Explore the Frontier of Global Academia

01.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2606.13405

Neuro-Symbolic Agents for Regulated Process Automation: Challenges and Research Agenda

Authors:

Alexander Rombach↗Chantale Lauer↗Nijat Mehdiyev↗

arXiv:2606.13405v1 Announce Type: new Abstract: LLM-based agents are entering regulated industries where they automate judgment intensive quality management processes. We argue that symbolic structures already embedded in these domains, including regulations, typed process models, and compliance constraints, should be treated not merely as external monitoring mechanisms but as core architectural components that shape the agent's decision-making and behavior. We propose compliance-by-construction as a complementary paradigm to guardrail-based monitoring: a structural foundation that prevents control-flow violations, while guardrails remain essential for catching semantic errors. We identify a structured set of neuro-symbolic research challenges on foundational and capability level and show that addressing them jointly enables compliance-by-construction. We call on the neuro-symbolic community to engage with regulated process automation as a high impact research domain.

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02.

arXiv (CS.CL) 2026-06-11 DOI: arXiv:2606.11722

ICA Lens: Interpreting Language Models Without Training Another Dictionary

Authors:

Sida Liu↗Feijiang Han↗

Finding interpretable directions in language-model representations is critical for understanding and controlling model behavior. Sparse autoencoders (SAEs) have become the standard tool for this purpose, but using them as the default first lens often requires training, storing, and evaluating large overcomplete dictionaries. This bottleneck limits rapid exploration and raises a fundamental question: how much interpretable structure is already visible from activation geometry before training another neural dictionary? Our intuition is simple: many interpretable directions are selective on tokens, and these directions should look less Gaussian than random directions. We therefore revisit independent component analysis (ICA), a classical method for finding non-Gaussian directions, as a compact lens for language-model interpretability. We find that ICA has been underestimated for LLM interpretability, because prior uses often relied on off-the-shelf ICA implementations that are brittle on LLM activations and lacked systematic tools for inspecting and evaluating the recovered directions. To bridge these gaps, we introduce ICALens, the first practical workflow for stable, efficient, and auditable ICA analysis of LLM representations. It combines an optimized GPU-parallel FastICA pipeline with LLM-specific stability recipes and better fitting diagnostics, enabling efficient and reliable layer-wise analysis. Across GPT-2 Small, Gemma 2 2B, and Qwen 3.5 2B Base, ICALens efficiently recovers compact, human-interpretable directions without per-layer gradient-based dictionary training. On SAEBench, ICA is competitive with public SAEs in sparse probing and outperforms them in targeted probe perturbation under small-to-medium budgets. These results suggest that ICA should not be viewed as a weak baseline, but as an efficient and complementary first lens for exploring language-model representations.

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03.

arXiv (CS.AI) 2026-06-17 DOI: arXiv:2507.11178

A Gradient-based Causal Discovery Framework with Applications to Complex Industrial Processes

Authors:

Meiliang Liu↗Huiwen Dong↗Xiaoxiao Yang↗Yunfang Xu↗Mingbao Yang↗Zijin Li↗Zhengye Si↗Xinyue Yang↗Zhiwen Zhao↗

arXiv:2507.11178v3 Announce Type: replace-cross Abstract: With the advancement of deep learning technologies, various neural network-based Granger causality models have been proposed. Although these models have demonstrated notable improvements, several limitations remain. Most existing approaches adopt the component-wise architecture, necessitating the construction of a separate model for each time series, which results in substantial computational costs. In addition, imposing the sparsity-inducing penalty on the first-layer weights of the neural network to extract causal relationships weakens the model's ability to capture complex interactions. To address these limitations, we propose Gradient Regularization-based Neural Granger Causality (GRNGC), which requires only one time series prediction model and applies $L_{1}$ regularization to the gradient between model's input and output to infer Granger causality. Moreover, GRNGC is not tied to a specific time series forecasting model and can be implemented with diverse architectures such as KAN, MLP, and LSTM, offering enhanced flexibility. Numerical simulations on DREAM, Lorenz-96, fMRI BOLD, and CausalTime show that GRNGC outperforms existing baselines and significantly reduces computational overhead. Meanwhile, experiments on real-world DNA, Yeast, HeLa, and bladder urothelial carcinoma datasets further validate the model's effectiveness in reconstructing gene regulatory networks.

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04.

arXiv (CS.LG) 2026-06-16 DOI: arXiv:2606.17022

Learning the Geometry of Data: A Mathematical Review of Shape Space Analysis

Authors:

Gary P. T. Choi↗Khanh Dao Duc↗Shira Faigenbaum-Golovin↗Karen Habermann↗Emmanuel Hartman↗Christoph von Tycowicz↗Chi Zhang↗Wenjun Zhao↗Felix Zhou↗

arXiv:2606.17022v1 Announce Type: cross Abstract: A central objective of machine learning is to identify structure and patterns in data. Advances in data acquisition have increasingly produced datasets whose observations possess rich geometric form, giving rise to shape spaces that encode variability in object geometry. Such datasets arise across a wide range of disciplines, including biology, medicine, anthropology, and computer vision, where subtle geometric differences often carry important scientific information. Traditional machine learning methods, however, are frequently ill-equipped to account for the nonlinear geometric structure underlying these data. This survey synthesizes a rapidly growing body of work on shape space analysis, which provides a mathematical and computational framework for the study of geometric data. Drawing on ideas from differential geometry, statistics, and machine learning, we organize the literature around a common analytical pipeline: shape representation and parameterization, the rigorous construction of robust geodesic metrics, statistical analysis on shape spaces, and geometry-aware learning methods. We discuss how these tools enable the characterization of shape variability, the comparison of geometric objects, and the analysis of structural trajectories across populations and time. To illustrate the breadth of the field, we highlight applications spanning multiple scales of biological organization, including studies of subcellular morphology and primate tooth evolution. Across these and many other domains, researchers face common challenges arising from complex, nonlinear, and often unaligned geometric variation. The review concludes by identifying key theoretical and computational challenges, as well as emerging opportunities driven by increasingly large and diverse geometric datasets.

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05.

arXiv (CS.LG) 2026-06-16 DOI: arXiv:2606.15280

Rethinking Structural Anomaly Detection: From Decision Boundaries to Projection Operators

Authors:

Alexander Bauer↗

arXiv:2606.15280v1 Announce Type: new Abstract: Most existing anomaly detection methods rely on estimating a probability density or learning an enclosing decision boundary, implicitly assuming that normal data occupies a region of non-zero volume in the ambient space. In contrast, structural anomaly detection considers data that lies near a low-dimensional manifold, creating a mismatch between the inductive bias of existing methods and the structure of the data, often resulting in degraded performance. To address this mismatch, we introduce a geometric perspective. Specifically, we learn a projection operator onto the manifold of normal samples and define a sample as anomalous if it is altered by this projection. This formulation naturally integrates the inductive bias of manifold-supported data and reframes anomaly detection in terms of a projection residual, thereby resolving issues arising from modeling degenerate distributions. Notably, it provides a unifying interpretation of reconstruction-based methods by explaining their success and failure in terms of projection quality. In particular, it explains the strong generalization ability of projection-aligned models as a consequence of contraction behavior toward the manifold. Moreover, by decoupling anomaly detection from probabilistic modeling, it reduces the tendency to misclassify rare but normal samples, a widely recognized limitation of existing approaches. Empirically, we demonstrate that projection-aligned methods achieve strong performance, outperforming boundary-based methods while improving upon existing reconstruction-based approaches.

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06.

arXiv (quant-ph) 2026-06-24 DOI: arXiv:2605.10424

Quantum Correlations of Neutrinos in the Kerr-Newman Space-time

Authors:

Ze-Wen Li↗Shu-Jun Rong↗

arXiv:2605.10424v2 Announce Type: replace-cross Abstract: Quantum phases provide a connection between gravitation and quantum information, which proposes a novel avenue to explore the properties of space-time. In this paper, we investigate the quantum correlations (QCs) of neutrinos in the Kerr–Newman space-time. Both radial and non-radial propagations are considered under the weak-field approximation. The results show that, for inward propagations, the oscillation probabilities and QCs differ significantly from those obtained in the Schwarzschild metric. In the case of radial outward propagation, the larger angular momentum $a$ increases the oscillation period of the survival probability $P_{ee}$, entanglement, and monogamy of nonlocality, whereas the larger charge $Q$ decreases the corresponding periods. For non-radial propagations, $M$ and $a$ can noticeably modulate the amplitudes of the considered QCs, which is not observed in the case of radial propagations. Furthermore, we find that, despite differences in their variation ranges, entanglement and coherence exhibit highly consistent oscillation behaviors in both radial and non-radial propagation cases. These findings provide a comprehensive understanding for the neutrinos-based relativistic quantum information.

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07.

arXiv (CS.CV) 2026-06-11 DOI: arXiv:2606.11446

3D-CBM: A Framework for Concept-Based Interpretability in Generative 3D Modeling

Authors:

Ahmad Al-Kabbany↗

This research introduces a framework for incorporating Concept Bottleneck Models (CBMs) into 3D generative architectures to address the inherent 'semantic gap' in deep geometric learning. As deep models become central to 3D content creation, explainability shifts from a peripheral feature to a fundamental requirement for trust and accountability in safety-critical domains such as healthcare and manufacturing. CBMs provide an intrinsic interpretability solution by constraining latent representations to align with human-defined concepts, yet their application to unstructured 3D data remains largely unexplored. We design, implement, and validate a formal 3D-CBM architecture that maps raw geometric inputs, including point clouds and meshes, into a multi-tiered taxonomy of interpretable primitives and functional attributes. The framework further identifies strategic datasets, such as PartNet and ShapeNet, specialized for concept-based supervision. Experimental results from a 3D part-manipulation proof-of-concept experiment demonstrate the framework's efficacy, achieving a concept prediction accuracy of 88.8\% and a Chamfer Distance of 0.0115. Critically, the model enables precise test-time intervention, allowing for the interactive correction of structural errors. This work establishes a foundation for semantically-steerable 3D generation and invites further exploration into collaborative human-in-the-loop design systems.

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08.

arXiv (math.PR) 2026-06-24 DOI: arXiv:2606.21122

Negative index, matchings, and nonnegative eigenvalues of tridiagonal stochastic matrices

Authors:

Bassam Mourad↗Issam Kaddoura↗Hassan Issa↗

arXiv:2606.21122v2 Announce Type: replace Abstract: We study negative eigenvalues of $n\times n$ stochastic matrices whose off-diagonal support is constrained by a sparse graph. The main tool is a matching-based inertia principle: if $G$ is bipartite with matching number $\mu(G)$, $S$ is a real symmetric matrix supported on $G$ with nonnegative diagonal entries and whose negative index (i.e. number of negative eigenvalues counted with their multiplicities) is denoted by $\nu_{-}(S) $, then \[ \nu_{-}(S)\leq \mu(G). \] In particular, every $n\times n$ nonnegative tridiagonal stochastic matrix $P$ satisfies $ \nu_{-}(P)\leq \left\lfloor \frac{n}{2}\right\rfloor. $ Consequently, after ordering the eigenvalues of $P$ in the decreasing order, we have $ \lambda_{\lceil n/2\rceil}(P)\geq0, \ and hence \ \lambda_2(P)\geq0, \mbox{ for } n\geq3. $ This gives an all-dimensional strengthening of the previously known $4\times4$ tridiagonal stochastic result. Next, we show that this tridiagonal bound is sharp in every dimension in both reducible and irreducible cases. Finally, we explore some possible extension and raise some open questions.

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09.

medRxiv (Medicine) 2026-06-11 DOI: HASH:5d813f98c2fd687f7c78c5f8cd824327

Corticospinal tract risk modifies motor recovery after minimally invasive surgery for intracerebral hemorrhage: a secondary analysis of MISTIE-III

Authors:

Murray↗O. N↗Jenkins↗Walborn↗Patel↗H. C↗Harston↗G. W↗Cootes↗T. F↗Klijn↗C. J. M↗…

Objective: Outcome after surgical hematoma evacuation for intracerebral hemorrhage (ICH) depends on hematoma location. As corticospinal tract (CST) integrity affects motor recovery after stroke, we hypothesized that CST integrity drives heterogeneity in surgical outcomes and investigated this in a secondary analysis of MISTIE-III participants. Methods: Risk of CST injury was categorized into four levels, based on the interaction between the CST, the hematoma, and perihematomal edema (PHE) on automatically segmented stability CT: no risk, PHE infiltration, hematoma infiltration, and complete interruption of the CST. Associations with outcome were tested using multivariable linear regression for motor National Institutes of Health Stroke Scale (NIHSS) at day 180 and ordinal regression for modified Rankin Scale (mRS) at day 365, introducing an interaction term between CST risk and treatment group. Results: Day 180 motor NIHSS was significantly lower for 'no risk' ({beta}:-3.77, [95% confidence interval [CI]: -5.8 to -1.70], p=0.0003) and 'PHE infiltration' ({beta}:-2.3, [95%CI: -3.5 to -1.1]; p=0.0002) vs. 'complete interruption'. Surgery was associated with lower Day 180 motor NIHSS in participants with hematoma infiltration ({beta}:-2.07, [95%CI: -3.8 to -0.4], p=0.016). Compared to complete interruption, 'no risk' (adjusted odds ratio [aOR]:0.27, [95%CI: 0.10 to 0.74], p=0.01) and 'PHE infiltration' (aOR:0.41, [95%CI: 0.23 to 0.74]; p=0.003) were associated with lower odds of unfavorable day 365 mRS. Surgery was associated with lower mRS in participants with no risk (aOR:0.23, [95%CI: 0.05 to 0.97, p=0.045). Interpretation: Increasing CST risk is associated with worse motor recovery (day 180) and disability (day 365). CST risk modifies the effect of the MISTIE-III procedure on motor recovery and disability.

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10.

arXiv (CS.CV) 2026-06-24 DOI: arXiv:2508.17728

Segmentation and Classification of Pap Smear Images for Cervical Cancer Detection Using Deep Learning

Authors:

Nisreen Albzour↗Sarah S. Lam↗

Cervical cancer remains a significant global health concern and a leading cause of cancer-related deaths among women. Early detection through Pap smear tests is essential to reduce mortality rates; however, the manual examination is time consuming and prone to human error. This study proposes a deep learning framework that integrates U-Net for segmentation and a classification model to enhance diagnostic performance. The Herlev Pap Smear Dataset, a publicly available cervical cell dataset, was utilized for training and evaluation. The impact of segmentation on classification performance was evaluated by comparing the model trained on segmented images and another trained on non-segmented images. Experimental results showed that the use of segmented images marginally improved the model performance on precision (about 0.41 percent higher) and F1-score (about 1.30 percent higher), which suggests a slightly more balanced classification performance. While segmentation helps in feature extraction, the results showed that its impact on classification performance appears to be limited. The proposed framework offers a supplemental tool for clinical applications, which may aid pathologists in early diagnosis.

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11.

arXiv (CS.CV) 2026-06-12 DOI: arXiv:2606.13267

TimeLens: On-Device Artifact Recognition with Retrieval-Augmented Question Answering for the Grand Egyptian Museum

Authors:

Rawan Hesham↗Ali Ashraf↗Amr Ahmed↗Malak Alaa↗Omar Ahmed↗Omar Wagih↗

TimeLens is an AI-powered bilingual mobile guide for the Grand Egyptian Museum (GEM). Pointing a phone at an exhibit, a visitor sees the artifact recognized in real time and can ask follow-up questions answered in English or Arabic. The work addresses three problems specific to in-gallery deployment: fine-grained visual similarity among 51 catalogued artifacts (many near-identical Ramesside statues), the gap between curated training data and handheld camera conditions, and the risk of an AI guide stating unsupported historical facts. Two engineering contributions are reported. First, an on-device artifact detector was developed through a data-quality-driven iteration study – from foundation-model auto-annotation (YOLO-World), through spatial label-cleaning rules, to a fully hand-annotated dataset – isolating label quality as the decisive factor: the final YOLOv8n model resolves every previously failing class while remaining a 5.97 MB TensorFlow Lite asset that runs in real time on a mid-range phone (mAP@0.5 = 0.995, mAP@0.5:0.95 = 0.924). Second, a bilingual Retrieval-Augmented Generation (RAG) guide, grounded in a 108-record ChromaDB knowledge base, was benchmarked across seven candidate language models, with Gemma 4 E2B (Q4 K M) selected; ten targeted optimizations reduce end-to-end latency from over 30 s to approximately 10 s. Both subsystems are integrated in a production Flutter application with bilingual interface, museum location gating, and text-to-speech support.

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12.

arXiv (CS.CL) 2026-06-11 DOI: arXiv:2606.11424

SOMA-SQL: Resolving Multi-Source Ambiguity in NL-to-SQL via Synthetic Log and Execution Probing

Authors:

Sai Ashish Somayajula↗Marianne Menglin Liu↗Chuan Lei↗Fjona Parllaku↗Daniel Garcia↗Rongguang Wang↗Syed Fahad Allam Shah↗Ankan Bansal↗Sujeeth Bharadwaj↗Tao Sheng↗Sujith Ravi↗Dan Roth↗…

Natural language interfaces to databases aim to translate user questions into executable SQL, yet remain brittle in real-world settings where questions are underspecified and schemas are large and ambiguous. Ambiguity across user questions, database schemas, and model interpretations are central failure modes in NL2SQL, leading to misaligned intent, incorrect schema grounding, and erroneous SQL generation. Existing approaches rely on human clarification or treat ambiguity as a schema representation problem, but these do not scale nor resolve ambiguity autonomously. We propose SOMA-SQL to automatically resolve ambiguity via targeted synthetic query log and ambiguity-driven probing. SOMA-SQL constructs synthetic query log to ground schema interpretation and guide candidate SQL generation; it then executes targeted probing queries, driven by a structured ambiguity taxonomy and candidate disagreements, to produce disambiguation evidence for final SQL selection and repair. This active approach to ambiguity discovery and resolution generalizes across unseen schemas and query distributions without human-in-the-loop. Experiments on six public benchmarks demonstrate that SOMA-SQL improves execution accuracy by 13.0% on average over state-of-the-art baselines, with gains of up to 16.7% on ambiguous questions.

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13.

medRxiv (Medicine) 2026-06-22 DOI: HASH:5bcc53f1f11c04b5dbcbb1bb322bfb48

Substantia Nigra and Subthalamic Nucleus Deep Brain Stimulation Exert Opposing Effects on Novelty Recognition in Parkinson's Disease

Authors:

Li↗Jiang↗Liu↗Yang↗Yao↗Zhang↗Xie↗Hollunder↗Strange↗Meng↗Wang↗Shi↗…

Episodic memory plays a critical role in supporting adaptive behavior; however, whether it can be causally regulated in humans via deep subcortical stimulation remains unclear. In the present study, we investigated the differential effects of substantia nigra (SN) and subthalamic nucleus (STN) stimulation on episodic memory, as well as the underlying mechanisms of its associated brain networks, using a recognition memory task combined with concurrent functional magnetic resonance imaging in patients with Parkinson's disease. SN-DBS increased recognition sensitivity and reduced false alarms at both frequencies, whereas 10 Hz STN-DBS reduced sensitivity and increased false alarms. Functional connectivity analyses in the absence of DBS stimulation identified a false recognition-related network linking nigral, pallidal, subthalamic, medial temporal, frontal, and occipital regions. SN-DBS-related false alarm reduction tracked modulation of this circuit and was marked by its baseline vulnerability state. These behavioral effects mapped onto target-dependent parieto-occipital and SN-visual retrieval pathways, supporting a model in which DBS bidirectionally regulates recognition memory through target- and frequency-dependent subcortical-cortical circuits.

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14.

arXiv (CS.AI) 2026-06-15 DOI: arXiv:2606.13742

A fully GPU-based workflow for building physics emulators of hypersonic flows

Authors:

Fabian Paischer↗Dylan Rubini↗Deniz A. Bezgin↗Aaron B. Buhendwa↗David Hauser↗Florian Sestak↗Johannes Brandstetter↗Sebastian Kaltenbach↗Nikolaus A. Adams↗

arXiv:2606.13742v1 Announce Type: cross Abstract: The ability to resolve complex physical phenomena with high fidelity and at low computational cost is central to addressing key challenges in modern engineering. A prime example lies in hypersonic flows, where the precise prediction of the full flowfield topology, in particular with respect to shock wave location and intensity, is critical. Yet supersonic and hypersonic flows continue to be a stumbling block for traditional reduced-order models and neural emulators that struggle to capture steep gradients in flow states with physical consistency in applications of industrial relevance. To that end, we introduce a fully GPU based workflow that integrates accelerated data generation with the training of neural emulators augmented by uncertainty quantification and physics-aware refinement. Our workflow is enabled by a differentiable high-fidelity solver (JAX-Fluids) which we employ for rapid dataset creation and residual-based improvement of the neural emulator to enhance physical consistency. Building on this framework, we first present a suite of model architectures and analyze their scaling behavior to expose their strengths and shortcomings. We then show that residual-based refinement enables training on cases where only mesh and input parameters are available, substantially reducing residuals and improving physical consistency. Together, differentiable simulation and residual-based refinement yield physics emulators that remain reliable beyond their training distribution, a key requirement for deploying surrogates in real-world engineering design loops.

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15.

arXiv (CS.CL) 2026-06-18 DOI: arXiv:2606.18587

Dual Dimensionality for Local and Global Attention

Authors:

Zhiyuan Wang↗Xuan Luo↗Sirui Zeng↗Xifeng Yan↗

Decoder-only Transformers compute attention over the KV cache of preceding tokens. Keys (and Values) are typically represented with the same dimensionality, regardless of its distance from the prediction target. In natural language, however, the next word is most strongly influenced by the immediately preceding tokens. We hypothesize that local and distant tokens impose asymmetric demands on representational capacity: local tokens are more critical for predicting immediate outputs and thus require richer representations, whereas distant tokens primarily serve as long-range memory, for which lower-dimensional representations may suffice. We formalize this idea as Distance-Adaptive Representation (DAR), implemented in a controlled setting that preserves full-dimensional representations within a local context window while assigning reduced-dimensional representations (e.g. 1/4 of the original dimensionality) to tokens beyond that window. Across multiple pretraining scales (70M to 410M parameters), as well as continued supervised fine-tuning on a 1B-scale model, this approach closely matches the performance of full-dimensional baselines. In contrast, uniformly reducing dimensionality across all token positions leads to worse performance. These results challenge the common assumption that key and value dimensionality should be uniform across token positions. Our findings suggest a new direction for designing attention architectures that adaptively allocate representational capacity across sequences, enabling further reductions in KV cache during inference.

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16.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2606.18463

Mixed-Precision Communication-Avoiding SGD for Generalized Linear Models on GPUs

Authors:

Aditya Devarakonda↗Irene Sim\'o Mu\~noz↗Giulia Guidi↗

arXiv:2606.18463v1 Announce Type: cross Abstract: Distributed stochastic gradient descent (SGD) is limited by communication rather than computation, since each iteration requires an AllReduce across processes. Communication-avoiding SGD (CA-SGD) amortizes communication over $s$ iterations by replacing $s$ consecutive AllReduces with a single AllReduce of an $sb\times sb$ Gram matrix, trading more computation and bandwidth for fewer synchronization points. Modern GPUs with matrix hardware and reduced-precision formats offset this by accelerating the Gram GEMM and shrinking BF16 traffic. We study mixed-precision CA-SGD for generalized linear models on NVIDIA GPUs. Our finite-precision analysis decomposes the local rounding error of one CA-SGD outer iteration into nine independent precision choices, depending on the hardware only through its low-precision unit roundoffs, so the resulting recipes transfer in principle across GPU generations. The recipe stores the input matrix and margin vector in low precision, computes the Gram matrix from low-precision inputs with high-precision accumulation, communicates it in high precision, and performs the inner recurrence and weight updates in high precision. On NERSC Perlmutter A100 GPUs, mixed-precision CA-SGD matches FP32 SGD loss within $0.5\%$ on logistic, linear, and Poisson problems and reaches $5.1$–$6.8\times$ speedup over FP32 SGD on epsilon, SUSY, HIGGS, synth, and Poisson-synth. Our software is available at https://doi.org/10.5281/zenodo.20448273

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17.

arXiv (CS.LG) 2026-06-17 DOI: arXiv:2606.17491

A Bayesian Boolean Matrix Factorization with Application to Copy Number Analysis in Cancer

Authors:

Adolphus Wagala↗Mehmet Samur↗Giovanni Parmigiani↗

arXiv:2606.17491v1 Announce Type: cross Abstract: Binary data factorization is common, but real-valued methods ignore discreteness and yield hard-to-interpret factors. Boolean Matrix Factorization (BooMF) instead decomposes a binary matrix into two lower-rank binary matrices via logical AND and OR, expressing the data as a Boolean disjunction of interpretable patterns. In cancer genomics, BooMF can reveal coordinated feature changes that may drive tumor evolution, unlike rotational or additive decompositions. Most existing BooMF methods are heuristic, greedy, sensitive to initialization, prone to local optima, and do not support principled model selection or uncertainty quantification. We introduce Bayesian Boolean Matrix Factorization (BBMF), a fully conjugate generative model with sparsity-inducing priors. It enforces Boolean constraints, yields interpretable latent factors with coherent uncertainty quantification, and admits Gibbs sampling with closed-form full conditionals. Because cancer evolution often involves widespread, near-simultaneous chromosome-number changes (e.g., whole-genome duplication followed by instability and selection), Boolean factorizations capture these patterns more naturally than additive models. Applied to arm-level copy-number alteration data in multiple myeloma, where entries indicate presence/absence of chromosomal-arm amplifications, BBMF finds a small set of interpretable bicliques linking patient subsets to recurrently co-altered chromosomal arms, providing a compact, biologically meaningful summary of tumor heterogeneity and demonstrating BBMF's utility for uncovering discrete latent structure in complex binary data.

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18.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2508.10178

Estimating carbon pools in the European Shelf sea environment: replacing reanalysis by model-informed machine learning?

Authors:

Jozef Skakala↗

arXiv:2508.10178v3 Announce Type: replace-cross Abstract: Shelf seas are important for the economy and the carbon cycle, but shelf sea observations for carbon pools are often sparse, or highly uncertain. An alternative can be provided by carbon reanalyses (whether assimilating proxy variables, such as chlorophyll-$a$, or directly carbon), but these are often expensive to run. We propose to use a computationally cheap ensemble of neural networks (i.e. deep ensemble) to learn the relationship between the directly observable (atmospheric, riverine and ocean) variables and marine carbon pools from a coupled physics-biogeochemistry model. The deep ensemble was trained on a North-West European Shelf (NWES) physical-biogeochemistry model free run simulation. After training, the deep ensemble was run using inputs from the NWES reanalysis instead of the free run, demonstrating that it can efficiently predict several NWES carbon pools (e.g., detritus, zooplankton, heterotrophic bacteria) in much better agreement with the reanalysis than the free run, while also providing uncertainty information. We further show that the deep ensemble performs similarly well when it is driven directly by the observations assimilated into the reanalysis, with the limitation that carbon pools can then be predicted only at the observed locations and times. We focus on explainability of the results and demonstrate potential use of the deep ensembles for future climate what-if scenarios. We suggest that model-informed machine learning presents a viable alternative to expensive reanalyses and could complement observations, wherever they are missing and/or highly uncertain.

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19.

arXiv (quant-ph) 2026-06-16 DOI: arXiv:2606.14985

Optical Creation of Synthetic Microgravity for Quantum Degenerate Gases

Authors:

Catie LeDesma↗Kendall Mehling↗Tristan Rojo↗Murray Holland↗

arXiv:2606.14985v1 Announce Type: cross Abstract: Microgravity environments provide unique opportunities for ultracold-atom experiments by enabling long interrogation times and reduced acceleration-induced dynamics. However, their realization has largely been restricted to specialized facilities such as drop towers, sounding rockets, and space-based laboratories. Here we realize synthetic microgravity for quantum degenerate gases using optically engineered force landscapes that compensate Earth's gravity to the milli-g level while maintaining continuous confinement of the atomic ensemble. These force landscapes are generated by dynamically painted optical dipole potentials and calibrated in situ through Bloch oscillations in a vertical optical lattice, enabling precise control of the residual acceleration. We use this capability to demonstrate matter-wave beam splitting with arm separations of several hundred microns. We further implement a Bloch-band atom interferometer in which interaction-induced dephasing is strongly suppressed through controlled three-dimensional expansion in the synthetic microgravity potential. This reduction of mean-field effects restores near-$\sqrt{N}$ scaling of interferometric sensitivity for large quantum degenerate ensembles. Our results establish a versatile platform for realizing synthetic microgravity with trapped quantum gases in terrestrial laboratories, bringing the advantages of microgravity experiments to continuously operating systems and opening new opportunities for quantum sensing, matter-wave interferometry, and precision measurements.

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20.

arXiv (CS.CL) 2026-06-24 DOI: arXiv:2606.23701

Evaluating LLM Usage for Efficient and Explainable Numerical and Classified Implicit Sentiment Analysis of Product Desirability

Authors:

Sherri Weitl-Harms↗John Hastings↗

Qualitative product feedback can reveal nuanced user experiences, but its implicit sentiment is difficult to measure. This paper presents a scalable and interpretable framework that uses large language models (LLMs) to quantify product desirability from such data. Using two Product Desirability Toolkit (PDT) datasets from ZORQ and CARMA comprising 106 respondent term groupings with gold-standard human annotation, zero-shot continuous numerical sentiment scoring and categorical sentiment classification are evaluated without relying on explicit review scores. Across the datasets, LLMs generated numerical sentiment scores directly from qualitative responses and closely matched expert labels, achieving Pearson correlations up to 0.97 and classification accuracy up to 94%. LLMs maintained robustness even when handling data presented in multiple forms and consistently expressed high confidence. In contrast, lexicon-based and transformer baselines did not produce statistically significant results. Among the models tested, GPT-4o-mini achieved performance comparable to larger models at 94% lower cost, supporting scalable deployment. The framework also incorporates model confidence ratings and human-readable rationale explanations (xAI), improving interpretability, transparency, and trust while supporting practical use in product satisfaction assessment. In general, using the PDT tool as a survey method along with a cost efficient LLM for sentiment analysis has the potential to provide for product evaluation with results that are rich in terms of sentiment scores (both numerical and classified sentiment) and in terms of the high-level user impressions of the product that can be used to identify ideas for product development and improvement, as well as marketing ideas for target audiences.

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21.

arXiv (CS.CL) 2026-06-16 DOI: arXiv:2606.06834

The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

Authors:

Chahat Baranwal↗Aaditya Baranwal↗Lakshya Nitin Tandon↗

High-grade gliomas integrate into neural circuits through functional synapses with neurons, raising the question of which noncoding elements shape synaptogenic gene expression in tumor cells. The regulatory program written across the dark genome, what we call the $dark regulome$, is the natural substrate to probe, and sequence foundation models offer a zero-shot route through in-silico mutagenesis (ISM); yet likelihood-based scoring is tautologically coupled to local sequence predictability, leaving the regulatory interpretation underdetermined. Across three architecturally distinct foundation models (Caduceus-Ph, HyenaDNA, Enformer) and 30,448 dark genome elements at 92 glioma-relevant loci, we introduce a residualization-and-permutation diagnostic that separates predictability-driven from regulation-driven RIS variance. A sharp 10kb proximal-regulatory horizon survives every control we apply, but the LM-derived element-class hierarchy does not: a six-feature linear baseline matches Caduceus top-decile membership at AUC $= 0.985$. Cross-architecture decomposition cleanly separates a sequence-predictability layer (the two language models co-rank long well-predicted transposable elements) from a regulatory-output layer (Enformer alone retains residual cCRE-discriminative signal), with literally zero overlap between the two top-100 lists. Conservation, brain cis-eQTL, and STRING-PPI cross-checks then anchor what biology survives: top-100 elements across all three models are $3.3\times$ enriched per model for matching brain eQTLs ($p_\mathrm{emp} < 5\times 10^{-3}$), while a tempting transposable-element regulatory layer and a striking NRXN1+NLGN1 protein-pair convergence both fail proper permutation tests once those tests are constructed. We deliver the diagnostic as a general methodological tool for any ISM-based regulatory study.

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22.

arXiv (quant-ph) 2026-06-15 DOI: arXiv:2507.15738

Symplectic coherence: a measure of position-momentum correlations in quantum states

Authors:

Varun Upreti↗Ulysse Chabaud↗

arXiv:2507.15738v2 Announce Type: replace Abstract: The interdependence of position and momentum, as highlighted by the Heisenberg uncertainty principle, is a cornerstone of quantum physics. Yet, position-momentum correlations have received little systematic attention. Motivated by recent developments in bosonic quantum physics that underscore their relevance in quantum thermodynamics, metrology, and computing, we establish a general framework to study and quantify position-momentum correlations in quantum states. We introduce symplectic coherence, a faithful and easily computable measure defined as the Frobenius norm of the block of the covariance matrix encoding position-momentum correlations, and demonstrate that symplectic coherence is monotone under relevant operations and robust under small perturbations. Furthermore, using a recent mapping by Barthe et al. (Phys. Rev. Lett. 134, 070604) which relates the covariance matrix of a bosonic state to the density matrix of a finite-dimensional system, we show that position-momentum correlations correspond to beyond-classical correlations in a virtual finite-dimensional quantum state, with symplectic coherence mapping naturally to geometric quantum discord. Taking energy constraints into account, we determine the maximal position-momentum correlations achievable at fixed energy, revealing structural insights about the corresponding optimal states. Finally, we illustrate the operational relevance of symplectic coherence through several examples in quantum information tasks and quantum thermodynamics. In the process, we establish new technical results on matrix norms and quantum covariance matrices, and demonstrate the conceptual significance of viewing covariance matrices as density matrices of virtual quantum states.

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23.

Nature (Science) 2026-06-24 DOI: HASH:04075d4df87a7ff150bbb275af565d9e

Why science needs the humanities more than ever

Authors:

Xin Fan↗

From AI to biotechnology, today’s scientific breakthroughs raise ethical and social challenges that technical expertise alone cannot solve. From AI to biotechnology, today’s scientific breakthroughs raise ethical and social challenges that technical expertise alone cannot solve.

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24.

arXiv (CS.LG) 2026-06-12 DOI: arXiv:2606.10678

One Step Closer to Ground Truth: A Multi-Scale Residual-Aware Representation Learning Pipeline for Predicting Time Series Data

Authors:

Amrijit Biswas↗Mustafa Kamal↗Robin Krambroeckers↗M. M. Lutfe Elahi↗Sifat Momen↗Nabeel Mohammed↗Shafin Rahman↗

arXiv:2606.10678v2 Announce Type: replace Abstract: Transformer-based models have emerged as leading paradigms in time-series forecasting in recent years, employing self-attention mechanisms to capture long-range dependencies. Despite their success, these single-stage forecasting architectures exhibit persistent systematic residual biases arising from structural discrepancies, unmodeled stochastic components, or inadequate multi-scale temporal representations. This limitation persists when residuals are treated as irreducible noise, precluding adaptive correction of structured error patterns. To address this limitation, we introduce a two-stage, model-agnostic framework that explicitly decouples forecasting and residual learning into distinct stages of representation learning. A base transformer first generates the initial predictions. Subsequently, a dedicated meta-corrector dynamically models structured error patterns across multivariate channels, preserves cross-variable dependencies, and iteratively refines the residual bias of the base transformer. By formalizing this pipeline as a hypothesis space expansion, our framework addresses approximation limitations inherent in single-stage architectures, removes reliance on restrictive assumptions, and enables end-to-end learning of complex error dynamics. Evaluated on eight popular benchmark datasets using established protocols, our approach achieves state-of-the-art performance, with significant improvements in standard metrics (MSE, MAE). The results demonstrate the framework's ability to mitigate systematic biases and enhance robustness to complex temporal dynamics, advancing the practical applicability of transformer-based forecasting models.

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25.

arXiv (quant-ph) 2026-06-11 DOI: arXiv:2606.11392

Compressed minimum-purity time evolution for late-time quantum dynamics

Authors:

Moksh Bhateja↗Jonas B. Rigo↗Markus Schmitt↗

arXiv:2606.11392v1 Announce Type: cross Abstract: Unitary time evolution of initially simple quantum many-body states rapidly generates entanglement and complex correlations, which limits direct numerical simulations. The late-time dynamics of physical observables, however, typically exhibits an effective simplicity in the form of hydrodynamics or kinetic theory. This leads to the question whether microscopic equations of motion can remain accurate and tractable up to long time scales by discarding irrelevant information in a controlled manner. Here, we introduce compressed minimum-purity time evolution (CoMPuTE) as an approach to keep track of a consistent set of reduced local density matrices, closing the hierarchical equations of motion using a minimum-purity principle. In benchmark applications we demonstrate (i) accurate description of energy diffusion in the one-dimensional mixed-field Ising model, (ii) the applicability to genuinely out-of-equilibrium Floquet dynamics starting from a pure state, and (iii) the limitations of the local reduced density matrix approximation when describing transport in the XXZ chain at $\Delta=1$ that is governed by increasingly non-local integrals of motion. The CoMPuTE method enhances computational efficiency in comparison to the closely related local-information time evolution algorithm, opening a possible route towards an extension to systems in higher spatial dimensions.

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