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01.
arXiv (CS.LG) 2026-06-15

Learning the Context of Errors: Black-Box Online Adaptation of Time Series Foundation Models

arXiv:2606.14222v1 Announce Type: new Abstract: The rapid evolution of Time Series Foundation Models (TSFMs) has advanced zero-shot forecasting across diverse domains. Inspired by the current form of Large Language Models, future TSFMs may be offered as commercialized, closed-source API services. However, many existing online adaptation methods still rely on white-box access for parameter fine-tuning or gradient backpropagation. This paradigm mismatch raises a question: In black-box online adaptation for TSFMs, what should we learn? We answer this with an insight: the predictive errors of the base model are conditioned on both the input and output of the base model (i.e., the context of errors). To validate this insight, we propose ORCA (Online Residual Contextual Adaptation). We conduct extensive experiments across 5 state-of-the-art TSFMs and 8 datasets to demonstrate the effectiveness of our approach. Furthermore, through ablation studies, we quantitatively analyze the impact of different adapter learning hypotheses on the final adaptation performance in black-box online adaptation. Code available at https://github.com/Fifthky/ORCA.

02.
arXiv (CS.CL) 2026-06-16

Revisiting the Systematicity in Negation in the Era of In-Context Learning

Understanding the meaning of negated sentences remains one of the challenges for language models, even in the era of large language models (LLMs). We analyze systematicity regarding LLM understanding of negation from two perspectives: behavioral systematicity and representational systematicity. For behavioral systematicity, we confirm that through demonstrations and in-context learning, LLMs can recognize negation expressions and scope within sentences to some extent, but they fail to achieve perfect performance. In particular, the difficulty of the negation scope recognition for models varies depending on the output format. For representational systematicity, we analyze the extent to which function vectors can be robustly constructed from in-context examples for tasks that are essential to understanding negation. The experiments suggest that while function vectors can be composed for negation cue extraction tasks, extracting function vectors for recognizing scope is more challenging.

03.
arXiv (CS.AI) 2026-06-16

Cognitive Debt: AI as Intellectual Leverage and the Dynamics of Systemic Fragility

Authors:

arXiv:2606.15078v1 Announce Type: new Abstract: We develop a formal theory of cognitive debt: the stock of unverified reasoning obligations that accumulates when individuals use AI as a substitute rather than a complement for first-principles cognition. The model features two state variables per agent, cognitive capital and cognitive debt, and a multiplicative production technology in which cognitive capital functions as collateral that determines the return to AI adoption. We establish six propositions. Rational agents incur positive cognitive debt because the costs are deferred, partially external, and masked by short-run productivity gains. Tranquil periods lower subjective risk assessments, raise AI substitution intensity, and compound leverage, generating a cognitive Minsky moment in which subjective risk falls while true systemic fragility rises. Expected crisis losses are convex in aggregate leverage. Post-crisis, output-target pressure can produce a false-correction loop in which agents patch AI failures with more AI. The decentralised equilibrium over-adopts substitutive AI relative to the social optimum because of systemic risk, cognitive public goods, and arms-race externalities. In a two-type heterogeneous-agent economy, high-cognitive-capital agents adopt AI more intensively and may eventually erode their unaided cognitive capital below that of initially lower-skilled agents.

04.
arXiv (quant-ph) 2026-06-11

Optimizing Encoder Circuits of Entanglement-Assisted Quantum LDPC Codes via Beam Search

arXiv:2606.11468v1 Announce Type: new Abstract: Entanglement-assisted (EA) quantum QC-LDPC codes offer strong error-correction capabilities with structured parity-check matrices, but their practical use depends on efficient encoder circuits and the availability of pre-shared Bell pairs (ebits). In all encoder implementations based on the stabilizer formalism, the dominant contribution to this complexity comes from the use of controlled gates. In this paper, we adopt the Sharma-Kumar-Garani (SKG) encoder construction. We formulate the encoder optimization as a search over GF(2) row operations that decompose the binary matrix derived from its CNOT sub-sequence. We solve this problem using a beam search algorithm guided by a Hamming-distance heuristic. For the tested EA quantum QC-LDPC code families, the proposed method achieves CNOT-count reductions of 7.3-34.0% relative to the SKG baseline encoder. The optimized circuits also yield lower CNOT counts than Patel-Markov-Hayes synthesis on all tested instances and are verified by stabilizer-tableau simulation. These results show that substantial encoder simplification is possible for structured EA QC-LDPC codes.

05.
bioRxiv (Bioinfo) 2026-06-21

SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning

Genome assembly is a computational pipeline designed to reconstruct chromosomes from small sequencing reads. Following their assembly, contiguous sequences (contigs) are arranged into chromosome-long sequences during scaffolding. Hi-C, a long-range linkage information between regions of the genome widely used in recent large sequencing projects, is often required to correctly order contigs. Several tools have been developed to automate this task following either statistical or deep-learning approaches. Statistical approaches summarise 2D Hi-C matrices into contact densities across sequences, thus ignoring informative visual patterns. The sole existing deep-learning tool uses a transformer-based computer vision model to correct the assembly. It has been trained on several species and uses Hi-C matrices directly. Yet it comes as a supplementary step in the scaffolding process, introducing extra computation time, and has been trained on a dataset that might contain labelling errors, which could provide sub-optimal results. We propose SPA-C, an hybrid pipeline combining the strengths of both approaches. Linkage prediction is handled with a frugal CNN-based model and a graph-solving algorithm is used to generate the scaffolds. Through our input's design, the model is able to both correct errors within assemblies and link contigs, leveraging small, local Hi-C contact matrices. We handled low-complexity regions that might induce erroneous predictions using an external tool, improving the overall accuracy of generated assemblies. On a benchmark of six various genomes and four standard metrics, SPA-C outperformed four out of four state-of-the-art methods while achieving comparable start-to-end computation time.Python and Bash scripts are available on GitHub (https://github.com/SPA-C/SPA-C.git) and Zenodo (https://doi.org/10.5281/zenodo.19000361).

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

PRISM: Perception Reasoning Interleaved for Sequential Decision Making

arXiv:2605.05407v2 Announce Type: replace Abstract: Scaling LLM-based embodied agents from text-only environments to complex multimodal settings remains a major challenge. Recent work identifies a perception-reasoning-decision gap in standalone Vision-Language Models (VLMs), which often overlook task-critical information. In this paper, we introduce PRISM, a framework that tightly couples perception (VLM) and decision (LLM) through a dynamic question-answer (DQA) pipeline. Instead of passively accepting the VLM's description, the LLM critiques it, probes the VLM with goal-oriented questions, and synthesizes a compact image description. This closed-loop interaction yields a sharp, task-driven understanding of the scene. We evaluate PRISM on the ALFWorld and Room-to-Room (R2R) benchmarks. We show that: (1) PRISM significantly outperforms state-of-the-art image-based models, (2) our Interactive goal-oriented perception pipeline yields systematic and substantial gains, and (3) PRISM is fully automatic, eliminating the need for handcrafted questions or answers.

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

FlowBender: Feedback-Aware Training for Self-Correcting Conditional Flows

Conditional diffusion and flow models routinely fail to satisfy the very constraints that define their task. For instance, a depth-conditioned model often produces images whose re-extracted depth disagrees with the input, even though the forward operator–the depth predictor defining the constraint–is available during both training and inference. Existing approaches generally fall into two categories: supervised models that treat the conditioning signal as a static cue and ignore alignment information at inference, and guidance-based methods that consult it through hand-tuned linear updates, typically trading fidelity to the condition against the plausibility of the generated sample. We argue that the fundamental gap in both paradigms is that the model is never trained to utilize its own alignment error. We introduce FlowBender, a closed-loop framework that treats this error as a first-class input, training the network to learn a correction policy conditioned on inference-time feedback. At each step, an unguided look-ahead pass estimates the clean signal, a task-specific deviation is computed via the forward operator, and a refinement pass consumes this signal to produce a corrected velocity. We propose several variants of FlowBender, including a gradient-based formulation for differentiable operators and a zero-order variant for non-differentiable settings such as JPEG compression. For efficient sampling, we introduce a prior-step shortcut that enables closed-loop correction at a minimal additional computational cost. Across image-to-image translation, restoration, and 3D mesh texturing, FlowBender consistently outperforms standard supervised baselines, alignment-loss-augmented training, and state-of-the-art inference-time guidance, improving fidelity and plausibility simultaneously rather than trading them against each other. Project page: https://flow-bender.github.io/

08.
arXiv (CS.CL) 2026-06-16

ttda704 at SemEval-2026 Task 6: Structured Chain-of-Thought Prompting for Political Evasion Detection

This paper describes our system for SemEval-2026 Task 6, which addresses the classification of political evasion strategies in English question-answer pairs extracted from U.S. presidential interviews. We systematically compare two distinct paradigms: (1) Parameter-Efficient Fine-Tuning of Qwen3 models (4B-32B) using QLoRA, enhanced with tiered upsampling and weighted cross-entropy loss to address severe class imbalance, and (2) structured Chain-of-Thought (CoT) prompting of reasoning-capable API models, namely DeepSeek-V3.2 and Grok-4-Fast. Our evaluation demonstrates that structured CoT prompting of reasoning-enabled models substantially outperforms our baseline parameter-efficient fine-tuning implementation in absolute Macro F1. Our best system, Grok-4-Fast with extended reasoning and few-shot hierarchical CoT prompting, achieves a Macro F1 of 0.5147 on Subtask 2 (9-class evasion) and 0.7979 on Subtask 1 (3-class clarity), ranking 8th out of 33 teams on Subtask 2 and 13th out of 41 teams on Subtask 1 on the official leaderboard. Furthermore, our ablation studies reveal key insights into effective prompt design for evasion detection: presenting labels within a hierarchical taxonomy helps structure model reasoning, while few-shot exemplars provide task calibration. However, the strongest prompt variants are not statistically distinguishable in Macro F1, and explicitly enabling extended reasoning modes yields substantial performance gains by facilitating the multi-step pragmatic analysis required to detect evasive intent.

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

APEX: Adaptive Principle EXtraction A Three-Layer Self-Evolution Framework for Production AI Agents

arXiv:2606.15363v1 Announce Type: new Abstract: Self-improvement in AI agents has emerged as a key research frontier: systems that modify their own prompts, workflows, and decision rules based on accumulated operational experience. The state-of-the-art Self-Harness framework [1] achieves 14–21% improvement on Terminal-Bench-2.0 by mining failure clusters and patching the agent harness. However, Self-Harness optimises only one dimension – the prompt harness – leaving behavioural principles and workflow topology unchanged. We propose APEX (Adaptive Principle EXtraction), a three-layer co-evolution framework that simultaneously evolves: (L1) the harness via failure-mode patching, (L2) behavioural principles via success-trace distillation [2], and (L3) the agent workflow topology via structural fitness-based selection [6]. We implement APEX on Joe [13], a production-grade super AI Agent built on NVIDIA Nemotron and designed as an Edge AI Agent Factory for the NVIDIA Agent Challenge 2026, managing a 15-node compute fleet using 114 real task traces collected over 18 days. APEX achieves an APEX Health Score of 0.570 (+90% vs. baseline 0.300) in a single evolutionary run, distilling 6 novel reusable principles and selecting a research-first workflow topology scoring 0.900 (+20%). Our results demonstrate that multi-dimensional co-evolution substantially outperforms single-axis harness optimisation, at a cost of only 4 LLM calls (~270 s) on a local qwen2.5-coder:32b instance.

10.
bioRxiv (Bioinfo) 2026-06-12

PeptiDIA: A Machine Learning Framework for Enhanced Peptide Identification in Fast-Gradient Data-Independent Acquisition Proteomics

Data-independent acquisition (DIA) mass spectrometry has become increasingly prevalent in proteomics as advances in instrumentation, chromatography, and computational analysis have enabled robust proteome identification across complex biological samples. However, analytical depth achieved with fast chromatographic gradients remains lower than that obtained using long-gradients, reflecting a throughput-depth trade-off. Here, we present PeptiDIA, a machine learning framework that enhances peptide identification in fast-gradient DIA data by leveraging paired fast and long-gradient acquisitions from identical samples. PeptiDIA processes DIA-NN outputs generated at relaxed false discovery rate thresholds to obtain expanded candidate peptide pools and trains gradient-boosted decision tree models using long-gradient identifications as reference labels. The model integrates DIA-NN features with engineered peptide descriptors and applies isotonic regression to calibrate probabilities, enabling controlled peptide recovery relative to the long-gradient reference. Applied to human and murine datasets spanning six tissues acquired on an Orbitrap Exploris 480, PeptiDIA increased peptide identifications by 25-34% at 1% target reference-discordance rate (RDR) and increased the number of protein groups containing at least one rescued peptide by 15-17%. Overall, PeptiDIA improves the identification depth of fast-gradient DIA-NN workflows without altering acquisition strategies. The framework is available as a web application and command-line tool at https://github.com/Jordano700/PeptiDIA.

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

ArFake: A Robust Framework for Multi-Dialect Arabic Speech Spoofing Detection Benchmark

With the rise of generative text-to-speech models, distinguishing between real and synthetic speech has become challenging, especially for Arabic that have received limited research attention. Most spoof detection efforts have focused on English, leaving a significant gap for Arabic and its many dialects. In this work, we introduce the first multi-dialect Arabic spoofed speech dataset. To evaluate the difficulty of the synthesized audio from each model and determine which produces the most challenging samples, we aimed to guide the construction of our final dataset either by merging audios from multiple models or by selecting the best-performing model, we conducted an evaluation pipeline that included training classifiers using two approaches: modern embedding-based methods combined with classifier heads; classical machine learning algorithms applied to MFCC features; and the RawNet2 architecture. The pipeline further incorporated the calculation of Mean Opinion Score based on human ratings, as well as processing both original and synthesized datasets through an Automatic Speech Recognition model to measure the Word Error Rate. Our results demonstrate that FishSpeech outperforms other TTS models in Arabic voice cloning on the Casablanca corpus, producing more realistic and challenging synthetic speech samples. However, relying on a single TTS for dataset creation may limit generalizability.

12.
PLOS Computational Biology 2026-06-08

Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings

by Julia Pilarski, Tanja Stadler, Sophie Seidel Multicellular organisms develop from a single cell by repeated rounds of cell division, differentiation, and death, which can be represented as a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking the ancestry of individual cells as populations grow and change over time. However, accurate reconstruction of the cell phylogeny and quantification of the corresponding phylodynamic parameters – cell division, differentiation, and death rates – from this tracking data remains challenging and needs to be systematically evaluated. We perform simulations and assess, using the Bayesian framework, the joint inference of time-scaled cell phylogenies and phylodynamic parameters from CRISPR lineage recordings with random or sequential edits. Principally, we characterize the inference improvements as the recorder capacity increases. We observe more accurate phylogenetic reconstruction from sequential compared to random recordings, but no substantial improvement in phylodynamic inference when using the additional information contained in the order of edits. Overall, we find that CRISPR lineage recordings carry a strong signal on the rates of cell division when appropriate models are used. However, we detect biases in the inferred rates of cell division and death under phylodynamic model misspecification, i.e., when fitting classic memoryless birth-death processes to synchronous cell divisions. Moreover, for scenarios when cells differentiate into distinct types, we demonstrate that Bayesian phylodynamic analysis of sparse end-point measurements can resolve these cell differentiation trajectories by lineage and time. Under prototypical dynamics, we recover cell type-specific division and death rates, and cell type transition rates in over 80% of simulations. Overall, this simulation study explores how much information on cellular development can be extracted from state-of-the-art genetic lineage tracing data using phylogenetic and phylodynamic methodology.

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

Detecting Hidden ML Training With Zero-Overhead Telemetry

arXiv:2606.19262v1 Announce Type: new Abstract: Hardware-enabled monitoring of GPU workloads underpins many proposals for AI compute governance, but if developers can defeat monitoring mechanisms, such schemes are unworkable. We evaluate the adversarial robustness of GPU workload classification using only zero-overhead, privacy-preserving NVML telemetry: content-agnostic signals that observe physical effects of computation without accessing model weights, training data, or hyperparameters. Across 5 rounds of monitor-evader iteration, we evaluate 20 evasion strategy families on 9 GPU models spanning 4 architecture generations. We develop a classifier that achieves 98.2% binary accuracy at identifying training workloads across the whole corpus, and 43-87% accuracy against the most challenging unexpected workloads even when they are adversarially disguised.

14.
arXiv (CS.AI) 2026-06-19

Policy-aware Vector Search: A Vision for Fine Grained Access Control in Vector Databases

arXiv:2606.19803v1 Announce Type: cross Abstract: Vector databases are increasingly used in security sensitive contexts with Retrieval Augmented Generation and organizational AI pipelines; however, their security capabilities remain limited. Specifically, Fine-grained Access Control (FGAC) which is required to ensure that data access adheres to user-specific policies is not fully supported in modern vector databases. Unlike relational databases, vector databases combine structured and unstructured attributes to provide semantic, approximate query results, which complicates FGAC implementation. This creates an inherent tension between enforcing FGAC policies correctly, achieving high ANN search recall and maintaining low query latency. In this paper, we present a vision for Policy-aware Vector Search by formalizing the FGAC policy model in vector databases as well as the enforcement problem. We compare various enforcement strategies, present preliminary findings, and identify key open challenges for future research in policy-aware vector search.

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

Quantum Algorithm for Open-System Battery Cathodes by Modeling Multiple Strongly Coupled Holstein Polarons with Chain-Mapped Caldeira-Leggett Dynamics

arXiv:2606.16017v1 Announce Type: new Abstract: Cathode lithiation occupies a chemical regime of tightly localized orbitals, narrow bandwidths, and strong electron-lattice coupling. The defining electrochemical observables (open-circuit voltage and differential capacity) are open-system, reservoir-equilibration quantities that closed-Hamiltonian quantum simulation cannot produce, set by exchange with electron, Li$^+$, and phonon baths. We present a fault-tolerant quantum algorithm that recovers them through a unitary chain-mapped Caldeira-Leggett embedding, rendering the baths Trotterizable. The resulting fourth-order Trotter step has a T-gate count polynomial in system size, validating its open-system dynamics against hierarchical equations of motion (HEOM) at strong coupling and the Lindblad limit at weak coupling. For single-carrier olivine LiFePO$_4$, a single voltage anchor on an otherwise DFT-fixed Hamiltonian places the differential-capacity peak within the $\pm5$ mV reproducibility of the experimental plateau. For multi-carrier spinel LiMn$_2$O$_4$, whose $1{:}1$ Mn$^{3+}$/Mn$^{4+}$ filling makes the inter-site Coulomb repulsion dynamically active, the same kernel yields a two-plateau voltage curve with a $125$ mV split, within $17\%$ of the observed $150$ mV. We deliver an end-to-end fault-tolerant resource estimate for such a multi-carrier, three-reservoir observable: $368$ logical qubits and $\sim3\times10^5$ T-gates per step, or $\sim1.7\times10^{12}$ T-gates for a full voltage curve (parallelizable over $\sim10^3$ trajectories), leaving the production-scale dynamical run as a milestone for future hardware. The same kernel reproduces macroscopic quantum coherence, two-band superconductivity, and the Mikheyev-Smirnov-Wolfenstein resonance without modification, placing dynamical battery chemistry and similar Hamiltonians within scope for fault-tolerant quantum simulation.

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

Stringalign: Moving beyond summary statistics with a transparent Unicode-aware tool for evaluating automatic transcription models

Comparing text strings is crucial when evaluating and understanding the performance of various text processing tasks such as document recognition and audio transcription. With an increasingly complex landscape of AI-based handwritten text recognition (HTR), optical character recognition (OCR) and automatic speech recognition (ASR) models, there is a need for tools that facilitate evaluation in a flexible and reproducible way. This paper presents Stringalign, a Python library designed to simplify the evaluation process for automatic transcription projects and facilitate transparent evaluation. Stringalign's tools to examine and visualise both the rate of errors and the types of errors a model makes, give insights into possible improvements and help inform model selection for a particular task. Widely used string comparison metrics, such as the character and word error rates (CER and WER), although useful, can be ambiguous due to varying definitions of what constitutes a character and a word. Stringalign addresses this challenge by ensuring all preprocessing (i.e. normalisation and tokenisation) is transparent and easily replicable, and by providing tools to move beyond summary statistics and analyse common model errors. Moreover, Stringalign adheres to FAIR (Findable, Accessible, Interoperable, and Reusable) principles for research software while staying lightweight and easy to adapt into researchers existing workflows. In this paper, we discuss challenges with character and word level string comparisons and show through examples that where existing tools can yield opaque and sometimes confusing results, Stringalign provides an easy-to-use and unambiguous alternative.

17.
arXiv (quant-ph) 2026-06-11

Controlled ion-ion interactions and cavity-enhanced emission of a coherent dinuclear Eu$^{3+}$ complex

arXiv:2606.11947v1 Announce Type: new Abstract: Molecular rare-earth-ion complexes offer unique opportunities for quantum technologies by combining the intrinsic coherence properties of rare-earth ions with chemically tunable molecular environments. A crucial capability is the realization of multi-qubit architectures with defined qubit couplings to enable two-qubit quantum gates. Here, we investigate the optical coherence properties and excitation-induced interactions of two Eu$^{3+}$-based molecular complexes, comparing a mononuclear reference system with a dinuclear analogue in which two Eu$^{3+}$ ions are positioned at a well-defined intramolecular distance of about 7 Angstrom. Using cryogenic ensemble spectroscopy, including spectral hole burning, free-induction decay, and photon echo measurements at temperatures down to 100 mK, we demonstrate long optical coherence times $T_{2,o}$ of up to 9 $\mu$s. As a key step toward scalable multi-qubit architectures, a control-target sequence was implemented to probe conditional ion-ion interactions, revealing a stronger interaction-induced dephasing in the dinuclear complex. Finally, we show the integration of the dinuclear complex into a fiber-based optical microcavity, and observe an 380-fold emission enhancement of the $\mathrm{}^5\mathrm{D}_0\rightarrow\mathrm{}^7\mathrm{F}_0$ transition. Together, these results position molecular rare-earth complexes as versatile and chemically tunable building blocks for scalable quantum technologies.

18.
arXiv (CS.AI) 2026-06-12

A Zero-shot Generalized Graph Anomaly Detection Framework via Node Reconstruction

arXiv:2606.12673v1 Announce Type: cross Abstract: Cross-domain graph anomaly detection (GAD) aims to identify abnormal nodes in unseen target graphs, showing strong potential in real-world applications with heterogeneous graph data. However, existing methods often depend on dataset-specific feature semantics and structural patterns, which limits their ability to generalize across different domains. To address this challenge, we propose AlignGAD, a zero-shot generalized graph anomaly detection framework. Our framework is built upon three key components: a Global Unification Module that aligns heterogeneous node features and normalizes graph signals in the spectral domain; a Clustering Module that constructs cluster-aware graph views to capture group-level abnormal patterns; and a Node Discrepancy Scoring Module that measures reconstruction discrepancy and aggregates anomaly evidence from different graph views. Experiments on multiple real-world datasets demonstrate the effectiveness of AlignGAD under the zero-shot GAD setting.

19.
arXiv (CS.LG) 2026-06-12

Kareus: Joint Reduction of Dynamic and Static Energy in Large Model Training

arXiv:2601.17654v2 Announce Type: replace Abstract: The computing demand of AI is growing at an unprecedented rate, but energy supply is not keeping pace. As a result, energy has become an expensive and contended resource that requires explicit management and optimization. Although recent works have made significant progress in large model training optimization, they focus on optimizing either dynamic or static energy consumption. We find that fine-grained kernel scheduling and frequency scaling jointly and interdependently impact both dynamic and static energy consumption. Based on this finding, we design Kareus, a training system that pushes the time-energy tradeoff frontier by optimizing both aspects. Kareus decomposes the intractable joint optimization problem into local, partition-based subproblems. It then uses a multi-pass multi-objective optimization algorithm to find execution schedules that push the time-energy tradeoff frontier. Compared to the state of the art, Kareus reduces training energy by up to 28.3% at the same training time, or reduces training time by up to 27.5% at the same energy consumption.

20.
arXiv (CS.AI) 2026-06-18

From Specification to Execution: AI Assisted Scientific Workflow Management

arXiv:2606.18425v1 Announce Type: cross Abstract: Scientific workflow management systems (WMS) support scalable and reproducible execution of complex pipelines, but workflow design, implementation, and debugging remain largely manual and require significant expertise. Recent approaches using large language models (LLMs) show promise for workflow generation from natural language, but often rely on direct code synthesis, which limits transparency, reproducibility, and integration with workflow systems. We present an AI-assisted approach to scientific workflow management that combines specification-driven workflow generation, automated debugging, and distributed execution. The method introduces a structured specification phase that separates workflow intent, design, and implementation, allowing validation prior to code generation. We also develop an LLM-based debugging agent that diagnoses and resolves failures across multiple system layers. To support distributed execution and user interaction, we integrate Pegasus, a widely used WMS, with a Model Context Protocol (MCP) layer, providing a unified interface for workflow submission, monitoring, and control. We evaluate the approach using a federated learning workflow for medical imaging, chosen for its parallel, iterative, and dependency-intensive structure. The system generated and executed large-scale workflows with thousands of jobs, reduced debugging effort, and allowed non-expert users to construct workflows with expert-level design patterns. These results indicate that end-to-end AI-assisted workflow generation and execution is feasible, and point toward AI-driven platforms for managing the scientific workflow lifecycle.

21.
arXiv (CS.CV) 2026-06-18

AMALIA-VL: A Native European Portuguese Open-Source Vision and Language Model

Large Vision and Language Models (LVLMs) have advanced rapidly, yet European Portuguese (pt-PT) remains systematically underserved by existing open-source multimodal models, which either conflate it with Brazilian Portuguese or severely under-represent it in their training data mixes. We introduce AMALIA-VL, the first open-source instruction-tuned LVLM built natively for pt-PT, pairing a high-resolution vision encoder with dynamic image tiling and a fully open pt-PT-optimized language model via a learned connector. We contribute with a purposefully designed three-stage training process - vision-language alignment, general visual instruction tuning, and preference optimization - together with a pt-PT-centric multimodal data mix combining curated and translated public datasets with novel datasets that address the near-total absence of European Portuguese multimodal resources. Our evaluation shows that AMALIA-VL establishes a strong baseline for open-source pt-PT LVLMs.We will release model weights, training data, and construction pipelines along with machine-translated pt-PT evaluation benchmarks to help democratize pt-PT LVLM development.

22.
Nature (Science) 2026-06-16

Daily briefing: How many elementary particles are there?

Authors:

Estimates range from 17 to 995.5. Plus, one man with paralysis is using a brain–computer interface at home and GLP-1 obesity drugs appear to boost testosterone and sperm quality. Estimates range from 17 to 995.5. Plus, one man with paralysis is using a brain–computer interface at home and GLP-1 obesity drugs appear to boost testosterone and sperm quality.

23.
arXiv (CS.AI) 2026-06-18

X+Slides: Benchmarking Audience-Conditioned Slide Generation

arXiv:2606.19256v1 Announce Type: new Abstract: Automatically generating slide decks from source documents is an important application of large language models (LLMs). Existing benchmarks primarily assess slide completeness and technical depth, while overlooking the target audience as a critical real-world factor. For instance, specialists demand rigorous proofs, whereas decision-makers prioritize actionable conclusions. To bridge this gap, we introduce X+Slides, a benchmark specifically designed for audience-conditioned slide generation. Built on a diverse corpus spanning 113 topics and seven presentation scenes, X+Slides employs a dynamic evaluation framework constructed from 8,133 deduplicated, source-grounded probes. By assigning audience-specific utility weights to the same source-grounded probes, X+Slides reports four complementary metrics: Audience Coverage measures how much audience-essential information is conveyed, Domain-wise Coverage shows which information types are covered, Efficiency measures delivered utility per unit of attention cost, and Correctness verifies whether slide claims are supported by the source. Experiments on DeepPresenter, SlideTailor, and NotebookLM show that current systems can recover a substantial but still incomplete part of audience-essential information: at $\tau_A=0.7$, DeepPresenter reaches a best Audience Coverage of 0.714, SlideTailor reaches 0.594, and the NotebookLM ablation reaches 0.853 while showing clear grounding differences. These results indicate that visual quality and broad topic coverage should not be treated as evidence support without source-grounded evaluation.

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

Not all Jensen-Shannon Divergence Estimators are Equal

arXiv:2606.16411v1 Announce Type: new Abstract: The Jensen-Shannon divergence is widely reported as a scalar measure of fidelity for synthetic tabular data. Yet, in practice, it is estimated from finite samples using protocols that are often underspecified. This creates a measurement problem. Although the population divergence is well defined, the empirical value depends on the estimator family, sampling protocol, calibration, dimensionality, and class balance. We show that different protocols can yield non-comparable values: marginal-based estimators ignore dependencies in the joint distribution and can severely underestimate divergence, while classifier-based estimators capture joint structure but exhibit strong estimator dependence. We systematically study this behavior across controlled settings with reference divergences and real-world synthetic tabular benchmarks. Our analysis reveals dependence blindness in marginal estimators, prior-shift bias under class imbalance, and estimator sensitivity in high dimensions. To address prior shift, we derive a closed-form posterior correction for classifier-based Jensen-Shannon estimation. Our results show that empirical Jensen-Shannon divergence values are inherently protocol-dependent, making explicit specification of the estimation procedure necessary for meaningful comparison. We provide practical guidelines and an open-source tool for estimator-aware Jensen-Shannon evaluation.

25.
arXiv (quant-ph) 2026-06-12

Coarse-grained quantum thermodynamics: Observation-dependent quantities, observation-independent laws

arXiv:2507.15918v2 Announce Type: replace Abstract: In both classical and quantum thermodynamics, physical quantities are typically assigned objective values defined independently of our observations. We then refer to the 'work performed by a gas', or the 'entropy of the gas', regardless of how they are evaluated. Here, we question this conception in the context of quantum thermodynamics, estimating how the definition of pivotal thermodynamic quantities is affected by experimental instruments of limited precision. We find that the coarse-grained thermodynamic quantities frequently lead to different conclusions from those drawn in fine-grained scenarios. For instance, the irreversibility of a process, or its work payoff, can significantly vary with the instrument precision. We show nonetheless that coarse-grained thermodynamic quantities satisfy the same relations (i.e., the second law inequality, the relation between dissipation and distinguishability of a process from its time-reverse, and the quantum work fluctuation theorems) as their fine-grained counterparts. These results highlight the observation-independence of relations linking thermodynamic quantities which are themselves observation-dependent.