment process mutually enhances vehicle localization accuracy and visual route consistency. To bridge the evaluation gap across different paradigms, we introduce practical route evaluation metrics and benchmark OLRA against OpenPilot, a representative direct-generation approach. Experimental results on the nuScenes dataset demonstrate that OLRA outperforms OpenPilot in complex road segments and in route estimation at distance beyond 20 meters, achieving lower overall Euclidean error. This study is expected to promote future research in low-cost, maplocalization-based route generation methods.

10.
arXiv (CS.LG) 2026-06-18

Optimal scenario design for climate emulation

arXiv:2606.19302v1 Announce Type: cross Abstract: As deep learning for physical systems continues to grow in popularity, efforts to improve generalizability have primarily focused on designing architectures that embed physical constraints. However, for machine-learning surrogate climate models (emulators), we show that the low structural diversity in existing scenarios commonly used to generate training data places a ceiling on predictive skill. Here, we examine whether training datasets themselves can be optimized to improve generalization. We introduce a method to create datasets that produce emulators capable of generalizing to new, structurally different scenarios absent from the training data. We use a differentiable Simple Climate Model (SCM) to calculate the sensitivity of emulator loss to perturbations in the training data, iteratively updating the training data to maximize emulator skill. For an SCM, training on one scenario optimized in this fashion outperforms an emulator trained on six standard ScenarioMIP pathways. We achieve this higher predictive skill despite training on a smaller dataset, finding that our emulator successfully isolates distinct physical behaviors of different climate forcing agents (e.g., greenhouse gases vs. aerosols) without single-forcing runs. We then demonstrate that scenarios optimized using an SCM, when used to drive an intermediate-complexity climate model, produce a training dataset that yields a more skillful emulator than training on ScenarioMIP outputs. Our results suggest that, in the compute-constrained environment of running full-scale climate models, generating a small number of dynamically rich scenarios provides greater marginal value for emulation and characterizing system responses than expanding the suite of traditional emissions pathways.

11.
arXiv (CS.CL) 2026-06-15

Does the Judge Prefer English? Evaluating Language-Switching Invariance in LLM-as-a-Judge

作者:

Large language models (LLMs) are now widely used as automatic judges for open-ended instruction-following evaluation. This practice is convenient, scalable, and often more semantically aware than reference-based metrics, but it also introduces a new reliability question: does a judge evaluate the quality of an answer, or does it also react to the language in which the comparison is presented? We propose Judge-LS, a lightweight meta-evaluation protocol that transforms LLMBar response-pair items into English, Chinese, and Chinese-English language-switched variants. A reliable judge should preserve its preference under label-preserving language transformations and should not prefer a language when two answers are translation-equivalent. We evaluate four API-accessible judges on the full 419-item LLMBar benchmark, producing 13,408 successful pairwise judgments. Across models, Chinese and language-switched presentations induce 10.7–14.4% preference flips relative to English, and all judges achieve their highest accuracy in English. However, translation-equivalent tie probes do not reveal a systematic English preference: most probes are judged as ties, and non-tie decisions more often favor Chinese. We add confidence intervals, paired significance tests, and an automatic transformation audit with a sensitivity analysis that excludes mechanically flagged high-risk variants. The experiment requires no model training, uses only API calls, and is feasible on modest local hardware.

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

Reservoir-controlled electromagnetically induced gratings in a weakly driven two-level medium

arXiv:2606.13085v1 Announce Type: cross Abstract: We theoretically investigate the transmission and diffraction of a weak probe field from an electromagnetically induced grating formed in a weakly driven two-level medium coupled to engineered quantum reservoirs. Using a perturbative solution of the optical Bloch equations in the weak-driving regime, we analyze how normal-vacuum, thermal, and broadband squeezed-vacuum environments modify the probe susceptibility and consequently reshape both the spatial transmission function and the far-field diffraction patterns. We show that reservoir statistics have a pronounced impact on the diffraction response by altering the amplitude and phase of the induced grating. Thermal reservoirs enhance the transmission modulation and increase the intensity of the dominant diffraction orders, whereas squeezed-vacuum reservoirs generate strongly phase-sensitive modifications that selectively redistribute optical power among diffraction channels. We further demonstrate that the detuning between the squeezed reservoir and the driving field provides an efficient mechanism for controlling diffraction directionality, leading to substantial amplification of selected angular orders. In two-dimensional geometries, squeezed-vacuum correlations produce highly structured phase landscapes and strongly anisotropic diffraction patterns, enabling directional enhancement of specific diffraction channels while suppressing others. These results establish reservoir engineering as a versatile approach for controlling transmission, diffraction efficiency, and angular selectivity in minimal two-level systems, with potential applications in programmable photonic devices, beam steering, and quantum optical platforms.

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

DriveJudge: Rethinking Autonomous Driving Evaluation with Vision-Language Models

Autonomous driving has shifted towards end-to-end policy learning, where reliable, interpretable policy evaluation is a fundamental challenge as driving quality is highly context-dependent. Commonly used rule-based driving metrics like EPDMS are interpretable but lack context-awareness, while recent VLMbased evaluations are context-aware but limited by ambiguous VLM outputs and weak physical grounding. To evaluate driving in a manner that is both interpretable and context-aware, we introduce DriveJudge. DriveJudge is a driving evaluation agent that combines rule-grounded evaluation with Vision-Language Model (VLM) reasoning and selectively invokes physically-grounded deterministic rule functions after interpreting the environmental context. To train and evaluate DriveJudge, we curate a large-scale dataset of 33,577 challenging driving samples with human annotations on whether the driving behavior is reasonable in the given scenario. With this dataset, we address the underexplored problem of driving metric evaluation, and introduce two human-aligned benchmark tasks: Driving Quality Classification and Trajectory Preference Selection. DriveJudge outperforms EPDMS for driving quality classification by 21.23 AUC, and the recent VLM-based DriveCritic for trajectory preference selection by 6.5%, setting a new standard for interpretable and precise driving evaluation.

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

E-mem: Multi-agent based Episodic Context Reconstruction for LLM Agent Memory

arXiv:2601.21714v5 Announce Type: replace Abstract: The evolution of Large Language Model (LLM) agents towards System~2 reasoning, characterized by deliberative, high-precision problem-solving, requires maintaining rigorous logical integrity over extended horizons. However, prevalent memory preprocessing paradigms suffer from destructive de-contextualization. By compressing complex sequential dependencies into pre-defined structures (e.g., embeddings or graphs), these methods sever the contextual integrity essential for deep reasoning. To address this, we propose E-mem, a framework shifting from Memory Preprocessing to Episodic Context Reconstruction. Inspired by biological engrams, E-mem employs a heterogeneous hierarchical architecture where multiple assistant agents maintain uncompressed memory contexts, while a central master agent orchestrates global planning. Unlike passive retrieval, our mechanism empowers assistants to locally reason within activated segments, extracting context-aware evidence before aggregation. Evaluations on the LoCoMo benchmark demonstrate that E-mem achieves over 54\% F1, surpassing the state-of-the-art GAM by 7.75\%, while reducing token cost by over 70\%.

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

GePBench: Evaluating Fundamental Geometric Perception for Multimodal Large Language Models

Geometric shapes play important roles in both physical world and human cognition. While multimodal large language models (MLLMs) have made significant advancements in visual understanding, their abilities to recognize geometric shapes and their spatial relationships, which we term geometric perception, are not explicitly and systematically explored. To address this gap, we introduce GePBench, a novel benchmark specifically designed to assess the geometric perception capabilities of MLLMs. Our extensive evaluations reveal that even the current state-of-the-art MLLMs exhibit significant deficiencies in geometric perception tasks. Furthermore, we show that models trained with GePBench data demonstrate considerable improvements on a wide range of downstream tasks, highlighting the critical role of geometric perception in enabling advanced multimodal applications. Our code and datasets are available at \href{https://github.com/Changhao-Xiang/GePBench}{https://github.com/Changhao-Xiang/GePBench}.

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

Clustering and Pruning in Causal Data Fusion

arXiv:2505.15215v3 Announce Type: replace-cross Abstract: Data fusion, the process of combining observational and experimental data, can enable the identification of causal effects that would otherwise remain non-identifiable. Although identification algorithms have been developed for specific scenarios, do-calculus remains the only general-purpose tool for causal data fusion, particularly when variables are present in some data sources but not others. However, approaches based on do-calculus may encounter computational challenges as the number of variables increases and the causal graph grows in complexity. Consequently, there exists a need to reduce the size of such models while preserving the essential features. For this purpose, we propose pruning (removing unnecessary variables) and clustering (combining variables) as preprocessing operations for causal data fusion. We generalize earlier results on a single data source and derive conditions for applying pruning and clustering in the case of multiple data sources. We give sufficient conditions for inferring the identifiability or non-identifiability of a causal effect in a larger graph based on a smaller graph and show how to obtain the corresponding identifying functional for identifiable causal effects. Examples from epidemiology and social science demonstrate the use of the results.

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

Pre-AF 13: An Interpretable Atrial Fibrillation Risk Score Mined from Discharge Reports

Background. Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia and a major determinant of prognosis. Established AF risk scores rely on factors (older age, hypertension) nearly ubiquitous among patients with cardiovascular disease (CVD), offering limited stratification in this high-risk group. Most target long-term (5-10 year) rather than medium-term prediction. We developed interpretable ML models predicting AF risk over a 24-month and entire follow-up horizon in CVD patients using routinely collected hospital data. Methods. Single-center retrospective study of electronic health records from the National Research Cardiology Center (Russia) for patients aged >=18 with CVD but without pre-existing AF, hospitalized more than once between January 2012 and May 2019. A custom NLP pipeline transformed unstructured discharge reports into 73 structured features, combining a rule-based parser with transformer-based NER. Using LightAutoML we built a full model (73 features), a simple model (reduced subset), and a linear model for a bedside risk score. Performance was assessed by ROC AUC, compared with CHARGE-AF, C2HEST, MHS, and HAVOC, and interpreted via SHAP. Results. Of 80,576 records from 45,000 patients, 17,562 met inclusion criteria; 1,438 (8.19%) developed AF. The full model reached ROC AUC 0.735 (24-month) and 0.696 (entire follow-up); the simple model was nearly identical (0.725, 0.696). All non-linear models outperformed the four clinical risk scores (ROC AUC 0.53-0.64). The simple model uses 13 features and is named Pre-AF 13. SHAP identified age and left atrial volume as dominant predictors. A linear risk score (Pre-AF 9) stratified observed 24-month AF incidence from ~7% to 36%. Conclusion. Interpretable ML models built from routinely collected EHR data identify high-AF-risk CVD patients, outperforming established clinical risk scores.

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

Near–Real-Time Conflict-Related Fire Detection in Sudan Using Unsupervised Deep Learning

Ongoing armed conflict in Sudan highlights the need for rapid monitoring of conflict-related fire-affected areas. Recent advances in deep learning and high-frequency satellite imagery enable near–real-time assessment of active fires and burn scars in war zones. This study presents a near–real-time monitoring approach using a lightweight Variational Auto-Encoder (VAE)–based model integrated with 4-band Planet Labs imagery at 3 m spatial resolution. We demonstrate that these impacted regions can be detected within approximately 24 to 30 hours under favorable observational conditions using accessible, commercially available satellite data. To achieve this, we adapt a VAE–based model, originally designed for 10-band imagery, to operate effectively on high-resolution 4-band inputs. The model is trained in an unsupervised manner to learn compact latent representations of nominal land-surface conditions and identify burn signatures by quantifying changes between temporally paired latent embeddings. Performance is evaluated across five case studies in Sudan and compared against cosine distance, CVA, and IR-MAD using precision, recall, F1-score, and the area under the precision-recall curve (AUPRC) computed between temporally paired image tiles. Results show that the proposed approach consistently outperforms the other methods, achieving higher recall and F1-scores while maintaining viable precision in highly imbalanced fire-detection scenarios. Experiments with 8-band imagery and temporal image sequences yield only marginal performance gains over single 4-band inputs, underscoring the effectiveness of the proposed lightweight approach for scalable, near–real-time conflict monitoring.

19.
arXiv (math.PR) 2026-06-15

Hierarchical symmetry selects log-Poisson cascades: classification, uniqueness, and stability

arXiv:2604.01632v2 Announce Type: replace Abstract: Within i.i.d. multiplicative cascades, a single axiom – the hierarchical symmetry, a linear contraction on incremental scaling exponents – is shown to be necessary and sufficient for the cascade multiplier to be log-Poisson. We prove: (1) a characterization theorem determining the log-Poisson law with explicit parameters, within the class of all multipliers with finite lattice moments; (2) a classification theorem locating the log-Poisson class inside the log-infinitely-divisible family and identifying the mechanism by which every rival sub-family fails the symmetry; (3) a stability theorem with sharp constants – $(1+\beta)^{1/2}$ when the limiting increment is known, $\sqrt{2}$ when it is fitted – and (4) an unconditional propagation theorem transferring the bound to the multiplier distribution at the sharp rate $\Theta(\sqrt{\varepsilon})$, with a matching lower bound. Beyond independence, the classification extends exactly at the level of asymptotic statistics (limiting cumulant generating function, large deviations, multifractal spectrum) and provably not at the level of laws: an explicit stationary ergodic Markov multiplier satisfies the symmetry exactly with a non-log-Poisson marginal, while exchangeable multipliers collapse to the i.i.d. log-Poisson cascade and finite-state Markov multipliers cannot satisfy the symmetry at all. In the continuous category of exactly scale-invariant log-infinitely-divisible multifractal random measures, no finite moment window of structure-function exponents identifies the cascade class, whereas at the level of the scale-invariance generator the symmetry selects exactly the Barral-Mandelbrot compound Poisson cascade, with scale-ratio-free stability constants. The proofs reduce to second-moment identities on [0,1] via the change of variables $u = e^{kx}$, boundedness of the multiplier, and multiplicative couplings.

20.
arXiv (math.PR) 2026-06-24

A parameterized family of balance indices for phylogenetic networks

arXiv:2606.24562v1 Announce Type: cross Abstract: We introduce a new family of balance indices for phylogenetic networks: the $H_\alpha$ indices, where $\alpha$ is a positive real number. This family includes the $B_2$ index as a special case ($\alpha = 1$) and provides a natural extension of the Sackin index to phylogenetic networks. We show that the $H_\alpha$ indices share many structural properties with the $B_2$ index, most notably a "grafting property" that makes it possible to express the $H_\alpha$ index of a network in terms of the $H_\alpha$ indices of its biconnected components. These properties allow us to identify networks that minimize / maximize $H_\alpha$ for various classes of phylogenetic networks, and to study its distribution for several models of random trees and networks (in particular, Galton-Watson trees and binary Markov branching trees, with a focus on the Yule and PDA models). Finally, we show how local limits can be used to analyze the asymptotic behavior of $H_\alpha$ for large trees and networks, and we obtain general results for the moments of $H_\alpha$ for a broad class of random phylogenetic networks known as blowups of Galton-Watson trees.

21.
bioRxiv (Bioinfo) 2026-06-11

Integrating Spatially Adjusted Protein Summaries for Survival Prediction in Spatial Proteomics

Recent advances in spatial proteomics, particularly imaging mass cytometry, enable the measurement of protein expression at the single-cell level while preserving a spatial context. Conventional survival analyses, however, typically rely on patient-level averages of protein intensities and therefore overlook spatial heterogeneity and tissue architecture. To address this limitation, we introduce a framework that incorporates spatial information into survival modeling by generating spatially adjusted protein summaries (SAPS). In this approach, cell-level protein intensities within each patient are modeled using spatial spline regression to capture spatial trends. From these models, we extract two complementary features: a spatially adjusted mean expression and a residual variance that reflects cell-to-cell variability unexplained by spatial effects. These summaries are then incorporated into Cox proportional hazards models in combination with clinical covariates. In simulation studies, our proposed framework achieved improved predictive performance compared to other alternative methods. The application of the method to breast cancer imaging mass cytometry data indicate that spatially adjusted summaries may enhance survival prediction and reveal biologically interpretable spatial protein patterns, suggesting high translational potential. This methodology offers an efficient means of translating complex spatial proteomics data into patient-level features, providing both improved survival prediction and new insights into the role of spatial heterogeneity in cancer outcomes.

22.
bioRxiv (Bioinfo) 2026-06-14

FENNEC: Fine-Tuned Ensemble Neural Networks Accelerate Chemically Modified siRNA Design and Screening

Small interfering RNAs (siRNAs) are a clinically validated therapeutic modality, yet designing potent chemically modified siRNAs remains a costly and iterative process, limited by scarce public data. Computational prediction of siRNA efficacy is therefore essential for rational design and accelerated preclinical development. However, despite the critical role of chemical modifications in therapeutic performance, current state-of-the-art machine learning methods either are not designed to model the chemical diversity of therapeutic siRNAs, or exhibit poor generalization performance. Here, we present FENNEC (Fine-Tuned Ensemble of Neural Networks for siRNA Efficiency Characterization), a machine-learning framework for predicting siRNA activity across chemically diverse design spaces. To support this effort, we curated the largest patent-derived dataset to date of chemically modified siRNAs from 42 patents using OCR-based table extraction and stringent filtering. FENNEC combines temporal convolutional networks with thermodynamic descriptors, experimental covariates, and embeddings from RNA foundation models to capture both local chemical determinants and broader target-context information. Importantly, we show that language-model-derived embeddings provide meaningful higher-order representations of target transcripts, particularly in data-scarce settings. FENNEC achieved robust predictive performance across both gene-level and scaffold-level validation settings, with additional experimental validation on a novel AHSA1-targeting dataset further supporting its generalizability across chemically modified siRNAs. In benchmarking, FENNEC outperformed classical machine-learning and state-of-the-art deep learning models, demonstrating generalization to unseen chemistry. Model interpretation recovered established design principles, including position-specific effects of glycol nucleic acid, 2'-fluoro modifications, and phosphorothioate backbones. Furthermore, in silico perturbation analyses suggest that FENNEC can serve not only as a predictive model, but also as an oracle for the design and optimization of chemically modified siRNAs. Together, our work addresses a key gap in the field by enabling chemically aware deep learning for siRNA design, supported by a large and diverse collection of chemically modified siRNA measurements.

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

Dr-DCI: Scaling Direct Corpus Interaction via Dynamic Workspace Expansion

Agentic search over large corpora relies on retriever-mediated interfaces (e.g., BM25 or ColBERT) for scalable candidate discovery. While effective at ranking relevant documents, these interfaces expose evidence only as ranked results or bounded document views, limiting agents' ability to reorganize material and verify constraints across documents. Direct Corpus Interaction (DCI) addresses this limitation by exposing shell-executable corpus operations for flexible search, filtering, comparison, and verification. However, full-corpus terminal commands become slow and unstable as the corpus grows, degrading performance and efficiency. We introduce DR-DCI, a retriever-steered DCI framework that treats retrieval as an agent-callable action for expanding a local workspace. Rather than operating directly over the full corpus, the agent dynamically pulls relevant documents into an evolving workspace and conducts DCI operations within it. This design combines retriever-level recall with DCI-style precision: retrieval keeps exploration scalable, while DCI preserves the local operations needed for effective evidence resolution. Experiments show that DR-DCI is both effective and efficient across scales. On Browsecomp-Plus, DR-DCI reaches 71.2\% accuracy, improving over raw DCI and ablated variants by up to 8.3 points while reducing tool usage, wall time, and estimated cost. With workspace-preserving context reset, accuracy further improves to 73.3\%. In corpus-scaling experiments, DR-DCI remains effective from 100K to 10M documents, whereas raw DCI becomes unstable and BM25 performs substantially worse. DR-DCI also scales to a 20M-scale file-per-document Wiki-18 QA setting, achieving an average score of 63.0 across six benchmarks and outperforming retrieval-based and trained search-agent baselines. Ablation analysis further shows that ranked previews and inter-document DCI are key to performance.

24.
arXiv (CS.CV) 2026-06-16

Structural Energy Guidance for View-Consistent Text-to-3D Generation

Text-to-3D generation based on diffusion models often suffers from the Janus problem, leading to inconsistent geometry across viewpoints. This work identifies viewpoint bias in 2D diffusion priors as the main cause and proposes Structural Energy-Guided Sampling (SEGS), a training-free and plug-and-play framework to improve multi-view consistency. SEGS constructs a structural energy in the PCA subspace of U-Net features and injects its gradient into the denoising process. It can be easily integrated into SDS/VSD pipelines without retraining. Experiments show that SEGS reduces the Janus Rate by about 10% on average and improves View-CS scores across multiple baselines, including DreamFusion, Magic3D, and LucidDreamer. This method effectively alleviates viewpoint artifacts while preserving appearance fidelity, providing a flexible solution for high-quality text-to-3D content generation.

25.
arXiv (CS.AI) 2026-06-16

Early Diagnosis of Wasted Computation in Multi-Agent LLM Systems via Failure-Aware Observability

arXiv:2606.01365v2 Announce Type: replace Abstract: Failure-aware observability diagnoses wasted computation in multi-agent LLM systems before final-answer evaluation can explain what went wrong. We propose a trace-based framework for a three-agent architecture – orchestrator, search agent, and execution agent – that converts structured events into online signals for loops, budget pressure, low information gain, and tool instability, then adds offline semantic grounding metrics and selective LLM-as-judge evaluation. On 165 GAIA validation traces under identical caps, 98 runs produce usable final answers and 67 fail or stop without one. Among warned failed runs, 58.1% of tokens are spent after the first warning on average, indicating substantial opportunity for intervention. A 10-task Level-2 pilot uses warnings to diversify search or require evidence, reducing post-warning token fraction from 0.638 in the baseline to 0.304. The results support a layered design: cheap online signals help the orchestrator redirect or halt redundant behavior, while deeper semantic checks identify whether completed answers are grounded enough to trust.