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01.
arXiv (quant-ph) 2026-06-24

High-harmonic generation driven by temporal-mode quantum states of light

arXiv:2512.06602v2 Announce Type: replace Abstract: We develop a theoretical framework for high-harmonic generation (HHG) driven by quantum states of light based on a temporal-mode expansion of the electromagnetic field. This approach extends previous single plane-wave mode treatments to realistic pulse configurations and arbitrary multi-mode states of light, resolving conceptual inconsistencies arising from non-normalizable infinite plane waves and establishing consistency between analytical and numerical methods. We derive a correction factor that quantifies deviations from the diagonal approximation (in which the yield becomes a statistical average over classical-field simulations) both for the response of a single atom and in the many-atom regime. Our results confirms that the HHG spectrum for atoms driven by any quantum state of light in free space is accurately described by averaging semi-classical calculations over the Husimi distribution, with no observable genuine quantum effects in the spectrum. We also demonstrate that in the many-atom regime, the mean-field coherent-state approximation underlying this treatment does not preserve probabilities, although unitarity is restored by in the diagonal approximation. The absence of genuine quantum effects in the HHG yield is attributed to the large photon numbers ($\sim 10^{11}$) required to reach HHG intensities in free space, which render quantum fluctuations negligible. We discuss nanophotonic environments with ultrasmall mode volumes as potential platforms where few-photon strong-field processes could exhibit genuine quantum signatures.

02.
arXiv (quant-ph) 2026-06-11

Dark state spectroscopy in nonlinear waveguide quantum electrodynamics

arXiv:2606.11997v1 Announce Type: new Abstract: Quantum systems face a fundamental trade-off: they must remain decoupled from the environment to maintain long coherence times, yet they require interactions with the environment to be accessible for measurement. As a prime example, emitter arrays coupled to waveguides facilitate collective modes that, owing to interference, can suppress radiation into the waveguide. While complete destructive interference creates perfectly dark states with infinite lifetimes, their inherent decoupling makes them unmeasurable in standard waveguide quantum electrodynamics. Consequently, current approaches must rely on system non-idealities that permit measurement but limit the coherence times. In this work, we lift this limitation by proposing the use of weakly squeezed light generated in \{chi}(2) nonlinear waveguides for the spectroscopy of completely dark states. We show that the fluorescence spectrum probes transitions between the dressed dark states of the emitter array. This work paves the way towards the measurement and control of dark states, with applications for robust quantum memories, computation, and communication.

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

Generalization Guarantees for Multi-Input Neural Operator Learning in Sobolev Spaces

arXiv:2606.17419v1 Announce Type: new Abstract: We develop approximation and generalization error estimates for multi-input neural operators, with the output error measured in Sobolev norms. In contrast to standard operator-learning settings with a single input function, our framework allows multiple input functions defined on possibly different domains, with different dimensions and Sobolev regularities. The derived rates explicitly quantify the contribution of each input space to the final error bound. In particular, in the balanced regime, the approximation and generalization rates are governed by the interaction between the input dimensions, regularities, and Sobolev orders, while the dependence on the model complexity retains a \(\log\log/\log\)-type structure. Our analysis provides a general theoretical framework for multi-input operator learning, including Sobolev training, and is applicable to operator learning problems arising from partial differential equations and scientific computing.

04.
arXiv (CS.AI) 2026-06-17

PLATE: Plasticity-Tunable Efficient Adapters for Geometry-Aware Continual Learning

arXiv:2602.03846v2 Announce Type: replace-cross Abstract: We develop a continual learning method for pretrained models that requires no access to old-task data, addressing a practical barrier in foundation model adaptation where pretraining distributions are often unavailable. Our key observation is that pretrained networks exhibit substantial geometric redundancy, and that this redundancy can be exploited in two complementary ways. First, redundant neurons provide a proxy for dominant pretraining-era feature directions, enabling the construction of approximately protected update subspaces directly from pretrained weights. Second, redundancy offers a natural bias for where to place plasticity: by restricting updates to a subset of redundant neurons and constraining the remaining degrees of freedom, we obtain update families with reduced functional drift on the old-data distribution and improved worst-case retention guarantees. These insights lead to \textsc{PLATE} (Plasticity-Tunable Efficient Adapters), a continual learning method requiring no past-task data that provides explicit control over the plasticity-retention trade-off. PLATE parameterizes each layer with a structured low-rank update $\Delta W = B A Q^\top$, where $B$ and $Q$ are computed once from pretrained weights and kept frozen, and only $A$ is trained on the new task. The code is available at https://github.com/SalesforceAIResearch/PLATE.

05.
medRxiv (Medicine) 2026-06-22

Biopsychosocial determinants of HPV vaccine perception in university students of both sexes in Cucuta, Colombia, 2024: a cross-sectional study

Colombia has been internationally recognised as a paradigmatic case of vaccine confidence crisis since the 2014 Carmen de Bolivar event, and national HPV vaccination coverage remains far below the World Health Organization 2030 target. Most published evidence focuses on female adolescents and on cervical cancer; the perception of the HPV vaccine in university-age populations of both sexes–and across the broader spectrum of HPV-attributable disease–remains comparatively understudied. We aimed to describe the influence of biopsychosocial determinants on HPV vaccine perception among university students of both sexes in Cucuta, Norte de Santander, Colombia. We conducted a cross-sectional study with a mixed quantitative-qualitative approach in 2024 among four universities (Universidad de Santander, Universidad Francisco de Paula Santander, Universidad de Pamplona and Universidad Libre; combined enrolment 21,033 students). Using convenience sampling stratified by institution, 750 actively enrolled undergraduate students of both sexes (18-60 years) completed a structured online questionnaire adapted from previously validated instruments. The instrument captured sociodemographic information, HPV knowledge and HPV vaccine perception. Data were analysed using Students t-test, one-way analysis of variance, Tukey post-hoc tests, effect sizes and 95% confidence intervals, with a 0.05 significance threshold. Of 750 respondents, 54.2% were women, 61.3% were under 20 years of age, and 75.1% attended public universities. HPV knowledge was high in 39.2%, intermediate in 42.4% and low in 18.4%; women and students aged 26 years or older displayed higher knowledge. Although 91.2% had heard of HPV and 82.5% knew that both sexes could acquire it, recognition of clinical manifestations and complications was uneven: cervical cancer 51.7%, penile cancer 30.5%, vaginal warts 45.9% and warts in the penis, larynx, anus or rectum 34.0%. Vaccine-specific knowledge was low in 77.1%, with men disproportionately represented (85.9% versus 69.5% in women). Overall positive perception of HPV vaccination was 66.6%, slightly higher in women (68.8%) than men (63.9%), in students aged 26 years or older (70.1%) and in students from private universities (68.1% versus 65.9%). Inferential analysis identified sex (Cohens d = -0.357), type of university (d = 0.189) and HPV knowledge (partial eta-squared = 0.096) as the only significant determinants. Age, socioeconomic stratum, age at sexual debut and vaccine-specific knowledge did not reach meaningful significance. HPV vaccine perception was predominantly positive but conditioned by three biopsychosocial determinants, with HPV knowledge as the primary driver. The persistent gender gap reflects historical anchoring of HPV messaging in cervical disease and female-targeted campaigns. Public-health strategies should adopt comprehensive, gender-inclusive educational interventions that explicitly visibilise non-cervical HPV-related cancers and address both sexes from a common evidence base.

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

HybridCodeAuthorship: A Benchmark Dataset for Line-Level Code Authorship Detection

arXiv:2606.12620v1 Announce Type: cross Abstract: Thanks to the rapid adoption of AI code assistants powered by large language models (LLMs), industry codebases are, increasingly, a hybrid of AI- and human-authored code. For risk management and productivity analysis purposes, it is crucial to enable fine-grained location detection of AI-generated code. To develop algorithms for this task, quality benchmarks are needed to assess performance. However, existing benchmarks tend to comprise academic, LeetCode-style problems and presume a code snippet is either completely human-authored or completely AI-authored, which is not reflective of the diverse intents and styles of industry codebases utilizing AI code assistants. To fill these gaps, we introduce HybridCodeAuthorship, a novel benchmark of Python code files with interleaved human- and AI-authored lines of code to simulate authentic utilization of AI code assistants. In this paper, we first present our dataset construction pipeline, which leverages CodeSearchNet, a massive collection of links to open sourced repositories on GitHub. We then benchmark the performance of two state-of-the-art AI-generated code detection algorithms at both the line- and chunk-level. Experimental results demonstrate that HybridCodeAuthorship is a challenging benchmark with a top-scoring algorithm, AIGCode Detector, obtaining a highest F1 score of 0.48 and 0.56 on chunk-level and line-level code detection tasks, respectively.

07.
arXiv (CS.CV) 2026-06-24

From Open Waters to Enclosed Cabins: ProteusVPR for Cross-Scene Visual Place Recognition in Maritime Perception and Cabin Inspection

Autonomous robotic inspection in maritime environments presents unique challenges for Visual Place Recognition (VPR) due to cross-scene perceptual shifts. Robots navigating ship-borne environments must transition between visually distinct domains: open decks with sparse textures and severe illumination changes, and enclosed cabins with repetitive structures and high visual ambiguity. Existing VPR methods, designed primarily for urban or indoor scenes, fail to generalize reliably across these starkly different scenarios. To address this, we propose ProteusVPR, a two-stage retrieval-refinement framework. The first stage employs any standard VPR model for initial image retrieval. The second stage introduces a geometric-visual estimation network that fuses the retrieved image with two temporally preceding frames, incorporating geometric descriptors, a local affine coordinate system, and camera azimuth encoding to achieve precise localization. To support this task, we introduce the XHZ dataset, an 8K-panoramic ship-borne dataset collected from an operational vessel, featuring multi-floor cabin structures, deck transition zones, and strict query-database separation for rigorous evaluation. Extensive experiments on the XHZ dataset demonstrate that ProteusVPR consistently improves the localization accuracy across multiple VPR backbones, reducing mean localization error by over 60\% on average and that ProteusVPR offers an effective and robust solution for precise visual localization in challenging, cross-scene maritime environments.

08.
bioRxiv (Bioinfo) 2026-06-19

ContinuumCellAgent: A Framework-Guided Agent for Long-Horizon Scientific Research

AI-scientist systems are beginning to automate parts of scientific research. We present ContinuumCellAgent, an autonomous agent that executes literature review, hypothesis formation, computational experimentation, manuscript drafting, and adversarial peer review as a single unattended run. Existing AI scientist systems remain difficult to diagnose because they lack modularity, systematic prompt grounding, and observability into long-running behavior. ContinuumCellAgent addresses these gaps with a modular supernode architecture for stage-wise backend swapping, protocols grounded in curated research-method checklists that also define reviewer rubrics, and a diagnostics layer that records file-based artifacts, message traces, and state transitions. We evaluate the system on open-domain QA benchmarks and biomedical/longevity case studies, showing that it can produce checkable research artifacts while exposing pipeline dynamics for rigorous AI co-scientist research.

09.
arXiv (CS.CL) 2026-06-17

A Framework for Evaluating Agentic Skills at Scale

Agent skills – structured, reusable knowledge artifacts that augment LLM agent capabilities – have been rapidly adopted in industry, yet their cross-domain impact and use across commercial and open-source models remain under-studied, and no reusable methodology exists for evaluating an individual skill. In this work, we present an evaluation framework that lets a skill author construct realistic tasks to rigorously assess the aspects of a skill that matter most to them, and that estimates skill utility by solving those tasks. Further, we apply our evaluation approach at scale to 500 real-world skills, generating 1,000 tasks derived from the skills' content, along with instruction-following and goal-completion scoring rubrics. Using these metrics, we evaluate how 19 agent-model configurations, both proprietary and open-source, perform on the tasks. Our results show that models vary widely in how closely they adhere to the instructions encoded in skills, leading to substantial differences in their performance gains. Furthermore, we show that access to a skill significantly changes model behavior compared to the no-skill setup, providing an essential mechanism for encoding opinionated workflows into LLM agents. We release our evaluation dataset to support future work on agent skills.

10.
arXiv (quant-ph) 2026-06-16

Non-Gaussian Phase Transition and Cascade of Instabilities in the Dissipative Quantum Rabi Model

arXiv:2507.07092v3 Announce Type: replace Abstract: The open quantum Rabi model describes a two-level system coupled to a harmonic oscillator. A Gaussian phase transition for the nonequilibrium steady states has been predicted when the bosonic mode is soft and subject to damping. We show that oscillator dephasing is a relevant perturbation, which leads to a non-Gaussian phase transition and an intriguing cascade of instabilities for $k$-th order bosonic operators, as well as a jump in the steady-state qubit polarization. For the soft-mode limit, the equations of motion form a closed hierarchy and spectral properties can be efficiently studied. To this purpose, we establish a fruitful connection to non-Hermitian Hamiltonians. The results for the phase diagram, stability boundaries, and relevant observables are based on mean-field analysis, exact diagonalization, perturbation theory, and Keldysh field theory.

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

scLLM-DSC: LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering for Single-Cell RNA Sequencing

arXiv:2606.13007v1 Announce Type: cross Abstract: Clustering is fundamental to scRNA-seq analysis, serving as a cornerstone for identifying cell populations and resolving tissue heterogeneity. However, existing methods focus on mining numerical statistical patterns, suffering from semantic agnosticism by neglecting the intrinsic biological functions encoded by genes. While Large Language Models (LLMs) offer promising semantic capabilities, their direct adaptation to cell clustering is hindered by the structural mismatch between generative pre-training objectives and discriminative downstream tasks. To bridge this gap, we propose scLLM-DSC, a novel LLM-Knowledge Enhanced Cross-Modal Deep Structural Clustering framework. Diverging from data-driven paradigms, scLLM-DSC establishes a semantically-grounded representation by synergizing two views: a Knowledge-Driven Semantic View derived from NCBI gene priors and contextualized Cell2Sentence embeddings, and a Structure-Aware Topological View extracted via a graph-guided encoder. Crucially, we introduce a cross-modal contrastive alignment mechanism to enforce consistency between biological semantics and transcriptomic features within a unified latent space. Extensive benchmarks demonstrate that scLLM-DSC significantly outperforms eleven state-of-the-art baselines in clustering accuracy.

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

ForecastBench-Sim: A Simulated-World Forecasting Benchmark

Forecasting benchmarks for general-purpose AI systems usually inherit the constraints of the real world: outcomes resolve slowly, tail events are rare, and counterfactual questions are difficult to score. We introduce ForecastBench-Sim, a simulated-world forecasting benchmark built on game rollouts from Freeciv, a turn-based strategy game modelled on the Civilization series. Forecasters receive a fixed world report (a structured snapshot of the current game state) and answer questions about hidden future states; the benchmark then continues the simulation and scores forecasts. Because the world is simulated, the same setup can generate continuous or binary forecasting questions at arbitrary time horizons, paired intervention worlds for conditional or causal questions, and resolved examples of rare or disruptive outcomes. We describe the benchmark pipeline, question families, scoring protocol, and release artifacts, and report validation slices from model evaluations and an anonymized human pilot. ForecastBench-Sim is intended to complement real-world forecasting benchmarks by providing controlled, immediately resolvable tasks for studying probabilistic reasoning under dynamic world states.

14.
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.

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

PlaceRep: Geospatial Place Representation Learning from Large-Scale Point-of-Interest Data

arXiv:2507.02921v4 Announce Type: replace-cross Abstract: Learning effective representations of urban environments requires capturing spatial structure beyond fixed administrative boundaries. Existing geospatial representation learning approaches typically aggregate Points of Interest (POIs) into pre-defined administrative regions such as census units or ZIP code areas, assigning a single embedding to each region. However, POIs often form semantically meaningful groups that extend across, within, or beyond these boundaries, defining places that better reflect human activity and urban function. To address this limitation, we propose PlaceRep, a geospatial representation learning method that constructs place-level representations by clustering spatially and semantically related POIs. PlaceRep summarizes large-scale POI graphs from U.S. Foursquare data to produce general-purpose urban region embeddings while automatically identifying places across multiple spatial scales. By eliminating model pre-training, PlaceRep provides a scalable and efficient solution for multi-granular geospatial analysis. Experiments using the tasks of population density estimation and housing price prediction as downstream tasks show that PlaceRep outperforms most state-of-the-art graph-based geospatial representation learning methods and achieves up to a x100 speedup in generating region-level representations on large-scale POI graphs. The implementation of PlaceRep is available at https://github.com/mohammadhashemii/PlaceRep.

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

Modeling light-matter coupled systems with neural quantum states

arXiv:2606.14352v1 Announce Type: cross Abstract: Recent advances in cold atom manipulation enable the study of many-body systems where short-range interactions between neighboring atoms coexist with long-range interactions mediated by photons. Such a combination of interactions makes a theoretical approach challenging beyond mean-field methods. In this work, we develop a neural quantum state based approach to study these systems numerically. We introduce a neural-network architecture capable of handling hybrid Hilbert spaces with large local bosonic dimensions in strongly interacting spin-photon systems. We benchmark this approach on a model of a two-dimensional lattice of Rydberg atoms coupled to a photon mode. The superradiant ground states found in the large spin-photon coupling regime allow us to demonstrate the efficiency of the method in the presence of high photon occupation. Furthermore, the ability to capture spin-spin and spin-photon correlations leads us to observe quantitative deviations in the ground state phase boundaries with respect to mean-field theory. The method extends to other systems with a similar hybrid Hilbert space structure, such as spin-phonon systems, and provides a scalable framework for investigating their ground state properties.

17.
arXiv (CS.AI) 2026-06-16

LaWAM: Latent World Action Models for Efficient Dynamics-Aware Robot Policies

arXiv:2606.15768v1 Announce Type: cross Abstract: Vision-Language-Action models (VLAs) leverage large-scale vision-language pretraining for semantic robot control, but often lack explicit foresight into how robot actions change the scene. World-Action Models (WAMs) address this limitation by conditioning policies on predicted futures, yet existing approaches typically rely on computationally expensive video generation with substantial pixel-level redundancy. We present LaWAM, a Latent World Action Model that exposes predictive dynamics to robot policies through compact latent visual subgoals instead of reconstructed future video. At the core of LaWAM is a latent-action-conditioned Latent World Model (LaWM). We obtain LaWM by training a latent action model in the latent space of a pretrained vision foundation model and repurposing its forward decoder to predict future observation features for scene evolution. LaWAM then conditions action generation on these predicted latent visual subgoals to enable dynamics-aware robot control. LaWAM achieves state-of-the-art or competitive success rates (SRs) across LIBERO (98.6% SR), RoboTwin (91.22% SR), and real-world manipulation tasks while retaining low-latency inference. LaWAM runs in 187 ms per action-chunk prediction and achieves up to 24x lower wall-clock latency than pixel-space WAMs.

18.
arXiv (CS.LG) 2026-06-11

Intermittent time series forecasting: local vs global models

arXiv:2601.14031v2 Announce Type: replace-cross Abstract: Forecasting intermittent time series, which contain zeros, is a crucial challenge in supply chains as inventory policies require probabilistic forecasts to establish safety levels. Intermittent time series are commonly forecast using local models, trained individually on each time series. In the last years global models, trained on a large collection of time series, have become popular for time series forecasting. Global models are often based on neural networks or gradient boosted trees. We carry out the first study comparing state-of-the-art probabilistic local and global models on intermittent time series. For global models we consider three different distribution heads suitable for intermittent time series: negative binomial, hurdle-shifted negative binomial and Tweedie. To the best of our knowledge, this is the first use of the latter two with neural networks. We perform experiments on five datasets comprising overall more than 40'000 real-world time series. Among global models, TiDE, a simple neural network architecture, achieves the best accuracy; it also consistently outperforms local models and has lower computational requirements. Large global models are instead much more computationally demanding and less accurate. Among the distribution heads, the Tweedie provides the best estimates of the highest quantiles.

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

Analyzing Error Propagation in Korean Spoken QA with ASR-LLM Cascades

We analyze how automatic speech recognition (ASR) errors propagate through ASR-LLM cascades in Korean spoken question answering (SQA), focusing on downstream semantic failures that conventional ASR metrics cannot fully capture. Our analysis shows that the relative downstream degradation caused by ASR errors is consistent across LLMs with different absolute performance, suggesting that cascade degradation largely tracks ASR-stage information loss. We further identify single-character Korean ASR errors as a Korean-specific loss channel, where even a minimal transcription difference can change the intended question and degrade downstream QA performance. Finally, an auxiliary comparison shows that a large audio language model outperforms an ASR-LLM cascade with an approximately matched language backbone in noisy Korean SQA, indicating the potential of direct audio input to mitigate transcript-induced information loss.

20.
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.

21.
arXiv (CS.AI) 2026-06-17

SoK: AI-Augmented Binary Reversing

arXiv:2606.17398v1 Announce Type: cross Abstract: Binary reversing is fundamental to software understanding, vulnerability discovery, malware investigation, and firmware auditing. However, it remains inherently challenging due to the irreversible loss of semantic information during compilation. Recent advances in machine learning, large language models (LLMs), and agentic AI systems have accelerated the adoption of AI-augmented binary reversing. Yet, the resulting body of work has become increasingly fragmented across reversing domains, artifact representations, learning approaches, and evaluation practices. This paper presents the first comprehensive systematization of knowledge on AI-augmented binary reversing. We analyze 144 research papers published since 2015, and organize them into 22 binary reversing domains according to the inference tasks. We further introduce a unified taxonomy spanning conventional and AI-augmented reversing pipelines. Our taxonomy connects traditional analysis techniques, binary-derived artifacts, representation strategies, learning paradigms, and downstream inference tasks, while clarifying the emerging roles of LLMs and agentic AI systems. By establishing a common vocabulary and structured framework, we provide a holistic view of the field's evolution over the past decade. Our study reveals common structures underlying seemingly disparate approaches, highlights persistent technical challenges and evaluation gaps, and identifies promising opportunities for future research. Collectively, these insights clarify the current state of the field and provide a foundation for the next generation of reliable and scalable AI-augmented binary reversing systems.

22.
Nature (Science) 2026-06-10

Gene ancestries reveal diverse microbial associations during eukaryogenesis

The origin of eukaryotes remains a central enigma in biology1. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon2,3. However, the nature, timing and contributions of other potential bacterial partners4–6 and the role of interactions with viruses7–9 remain contentious. To address these questions, we used advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided a revised reconstruction of the last eukaryotic common ancestor (LECA) proteome, in which we traced the phylogenetic origin of each protein family. We found compelling evidence for multiple waves of horizontal gene transfer from diverse bacterial donors, with some likely to have preceded mitochondrial endosymbiosis. We inferred plausible traits of the major donors and their functional contributions to the LECA. Our findings support a contribution of horizontal gene transfers to shaping the proteomes of pre-LECA ancestors and suggest a facilitating role of Nucleocytoviricota viruses. Taken together, our results suggest that ancient eukaryotes may have originated within complex microbial ecosystems through a succession of diverse associations that left a footprint of horizontally transferred genes. Phylogenomic reconstruction of the proteome of the last eukaryotic common ancestor sheds light on the origin of eukaryotes, indicating an important role of horizontal transfer of genes from diverse bacterial and viral donors.

23.
arXiv (CS.AI) 2026-06-19

LoRDO: Distributed Low-Rank Optimization with Infrequent Communication

arXiv:2602.04396v2 Announce Type: replace-cross Abstract: Distributed training of foundation models via $\texttt{DDP}$ is limited by interconnect bandwidth. While infrequent communication strategies reduce synchronization frequency, they remain bottlenecked by the memory and communication requirements of optimizer states. Low-rank optimizers can alleviate these constraints; however, in the local-update regime, workers lack access to the full-batch gradients required to compute low-rank projections, which degrades performance. We propose $\texttt{LoRDO}$, a principled framework unifying low-rank optimization with infrequent synchronization. We first demonstrate that, while global projections based on pseudo-gradients are theoretically superior, they permanently restrict the optimization trajectory to a low-rank subspace. To restore subspace exploration, we introduce a full-rank quasi-hyperbolic update. $\texttt{LoRDO}$ achieves near-parity with low-rank $\texttt{DDP}$ in language modeling and downstream tasks at model scales of $125$M–$720$M, while reducing communication by $\approx 10 \times$. Finally, we show that $\texttt{LoRDO}$ improves performance even more in very low-memory settings with small rank/batch size.

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

Crossing the Validation Crisis: Cross-Validation Reduces Benchmarking Variance Surprisingly Well

arXiv:2606.12552v1 Announce Type: new Abstract: Modern machine learning progresses through empirical work, benchmarking new methods to evaluate relative performance. However, the statistical variability inherent to evaluation - exacerbated by the stochastic nature of many algorithms - often makes performance estimation unreliable due to the limited test samples available, leading to a validation crisis in which genuine advances are difficult to discern. In this work, we show that cross-validation improves markedly confidence when evaluating and comparing learning algorithm performances. We introduce the concept of sample gain, which quantifies the virtual data augmentation achieved by using multiple cross-validation splits to reduce benchmarking variance. Experiments on both synthetic and real-world datasets (histopathologic scans and NLP fine-tuning) demonstrate that multiple splits can substantially improve the reliability and stability of performance estimates, with diminishing returns often setting in later than expected. We also introduce a procedure to dynamically early-stop cross-validation by estimating from the first few folds if subsequent folds will bring large sample gains. Our findings highlight the value of pushing cross-validation on available samples to achieve robust and reliable benchmarking.

25.
arXiv (quant-ph) 2026-06-16

A Gauge-Covariant Geometric Framework for Non-Hermitian Quantum Systems

arXiv:2606.15922v1 Announce Type: new Abstract: We develop a comprehensive, gauge-covariant geometric framework for non-Hermitian quantum systems in the quasi-Hermitian regime, that is, the region of parameter space where the non-Hermitian Hamiltonian admits a real spectrum and a positive-definite metric operator. We build this framework by elevating the Dyson map to a central geometric object. This map is the transformation that converts a non-Hermitian Hamiltonian into an equivalent Hermitian one. From it we construct the Dyson connection and decompose it into Hermitian and anti-Hermitian parts, identified respectively as {\it stretching } and {\it rotation } components. This decomposition cleanly separates the genuine physical metric deformations from the unitary gauge redundancies. Working with manifestly gauge-covariant states, we then derive the complex non-Hermitian Berry phase and the quantum geometric tensor (QGT), and show that the non-Hermitian geometric curvature originates from the non-commutativity of the stretching components at the operator level. We further analyse the geometric singularities near an exceptional point (EP) and uncover a distinct hierarchy of divergences. For a general two-level non-Hermitian model, the quantum metric tensor (QMT) exhibits a leading-order divergence $\sim |\epsilon_\mu|^{-2}$, while the Berry curvature shows a weaker, subleading divergence $\sim |\epsilon_\mu|^{-3/2}$, with $\epsilon_\mu$ denoting the parameter displacement from the EP along an individual parameter axis $\mu$. Finally, we examine physical realizations of this model, including the non-Hermitian Su–Schrieffer–Heeger (SSH) and Hatano–Nelson (HN) models, where exact analytical results confirm the predicted critical scaling laws and illustrate the metric-deformation-driven non-Hermitian geometries.