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01.
arXiv (CS.LG) 2026-06-16

Polynomial-Time Mistake-Bounded Language Generation

arXiv:2606.16077v1 Announce Type: cross Abstract: In this note, we introduce a polynomial-time version of the mistake-bounded language generation (MBLG) framework due to Kleinberg, Peale, and Reingold (2026). We observe that the family of parities of variables, and the family of conjunctions of literals, are polynomial-time MBLG. Our main result states that the family of monotone Boolean functions with polynomially-many maxterms is polynomial-time MBLG. This family includes all monotone Boolean functions, computable by polynomial-size decision trees. Our technique can be presented as a new combinatorial game about writing numbers on a board.

02.
arXiv (CS.AI) 2026-06-19

Concept Flow Models: Anchoring Concept-Based Reasoning with Hierarchical Bottlenecks

arXiv:2606.19489v1 Announce Type: cross Abstract: Concept Bottleneck Models (CBMs) enhance interpretability by projecting learned features into a human-understandable concept space. Recent approaches leverage vision-language models to generate concept embeddings, reducing the need for manual concept annotations. However, these models suffer from a critical limitation: as the number of concepts approaches the embedding dimension, information leakage increases, enabling the model to exploit spurious or semantically irrelevant correlations and undermining interpretability. In this work, we propose Concept Flow Models (CFMs), which replace the flat bottleneck with a hierarchical, concept-driven decision tree. Each internal node in the hierarchy focuses on a localized subset of discriminative concepts, progressively narrowing the prediction scope. Our framework constructs decision hierarchies from visual embeddings, distributes semantic concepts at each hierarchy level, and trains differentiable concept weights through probabilistic tree traversal. Extensive experiments on diverse benchmarks demonstrate that CFMs match the predictive performance of flat CBMs, while substantially mitigating information leakage by reducing effective concept usage. Furthermore, CFMs yield stepwise decision flows that enable transparent and auditable model reasoning with hierarchical class structures.

03.
arXiv (CS.LG) 2026-06-11

PCA-Enhanced Adaptive NVAR Framework for High-Resolution Sea Surface Temperature Forecasting in the East Sea

arXiv:2606.12141v1 Announce Type: new Abstract: Accurate forecasting of sea surface temperature (SST) in regional seas such as the East Sea is crucial for monitoring marine ecosystems, assessing climate risks, managing fisheries, and conducting naval operations. Traditional numerical ocean models provide reliable predictions but are computationally expensive and often unsuitable for real-time forecasting. Many deep learning methods also struggle with high-dimensional spatiotemporal ocean data and experience error accumulation over longer forecasting periods. This study builds on our previously proposed Adaptive Next-Generation Reservoir Computing (Adaptive NVAR) framework, initially introduced and tested on synthetic dynamical systems, and extends it to ocean forecasting. We present a reduced-order forecasting framework that combines Singular Value Decomposition (SVD) with Adaptive NVAR to predict SST dynamics in the East Sea. SST fields are compressed into a low-dimensional representation using SVD, which extracts dominant modes of ocean variability. Adaptive NVAR models the temporal evolution of these latent states, and the predicted states are reconstructed into SST forecasts. We evaluate the framework using regional ocean datasets and compare it with the standard NG-RC/NVAR. Results show that Adaptive NVAR consistently achieves lower forecasting errors across multiple prediction horizons. In addition, SVD reduces computational complexity, resulting in a fast and scalable framework suitable for real-time ocean forecasting.

04.
arXiv (CS.CL) 2026-06-16

AthDGC: An Open Diachronic Greek Treebank with Indo-European Parallels

AthDGC ("Athens-PROIEL") is an open, end-to-end workflow and dataset. It is, to the best of our knowledge, the first openly licensed dependency-parsed treebank of Greek that spans eight diachronic periods, namely Archaic, Classical, Koine, Late Antique, Byzantine, Late Byzantine, Early Modern, and Modern Greek, under a single PROIEL XML 2.0 schema, with verse-level cross-alignment of the New Testament to Latin (Vulgate), Gothic (Wulfila), Old Church Slavonic (Marianus), and Classical Armenian. AthDGC builds on the PROIEL Treebank Family (Haug and Johndal 2008; Eckhoff et al. 2018), which established the schema and the Koine-Greek reference set for the project. Annotation uses the Stanford Stanza PROIEL-trained workflow; sentence-level alignment uses LaBSE, a multilingual sentence-embedding model; word-level alignment uses multilingual-BERT attention through the AwesomeAlign procedure. The v0.4 release provides curated samples and the open-source toolkit; the full annotated corpus partitions remain under v0.5 audit on the Greek national HPC. Quantitative scale, per-witness verse counts, and per-period annotated-row counts are reported in the v0.5 release notes, after the audit pass completes. Concept DOI: 10.5281/zenodo.20439182.

05.
arXiv (CS.AI) 2026-06-12

Echo2ECG: Enhancing ECG Representations with Cardiac Morphology from Multi-View Echos

arXiv:2603.08505v2 Announce Type: replace-cross Abstract: Electrocardiography (ECG) is a low-cost, widely used modality for diagnosing electrical abnormalities like atrial fibrillation by capturing the heart's electrical activity. However, it cannot directly measure cardiac morphological phenotypes, such as left ventricular ejection fraction (LVEF), which typically require echocardiography (Echo). Predicting these phenotypes from ECG would enable early, accessible health screening. Existing self-supervised methods suffer from a representational mismatch by aligning ECGs to single-view Echos, which only capture local, spatially restricted anatomical snapshots. To address this, we propose Echo2ECG, a multimodal self-supervised learning framework that enriches ECG representations with the heart's morphological structure captured in multi-view Echos. We evaluate Echo2ECG as an ECG feature extractor on two clinically relevant tasks that fundamentally require morphological information: (1) classification of structural cardiac phenotypes across three datasets, and (2) retrieval of Echo studies with similar morphological characteristics using ECG queries. Our extracted ECG representations consistently outperform those of state-of-the-art unimodal and multimodal baselines across both tasks, despite being 18x smaller than the largest baseline. These results demonstrate that Echo2ECG is a robust, powerful ECG feature extractor. Our code is accessible at https://github.com/michelleespranita/Echo2ECG.

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

Rethinking Reward Supervision: Rubric-Conditioned Self-Distillation

Post-training of reasoning language models is commonly driven by supervised distillation and reinforcement learning with verifiable rewards. Distillation often relies on chain-of-thought annotations that are expensive to obtain and may themselves be noisy, incomplete, or partially incorrect; even when the final solution is correct, an imperfect rationale can interfere with learning. Reinforcement learning with verified rewards, on the other hand, typically compresses evaluative feedback into a scalar signal, obscuring which aspects of a response should be improved. We propose Rubric-Conditioned Self-Distillation, a framework that incorporates rubrics as structured, fine-grained feedback for on-policy self-distillation. Our method conditions the teacher model on criterion-level rubrics and uses it to provide token-level guidance on the student's own sampled trajectories. This design avoids treating a single reference rationale as the sole supervision target. Instead, rubrics specify what a strong response should satisfy, enabling more fine-grained credit assignment over the reasoning process than scalar reward optimization. We instantiate this framework with a two-stage pipeline that first learns to generate task-specific rubrics and then trains a rubric-guided reasoner. We evaluate on a diverse suite of science reasoning benchmarks and results show that rubric-conditioned self-distillation effectively converts rubric-level criteria into token-level guidance over the reasoning process, surpassing GRPO by 1.0 points and OPSD by 0.9 points on average.

07.
arXiv (CS.AI) 2026-06-19

Execution-bound advisory automation for agentic AI: a reproducible AIBOM-driven CSAF-VEX framework

arXiv:2606.19390v1 Announce Type: cross Abstract: A protocol driven framework is presented that binds SBOM and AIBOM artefacts to deterministic environment capture and structured runtime telemetry. Exploitability is computed from declared artefacts, observed activation conditions, and enforced execution policies. CSAF VEX advisories are generated from combined static and runtime evidence, cryptographically signed, and validated through deterministic replay. Evaluation uses approximately 10000 component entries across synthetic Agentic AI workloads 50 to 5000 components, incorporating OSV, GitHub Advisory, KEV, and EPSS datasets.

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

An Explainable AI Assistant for Introductory Programming Education: Improving Feedback Reliability with Instructor-AI Collaboration

arXiv:2606.12425v1 Announce Type: cross Abstract: Active learning is widely recognized as an effective approach for improving learning outcomes in introductory programming courses. However, insufficient instructional support often limits students' access to timely, personalized feedback, which is crucial for mastering foundational programming concepts. Although recent advances in AI, particularly large language models, offer scalable opportunities for feedback, concerns about explainability and reliability remain. In this paper, we present an AI-driven classroom assistant that leverages an explainable AI model to analyze student code, map logical errors to instructor-identified misconceptions, and deliver instructor-authored feedback, thereby grounding reliability in instructor-defined pedagogical knowledge. To evaluate the effectiveness of our framework, we conducted an expert evaluation to examine its alignment with instructor-verified feedback and deployed the system in a classroom setting to assess students' perceptions of its usability. Results indicate that the assistant can provide accurate, instructor-verified feedback to students while fostering a positive experience.

09.
arXiv (CS.CL) 2026-06-24

Best Preprocessing Techniques for Sentiment Analysis

Sentiment analysis in Twitter datasets is important because it enables monitoring public opinion on products and analysis of political and social movements. One critical step is preprocessing: the automated processing of text for machine learning algorithms. Preprocessing plays a critical role in reducing noise and improving efficiency. However, little research has systematically examined the order in which preprocessing techniques are implemented. We find that, when accounting for order, spelling correction is the least impactful preprocessing technique, whereas tokenisation is the most impactful. Stemming and stop-word removal are interchangeable, and it is better to remove stop words without removing negation. The best order for applying the preprocessing techniques was tokenisation, text cleaning, stemming, and then stopword removal. Our results provide a systematic approach for practitioners to deploy preprocessing to improve model output without the costly preprocessing exploratory phase.

10.
arXiv (quant-ph) 2026-06-11

Global vs. Local Discrimination of Locally Implementable Multipartite Unitaries

arXiv:2509.10430v2 Announce Type: replace Abstract: We study single-shot distinguishability of locally implementable multipartite unitaries under Local Operations and Classical Communication (LOCC) and global operations. As unitary discrimination depends on both the choice of probing states and the measurements on the evolved states, we classify LOCC and global distinguishability into two categories: adaptive strategies, where probing states are chosen based on measurement outcomes from other subsystems, and restricted strategies, where probing states remain fixed. Our findings uncover three surprising features in the bipartite setting and establish new structural limits for unitary discrimination: (i) Certain pairs of unitaries are globally distinguishable with restricted strategies but indistinguishable under LOCC, even with adaptive strategies. (ii) There exist sets of four unitaries that are distinguishable via LOCC, yet remain globally indistinguishable with restricted strategies. (iii) Some sets of unitaries are globally indistinguishable under adaptive strategies, when probed with separable states, but become distinguishable via LOCC.

11.
arXiv (quant-ph) 2026-06-24

Thermodynamics of quantum processes: An operational framework for free energy and reversible athermality

arXiv:2510.12790v4 Announce Type: replace Abstract: We explore the thermodynamics of quantum processes (quantum channels) by axiomatically introducing the free energy for channels, defined via the quantum relative entropy with an absolutely thermal channel whose fixed output is in equilibrium with a thermal reservoir. This definition finds strong support through its operational interpretations in designated quantum information and thermodynamic tasks. We construct a resource theory of athermality for quantum processes, where free operations are Gibbs preserving superchannels and golden units are unitary channels with respect to absolutely thermal channel having fully degenerate output Hamiltonian. We exactly characterize the one-shot distillation and formation of quantum channels using hypothesis-testing and max-relative entropy with respect to the absolutely thermal channel. These rates converge asymptotically to the channel free energy (up to a multiplicative factor of half the inverse temperature), establishing its operational meaning and proving the asymptotic reversibility of the athermality. We show the direct relation between the resource theory of athermality and quantum information tasks such as private randomness and purity distillation, and thermodynamic tasks of erasure and work extraction. Our work connects the core thermodynamic concepts of free energy, energy, entropy, and maximal extractable work of quantum processes to their information processing capabilities.

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

CRC-Screen: Certified DNA-Synthesis Hazard Screening Under Taxonomic Shift

Authors:

arXiv:2605.00074v2 Announce Type: replace-cross Abstract: DNA-synthesis providers screen incoming orders by searching the requested sequence against curated hazard lists. We show that this baseline collapses to a 100% false-flag rate when the hazardous sequence comes from a taxonomic family absent from the reference set: under Conformal Risk Control's certified miss-rate constraint, a low-discrimination signal forces the threshold below the entire test-benign mass. We compose three signals derived from a synthesis order's public annotation: $k$-mer Jaccard similarity to known toxins, the trimmed-mean score of a five-LLM judge panel, and cosine similarity to clustered embedding centroids. Fused under a monotone logistic aggregator and calibrated by Conformal Risk Control, the resulting screener certifies $\mathbb{E}[\mathrm{FNR}] \le \alpha + \mathrm{TV}$, where the additive term is the calibration-to-test distribution shift under family holdout (a certified ceiling of 24-49% across folds). Across ten leave-one-taxonomic-family-out folds at $\alpha=0.05$ on UniProt KW-0800 reviewed toxins, the calibrated screener achieves 0% empirical test miss rate on every fold and 0% test false-flag rate on nine of ten folds. The bound's finite-sample slack $1/(n_{\mathrm{cal}}+1)$ caps the certifiable miss rate at 1.77% on our 200-hazard subsample; reaching procurement-grade $\alpha=10^{-3}$ requires an $18\times$ larger calibration set, which the full reviewed UniProt KW-0800 corpus is large enough to deliver. The binding constraint on certifiable DNA-synthesis screening is calibration data, not algorithms. Code: https://github.com/najmulhasan-code/crc-screen

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

Fusion of Pervasive RF Data with Spatial Images via Vision Transformers for Enhanced Mapping in Smart Cities

In this paper, we present a deep learning-based approach that integrates the DINOv2 architecture to improve building mapping by combining (possibly erroneous) maps from open-source platforms with pervasive radio frequency (RF) data collected from multiple wireless user equipments and base stations. Unlike prior methods, our approach leverages a vision transformer-based architecture to jointly process both RF and map modalities within a unified framework, effectively capturing spatial dependencies and structural priors for enhanced mapping accuracy. For the evaluation purposes, we employ a synthetic dataset co-produced by Huawei. To address the challenges associated with real-world data imperfections, we introduce controlled noise to its RF data so as to simulate real-world conditions. Additionally, we develop and train a model that leverages only aggregated path loss information to tackle the mapping problem. We measure the results according to three performance metrics: the Jaccard index (intersection over union, IoU), the Hausdorff distance, and the Chamfer distance. Our design achieves a macro IoU of 65.3%, significantly surpassing (i) the erroneous maps baseline, which yields 40.1%, (ii) an RF-only method from the literature, which yields 37.3%, and (iii) a non-AI fusion baseline that we designed which yields 42.2%. The comparative evaluation highlights the limitations of relying solely on RF data or on spatial data, as well as the effectiveness that AI can have on fusing data towards enhancing smart city mapping accuracy. We further validate our method on real-world data from the Oslo region, complementing the synthetic evaluation with a real deployment setting, where our best fusion model reaches 64.9% macro IoU. We additionally outline a strategy for deploying the model over larger areas by tiling the region with overlapping windows.

14.
arXiv (CS.LG) 2026-06-11

IAPO: Input Attribution-Aware Policy Optimization for Tool Use in Small Multimodal Agents

arXiv:2606.11652v1 Announce Type: new Abstract: This paper investigates reinforcement learning (RL) methods for improving tool-calling capabilities in multimodal small language model (SLM) agents. While existing works have explored various reward designs to improve agentic tool-calling ability, these approaches face inherent limitations for SLM training, especially under multimodal scenarios. First, many existing methods evaluate tool use correctness through exact matching against certain ground-truth or predefined formats. However, this assumption is often unsuitable for multimodal tasks, where multiple tool use paths may be valid and annotated tool trajectories are typically unavailable. Second, such sparse and brittle binary rewards provide little guidance on how to improve the underlying decision process, making them particularly difficult for multimodal SLM to learn from. To address these issues, we propose Input Attribution-Aware Policy Optimization (IAPO), an RL algorithm for improving tool use in multimodal SLM by aligning the model's attribution across input components with that of a stronger teacher. Experiments on Qwen2.5-VL-3B show that the proposed method improves visual question answering accuracy by an average of 3% across six test sets compared with existing visual tool use work, by helping the model attend to the most relevant input evidence.

15.
arXiv (CS.CV) 2026-06-18

Physics-IQ Verified

Video generative models ( VGMs) have become a new frontier that can be used not just for video generation but for a multitude of downstream tasks, including world modeling. To advance these tasks, a good video model must understand the physical reality of the world. Evaluating this understanding is an emerging field and has led to the Physics-IQ benchmark, which quantifies this explicitly by comparing model-generated videos to real-world videos of physical experiments. In this work, we present a systematic audit of the Physics-IQ benchmark, expose shortcomings and propose three solutions that sharpen how we can measure physical understanding of VGMs. Specifically, we improve prompt and ground-truth quality to reduce the influence of confounding factors and further introduce a sample-level scoring system that weights each sample and metric equally. Our resulting benchmark, Physics-IQ Verified, refines 57.6\% of all samples and improves over 34.8\% of prompts. In a comparison study using six image-to-video generative models, we observe moderate but meaningful ranking changes (Kendall's $\tau = 0.46$). We hope Physics-IQ Verified advances the community by providing a more reliable signal toward physically accurate VGMs. The code for the benchmark can be accessed at https://github.com/google-deepmind/physics-iq-benchmark

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

A Systematic Evaluation of Large Language Models for PTSD Severity Estimation: The Role of Contextual Knowledge and Modeling Strategies

Large language models (LLMs) are increasingly being used in a zero-shot (generative) fashion to assess mental health conditions, yet we have limited knowledge on what factors affect their accuracy. In this study, we use a clinical dataset of natural language narratives and self-reported PTSD severity scores from 1,437 individuals to comprehensively evaluate the performance of 11 state-of-the-art LLMs. To understand the factors affecting model's assessment accuracy, we systematically varied (i) contextual knowledge prompted to the models like subscale definitions, distribution summary, and interview questions, and (ii) modeling strategies including zero-shot vs few shot, amount of reasoning effort, model sizes, structured subscales vs direct scalar prediction, output rescaling and nine ensemble methods. Our findings indicate that (a) LLMs are most accurate when provided with detailed construct definitions and context of the narrative, even exceeding human raters agreement with self-reported scores; (b) increased reasoning effort leads to better estimation accuracy; (c) performance of open-weight models (Llama, DeepSeek) plateaus beyond 70B parameters while closed-weight (gpt-o3-mini, gpt-5) alternatives improve with newer generations; and (d) best performance is achieved when ensembling a supervised model with the zero-shot LLMs. Beyond agreement with self-reports, LLMs' estimates discriminated PTSD severity from depression, anxiety, and alcohol use, and prospectively predicted future mental healthcare expenditure. Together, these results suggest that contextual knowledge and modeling strategies meaningfully affect accuracy and clinical utility of LLM-based assessments of PTSD severity.

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

LAUKIN: A Multi-jurisdictional Common Law Contract Dataset

Multinational companies increasingly require cross-jurisdictional contract review, yet existing legal NLP datasets are largely restricted to a single jurisdiction. We introduce LAUKIN (Legal equivalence dataset of Australia, UK, and INdia), a dataset of clause pairs (AU-UK, UK-IN, IN-AU) labelled for boolean legal equivalence. We develop a novel multi-stage retrieval and reranking pipeline to construct the initial clause pair mapping, with a subset of clause pairs subsequently annotated by legal experts as Equivalent or Not Equivalent. The dataset comprises 14,727 clause pairs from 204 contracts across 8 agreement types, of which 3,000 are manually labelled: 900 train, 600 dev, and 1,500 test. We evaluate 12 models across 4 techniques, achieving a best macro-F1 of 65.11%, establishing LAUKIN as a challenging benchmark. Results reveal that, despite shared legal heritage, drafting conventions diverge significantly across jurisdictions, making cross-jurisdictional equivalence classification non-trivial. LAUKIN also includes 11,727 unlabelled training pairs to support future semi-supervised learning research in legal NLP.

18.
arXiv (quant-ph) 2026-06-11

A semi-definite programming formulation of the device-dependent guessing probability

arXiv:2606.12079v1 Announce Type: new Abstract: In quantum mechanics, a measurement applied to a state in general produces some amount of intrinsic randomness. This is not only a fundamental feature of the theory, but is also at the basis of any quantum process to generate random numbers. The simplest of such processes consists of a single, fully charaterized, measurement acting on a single, fully characterized, state. Unfortunately, no general method to estimate the intrinsic randomness produced in such setups is known. In this work, we address this issue by presenting a semidefinite programming formulation of the maximum probability with which an adversary, Eve, can guess the outcomes of characterized but untrusted prepare-and-measure setups. We then present several applications of this construction. First, we apply our method to a variety of specific setups, allowing us both to benchmark the approach and, more importantly, to determine the exact amount of certifiable randomness in scenarios where only upper bounds were previously available. Then, we show that the presence of entanglement between the device preparing the state and the measurement strictly increases Eve's predictive power, already in the most elementary setup of a binary measurement acting on a qubit state.

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

Revisiting Active Speaker Detection: An In-the-Wild Benchmark for Generalization and Robustness

We present UniTalk, a novel dataset emphasizing challenging scenarios to enhance model generalization for the task of active speaker detection (ASD). Previously established benchmarks such as AVA predominantly comprise old movies and thus exhibit significant domain gaps with real-world video. In contrast, UniTalk covers diverse video types reflecting challenging real-world conditions, including underrepresented languages, noisy backgrounds, and crowded scenes, while being on par with AVA in scale. Extensive evaluations reveal that ASD remains unsolved under realistic conditions: state-of-the-art models near-perfect on AVA fail to reach saturation on UniTalk. Conversely, models trained on UniTalk generalize better to modern in-the-wild datasets including Talkies and ASW. UniTalk thus establishes a new benchmark for ASD, providing researchers with a valuable resource for developing and evaluating versatile and resilient models.

20.
arXiv (CS.AI) 2026-06-16

Dual-Granularity Orthogonal Disentanglement for Generalizable Audio Deepfake Detection

arXiv:2606.16532v1 Announce Type: cross Abstract: Audio deepfake detectors often fail to generalize across speakers, as they learn speaker-identity features rather than synthesis artifacts, known as implicit identity leakage. Existing methods address this but incur architectural complexity or training instability. This paper proposes a dual-granularity orthogonal disentanglement framework enforcing feature independence at two levels: sample-level cosine orthogonality captures directional decorrelation, while batch-level cross-covariance regularization eliminates linear correlations across embedding dimensions. A curriculum disentanglement schedule progressively strengthens the orthogonality constraint without auxiliary networks or adversarial dynamics. Experiments on ASVspoof 2019 LA, ASVspoof 2021 DF, and In-the-Wild datasets demonstrate that the proposed method achieves 1.35%, 7.88%, and 21.58% equal error rates (EER), respectively, surpassing gradient reversal disentanglement by 2.60% absolute on cross-dataset transfer.

21.
arXiv (quant-ph) 2026-06-24

Exceptional by Design: Long-Range Hopping as a Knob for Exceptional Point Control

arXiv:2606.24705v1 Announce Type: new Abstract: Exceptional points are degeneracies unique to non-Hermitian systems, where eigenvalues and eigenvectors coalesce, rendering the Hamiltonian defective. We investigate the exceptional-point structure and topological properties of a generalized non-Hermitian Rice-Mele model with balanced gain and loss, as well as next-nearest-neighbor hopping. The system hosts only second-order exceptional points under both periodic and open boundary conditions. Under periodic boundary conditions, the exceptional points in parameter space lie on lines and ellipses that are independent of the next-nearest-neighbor hopping, since the latter enters the bulk Hamiltonian only as an identity contribution. Under open boundary conditions, this independence is broken: the next-nearest-neighbor hopping not only shifts the energy of existing exceptional points but also generates new ones, with a specific condition signaling a topological gap closing observed only in the open-boundary spectrum. At special parameter points, multiple simultaneous second-order exceptional points yield degenerate configurations whose degeneracy grows with system size. Exceptional point locations are identified numerically via the condition number of the eigenvector matrix and confirmed by Jordan decomposition. The topological phase diagram, computed via a winding number framework for non-Hermitian systems without symmetry protection, reveals sectors with zero, one, and two edge states; the bulk-boundary correspondence is confirmed, and the non-Hermitian skin effect is absent.

22.
PLOS Computational Biology 2026-06-17

Combining machine learning and iterative experiments to keep pace with emerging viral variants of concern

by Thomas Sheffield, Ryan C. Bruneau, Stephen Won, Kenneth L. Sale, Brooke Harmon, Le Thanh Mai Pham Modeling and predicting viral mutations before they emerge plays a crucial role in pandemic preparedness, enabling the early identification of emerging variants of concern (VOCs) and guiding timely updates to vaccines, diagnostic tests, and therapeutic strategies. However, existing machine learning models and large-scale experiments lose their predictive power as viral variants evolve further from the original strains in sequence space. Here, we present a scalable framework that integrates random forest and neural network machine learning models with targeted high-throughput experimentation to anticipate and evaluate emerging SARS-CoV-2 receptor-binding domain (RBD) variants. Using public datasets, we trained predictive models for binding to human Angiotensin-converting enzyme 2 (ACE2), RBD expression, and antibody escape, and refined these models through iterative integration of experimental data focused on over 200 variants derived from wild-type (WT) and Omicron strains. Through an indirect transfer learning approach, our machine learning models achieved high accuracy having correlation coefficients of up to 0.79 for antibody binding. The models were also generalizable across diverse antibody types including heavy-chain-only antibodies (HCAbs) by encoding complementarity-determining regions (CDRs) as input features. This dynamic approach enables rapid assessment of emerging variants, facilities prioritization of the therapeutic strategies, and supports a proactive, data-driven response to evolving viral threats.

23.
arXiv (CS.CL) 2026-06-15

Trusted Uncertainty in Large Language Models: A Unified Framework for Confidence Calibration and Risk-Controlled Refusal

Deployed language models must decide not only what to answer but also when not to answer. We present UniCR, a unified framework that turns heterogeneous uncertainty evidence including sequence likelihoods, self-consistency dispersion, retrieval compatibility, and tool or verifier feedback into a calibrated probability of correctness and then enforces a user-specified error budget via principled refusal. UniCR learns a lightweight calibration head with temperature scaling and proper scoring, supports API-only models through black-box features, and offers distribution-free guarantees using conformal risk control. For long-form generation, we align confidence with semantic fidelity by supervising on atomic factuality scores derived from retrieved evidence, reducing confident hallucinations while preserving coverage. Experiments on short-form QA, code generation with execution tests, and retrieval-augmented long-form QA show consistent improvements in calibration metrics, lower area under the risk-coverage curve, and higher coverage at fixed risk compared to entropy or logit thresholds, post-hoc calibrators, and end-to-end selective baselines. Analyses reveal that evidence contradiction, semantic dispersion, and tool inconsistency are the dominant drivers of abstention, yielding informative user-facing refusal messages. The result is a portable recipe of evidence fusion to calibrated probability to risk-controlled decision that improves trustworthiness without fine-tuning the base model and remains valid under distribution shift.

24.
arXiv (CS.AI) 2026-06-19

Dual-Agent Framework for Cross-Model Verified Translation of Natural-Language Protocols into Robotic Laboratory Platform

arXiv:2606.20120v1 Announce Type: cross Abstract: Biological experiment protocols are written in natural language, whereas automation systems rely on predefined control commands, creating a semantic gap that limits autonomous execution. Microplate-based automatic experiments are particularly challenging due to the need to simultaneously control well mapping, sample-reagent combinations, replicate placement, and parallel dispensing. This study proposes an agent-based protocol translation framework that converts natural-language microplate-based protocols into executable control commands for a robotic laboratory platform. A Parser Agent formalizes the natural-language protocol into a structured representation, and a rule-based mapping engine deterministically incorporates the operational constraints of the robotic laboratory platform to generate device-level control commands. A heterogeneous LLM Validation Agent verifies completeness, parameter accuracy, and execution order, and triggers a self-correction loop with structured feedback when errors are detected. A sweep involving 7 Parsers and 3 Validators on randomly selected ELISA protocols evaluates how model scale and Validator type affect translation accuracy and pass rates under cross-model verification. The accuracy-latency trade-off is further verified by comparing the rule-based mapping of the proposed framework with LLM end-to-end direct mapping. Finally, Bradford assay-based protein quantification using a microplate was demonstrated on a robotic laboratory platform, validating end-to-end autonomous execution from natural-language protocols to real-world experiments. The proposed framework provides a flexible approach to narrowing the semantic gap between natural-language protocols and microplate-based self-driving laboratories.

25.
arXiv (CS.CV) 2026-06-19

Cinematic Compositing Using Character-Environment-Harmonized Video Generation Models

Cinematic compositing aims to integrate green-screen characters into novel environments while maintaining physical and photometric realism. Previous methods often fail to capture the complex bidirectional interactions between characters and their surroundings, which we characterize as Character-to-Environment (C2E) physical interaction and Environment-to-Character (E2C) lighting harmonization. To address this, we propose an end-to-end video diffusion framework that jointly models C2E and E2C interactions, specifically handling the challenges of interactive props. Our approach introduces a tri-mask-guided architecture with RGB-D joint denoising to ensure physically consistent interactions among the character, props, and environment. We further develop an efficient prior-driven data curation pipeline to construct high-quality relighting pairs without expensive rendering. Finally, a reference-conditioned mechanism enables controllable environment synthesis and precise prop replacement. Extensive experiments demonstrate that our framework significantly outperforms existing methods in cinematic-quality dynamic video compositing.