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01.
arXiv (CS.LG) 2026-06-11

Online Learning for Supervisory Switching Control

arXiv:2603.14762v4 Announce Type: replace-cross Abstract: We study supervisory switching control for partially-observed linear dynamical systems. The objective is to identify and deploy a suitable controller for the unknown system by periodically selecting among a collection of $N$ candidate controllers, some of which may destabilize the underlying system. While classical estimator-based supervisory control guarantees asymptotic stability, it lacks quantitative finite-time performance bounds. Conversely, current non-asymptotic methods in both online learning and system identification require restrictive assumptions that are incompatible in a control setting, such as system stability, which preclude testing potentially unstable controllers. To bridge this gap, we propose a novel, non-asymptotic analysis of supervisory control that adapts multi-armed bandit algorithms to a control-theoretic setting. The proposed data-driven algorithm evaluates candidate controllers via scoring criteria that leverage system observability to isolate the effects of state history, enabling both detection of destabilizing controllers and accurate system identification. We present two algorithmic variants with dimension-free, finite-time guarantees, where each identifies the matching controller in $O(N \log^2 N)$ steps, while simultaneously achieving finite $L_2$-gain with respect to system disturbances.

02.
arXiv (CS.CV) 2026-06-11

DarkVGGT: Seeing Through Darkness Using Thermal Geometry without Daylight Tax

Recent feed-forward 3D reconstruction methods have demonstrated strong performance and flexibility in efficient end-to-end scene geometry estimation from image streams. However, their reliance on visible-light appearance makes them vulnerable in dark and low-visibility environments, where RGB cues are severely degraded and geometric evidence becomes ambiguous. To address this challenge, we propose DarkVGGT, an RGB-T feed-forward geometry framework that uses physics-aware thermal modeling for robust 3D estimation in low-light scenes. DarkVGGT introduces two complementary modules. First, physics-inspired thermal factorization extracts emissive-dominant, geometry-consistent thermal cues while isolating sparse reflective residuals that may introduce geometric ambiguity. Second, geometry-shared thermal routing isolates modality-invariant geometric structures from thermal-specific patterns, selectively injecting reliability-aware structural guidance into the RGB stream. Together, these components enable accurate thermal-informed geometry estimation under degraded RGB conditions while largely preserving performance in well-lit environments. Experiments on low-visibility RGB-T benchmarks demonstrate consistent improvements in both depth and camera pose estimation over existing feed-forward geometry baselines.

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

See First, Answer Later: Visual Evidence Pre-Alignment via Sufficiency-Driven RL

Multimodal large language models (MLLMs) integrate strong text reasoning with visual inputs, yet their responses can be inconsistent with the underlying images, indicating ineffective utilization of visual evidence during inference. The prevailing training paradigm relies on large-scale caption-based pretraining for general alignment, followed by supervised fine-tuning and reinforcement learning to enable instruction following and complex reasoning. However, such pretraining provides only weak visual grounding: short, coarse captions bias models toward salient objects while neglecting fine-grained visual evidence. In this paper, we introduce Visual Evidence Pre-Alignment (VEPA), an intermediate stage between pretraining and post-training that explores a novel sufficiency-driven objective with Group Relative Policy Optimization (GRPO) to optimize question-conditioned visual evidence descriptions. Extensive experiments across diverse benchmarks show that our VEPA consistently enhances performance on visually demanding evaluations and complements standard supervised post-training. Further analyses show that the income stems from strengthened, transferable visual grounding, rather than from additional task-specific training.

04.
arXiv (CS.LG) 2026-06-19

Influence-Guided Concolic Testing of Transformer Robustness

arXiv:2509.23806v2 Announce Type: replace-cross Abstract: Concolic testing for neural networks alternates concrete execution with constraint solving to search for inputs that flip model decisions. We present a concolic tester for Transformer classifiers that uses SHAP estimates to rank pending path predicates by their impact on the current prediction. To support self-attention with multiple heads in execution backed by SMT solving, we implement attention semantics in pure Python that are compatible with the solver and make the softmax boundary explicit by concretizing exponentiation arguments. We evaluate our method on CIFAR-10 across three compact Transformer classifiers, ResNet18, and VGG16 under a one-pixel budget and a 900s horizon. Across the 500 model–input pairs in this matched comparison, our method achieves 60% success, compared with 15% for a differential evolution baseline that treats the model as a black box. In the primary two-layer Transformer branch-ordering study, SHAP-based predicate prioritization raises success from 56% to 60% and reduces median attack time by 51%. These results show that influence-guided path exploration can make concolic testing a practical way to find adversarial examples in Transformer models.

05.
Nature Biotechnology 2026-06-23

Efficient generation of epitope-targeted antibodies with Germinal

Obtaining antibodies to specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low success rates that require resource-intensive screening. Here we introduce Germinal, a broadly enabling generative pipeline that designs antibodies against specific epitopes with nanomolar binding affinities while requiring only low-n experimental testing. Our method co-optimizes antibody structure and sequence by integrating a structure predictor with an antibody-specific protein language model to perform de novo design of functional complementarity-determining regions onto a user-specified structural framework. When tested against four diverse protein targets, Germinal designed functional antibodies across all targets and binder formats, testing only 43–101 designs for each antigen. Validated designs also exhibited robust expression in mammalian cells and high sequence and structural novelty. We provide open-source code and full computational and experimental protocols to facilitate wide adoption. Germinal achieves epitope-targeted, de novo complementarity-determining region design with high experimental success rates.

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

Emergent de Sitter Space and Non-Unitary Tensor Networks from Non-Hermitian Quantum Criticality

arXiv:2606.17983v1 Announce Type: new Abstract: Extending the holographic principle to de Sitter (dS) spacetimes remains one of the most vital open frontiers in quantum gravity, where a microscopic, bottom-up tensor-network framework that relates boundary quantum data to emergent de Sitter spacetime is still lacking. In this work, we first show the emergence of de Sitter spacetime from boundary entanglement by formulating a non-unitary continuous multi-scale entanglement renormalization ansatz (cMERA) for a concrete non-Hermitian critical fermion chain. Within this emergent spacetime, we analyze the associated geodesics and show that they act as extremal Ryu-Takayanagi (RT) surfaces undergoing a smooth timelike-to-null transition. Remarkably, we demonstrate that this continuum trajectory dictates a distinct tensor-network architecture in which the bond-counting contribution naturally truncates at the discrete timelike-to-null transition toward the deep infrared. In the resulting architecture, the null ray along the horizon is represented by zero-cost links, since the associated cut severs no tensor legs. This network structure successfully reproduces the logarithmic scaling of non-unitary critical entanglement entropy, offering a bond-counting picture for the de Sitter RT formula. Our results provide the long-sought dS/(c)MERA correspondence at the level of both emergent spacetime and discrete holographic entanglement.

07.
arXiv (CS.AI) 2026-06-11

Privacy-Preserving Federated Autoencoder for ECG Anomaly Detection on Edge Devices

arXiv:2606.11556v1 Announce Type: cross Abstract: Continuous electrocardiography (ECG) monitoring could surface rhythm abnormalities before they escalate into cardiovascular events. However, a deployable system must satisfy three requirements simultaneously: legal-grade privacy (GDPR, HIPAA), real-time inference on constrained edge hardware, and detection quality under non-IID cross-hospital data. We design and evaluate an end-to-end federated system addressing all three for unsupervised 12-lead ECG anomaly detection on PTB-XL dataset, combining three autoencoder families (VanillaAE, ConvAE, VAE), Flower-based federated averaging (FedAvg) across ten simulated hospitals, client-side differentially private SGD (DP-SGD) with a Rényi-DP accountant, and 8-bit integer (INT8) post-training quantization with Raspberry Pi 4 benchmarking. Our main contributions are: an empirical characterization of how these mechanisms compose, practical DP-specific recommendations, and technical and security insights for a clinically sensitive setting. Federated learning matches or exceeds the centralized baseline across all architectures (ConvAE federated area under the ROC curve, AUROC, $0.782$), and an $\varepsilon$ sweep identifies $\varepsilon=4$ as the recommended clinical operating point. INT8 quantization roughly halves model size and cuts Pi 4 latency by up to $44%$ with $

09.
arXiv (quant-ph) 2026-06-16

Measuring Non-Stabilizerness in an SU(2) Lattice Gauge Theory

arXiv:2606.14842v1 Announce Type: new Abstract: One of the goals of quantum simulation is to provide novel insights into quantum systems, such as the gauge theories that are relevant for high-energy and nuclear physics. Recent years have seen rapid improvements in both the hardware and software necessary for these simulations. A central consideration in the design of such simulations is the quantum complexity of a given quantum state. This work takes a step towards studying a specific kind of complexity, namely the non-stabilizerness, in a simple yet non-trivial system: SU(2) lattice gauge theory of two plaquettes. The non-stabilizerness of low-energy eigenstates is studied and the implications for quantum simulations are discussed. The real-time evolution of this system is simulated on ibm_marrakesh and the non-stabilizerness is measured using a random measurement protocol. New techniques enhancing the efficiency of this protocol are developed, including both a new way to calculate the estimator for non-stabilizerness and a flexible error mitigation technique called Bit String Decoherence Renormalization. This mitigation method is central to accurately resolving the experimental time dependence of non-stabilizerness, and is anticipated to have broad applicability in digital quantum simulations.

10.
arXiv (CS.LG) 2026-06-16

SILAGE: Memory-Efficient, Full-Gradient-Free Nonconvex Optimization for Nested Finite Sums

arXiv:2606.15832v1 Announce Type: new Abstract: Empirical risk minimization on massive datasets naturally exhibits a nested double finite-sum structure, where $N=nm$ total samples are logically or physically partitioned into $n$ blocks of size $m$ (e.g., in pooled data silos, out-of-core learning, or deliberate stratification). While variance-reduced methods achieve optimal oracle complexities for nonconvex objectives, they suffer from severe scaling bottlenecks in this centralized regime. Recursive estimators, such as PAGE, require periodic global full-gradient refreshes over all $nm$ samples, which are computationally expensive. Conversely, single-loop methods, such as SILVER, avoid such refreshes but require an impractical $\mathcal{O}(nm)$ memory footprint to store a control variate for every sample. In this paper, we propose SILAGE, a variance-reduced algorithm that addresses this trade-off. By actively exploiting the double-sum structure, SILAGE eliminates periodic global full-gradient refreshes over all $nm$ components (evaluating at most one local group gradient per iteration) while requiring only $\mathcal{O}(n)$ memory. Furthermore, we provide a tight convergence analysis that avoids pessimistic worst-case Lipschitz constants. Instead, SILAGE's complexity natively adapts to the underlying data geometry via nested functional similarities: across-group ($\delta_1$) and within-group ($\delta_2$) heterogeneity. Our results improve existing state-of-the-art bounds in several practically relevant regimes.

11.
medRxiv (Medicine) 2026-06-17

Cardio Heart Connect: Protocol for a Randomized Trial of a Commercially Available mHealth Fitness Intervention for Cardiac Rehabilitation After Transcatheter Aortic Valve Replacement

Background: Despite ample evidence of the benefits of cardiac rehabilitation (CR), few transcatheter aortic valve replacement (TAVR) patients participate. Commercially available mobile health offers an opportunity to deliver activity-promotion content to populations that are challenged to participate in CR. This study aims to test the efficacy of clinically controlled, commercially available fitness programming for improving physical activity and cardiovascular health outcomes designed to be initiated while patients are on waitlists for traditional CR. Methods: The Cardio Heart Connect study is a hybrid type I effectiveness-implementation trial aiming to enroll N=200 patients who have been placed on a cardiac rehab waitlist following a TAVR procedure from the University of Colorado Hospital Heart and Vascular Center. Participants will be randomized 1:1 to the Cardio Heart Connect intervention with commercially available fitness or attention control, designed to control for technology access. At baseline, post-intervention (8 weeks), and follow-up (12 months), we will assess the primary outcome of participants? daily steps as measured by smartwatch accelerometer and secondary outcomes of interest including functional capacity (Duke Activity Status Index; VO2max), quality of life (Kansas City Cardiomyopathy Questionnaire), and cardiovascular health status (Life Essential 8). In addition, we will use mixed methodologies to evaluate the implementation of intervention using the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) Framework. Conclusions: Commercially available fitness programs have the potential to provide more accessible opportunities for patients recovering from TAVR to engage in physical activity and may be preferred due to their customizability, convenience, and ease of scheduling. Overall, this study will provide insight into the use of commercial mHealth to promote activity following TAVR.

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

Neural Additive and Basis Models with Feature Selection and Interactions

arXiv:2606.19850v1 Announce Type: cross Abstract: Deep neural networks (DNNs) exhibit attractive performance in various fields but often suffer from low interpretability. The neural additive model (NAM) and its variant called the neural basis model (NBM) use neural networks (NNs) as nonlinear shape functions in generalized additive models (GAMs). Both models are highly interpretable and exhibit good performance and flexibility for NN training. NAM and NBM can provide and visualize the contribution of each feature to the prediction owing to GAM-based architectures. However, when using two-input NNs to consider feature interactions or when applying them to high-dimensional datasets, training NAM and NBM becomes intractable due to the increase in the computational resources required. This paper proposes incorporating the feature selection mechanism into NAM and NBM to resolve computational bottlenecks. We introduce the feature selection layer in both models and update the selection weights during training. Our method is simple and can reduce computational costs and model sizes compared to vanilla NAM and NBM. In addition, it enables us to use two-input NNs even in high-dimensional datasets and capture feature interactions. We demonstrate that the proposed models are computationally efficient compared to vanilla NAM and NBM, and they exhibit better or comparable performance with state-of-the-art GAMs.

13.
arXiv (CS.AI) 2026-06-11

Are LLMs Bad at Moral Reasoning?

arXiv:2606.11635v1 Announce Type: cross Abstract: For highly capable AI systems to operate safely in dynamic, open-ended environments, they must be able to identify, understand, and respond to moral reasons for action, and constrain their behaviour accordingly. A growing body of research aims to evaluate this capacity – moral competence – in today's most capable AI systems, recently reaching broadly pessimistic conclusions. One of the most ambitious such papers collects gold-standard human-authored rubrics for evaluating moral reasoning in 1,000 cases, and benchmarks frontier AI models against those rubrics, with underwhelming results. In this paper, we argue that the MoReBench dataset can be redeployed to give a much more optimistic picture of LLMs' moral reasoning (an essential part of moral competence). We show that if, instead of scoring LLMs' responses to these cases against these rubrics, we instead give the LLMs the same task given to humans – to generate scoring rubrics for the moral analysis of particular cases – the rubrics they generate are both better calibrated to the human rubrics than their open-ended responses, and, where they differ, plausibly reflect nothing more than the vast dimensionality of most moral problems, as well as highlighting some human departures from the "rubric for creating rubrics". Taking these points into consideration, the MoReBench dataset suggests that LLMs are significantly more capable at moral reasoning than was previously believed.

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

AgentArmor: A Framework, Evaluation, \& Mitigation of Coding Agent Failures

arXiv:2606.19380v1 Announce Type: cross Abstract: Software engineering and deployment are increasingly being delegated to AI coding agents. The scale of their adoption is surfacing rare, but highly destructive, failure modes. In this paper, we study these failure modes as stemming from three distinct mechanisms: underspecification, where default model behavior is unsafe; capability errors, where the safe action is available but the model does not adhere to it due to bias or capability limitations; and agent harness errors, where the model fails to execute the safe action through the harness. We evaluate these across 8 different evaluations, each inspired by real-life deployment failures, totaling 20 coding environments and 59 synthetic transcript templates. Based on this evaluation, we propose AgentArmor, an agent harness modification, to mitigate these errors. By adding an extended system prompt, a separate command classifier, a ``3 strikes'' policy, deterministic guardrails, and tools for the agent to edit its own context, we show that AgentArmor is safer across a statistically significant number of samples. Thus, we suggest concrete mitigations for current coding agents and a design philosophy for future agent harness features.

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

Learning to Share: Selective Memory for Efficient Parallel Agentic Systems

arXiv:2602.05965v2 Announce Type: replace-cross Abstract: Agentic systems solve complex tasks by coordinating multiple agents that iteratively reason, invoke tools, and exchange intermediate results. To improve robustness and solution quality, recent approaches deploy multiple agent teams running in parallel to explore diverse reasoning trajectories. However, parallel execution comes at a significant computational cost: when different teams independently reason about similar sub-problems or execute analogous steps, they repeatedly perform substantial overlapping computation. To address these limitations, in this paper, we propose Learning to Share (LTS), a learned shared-memory mechanism for parallel agentic frameworks that enables selective cross-team information reuse while controlling context growth. LTS introduces a global memory bank accessible to all teams and a lightweight controller that decides whether intermediate agent steps should be added to memory or not. The controller is trained using stepwise reinforcement learning with usage-aware credit assignment, allowing it to identify information that is globally useful across parallel executions. Experiments on the AssistantBench and GAIA benchmarks show that LTS significantly reduces overall runtime while matching or improving task performance compared to memory-free parallel baselines, demonstrating that learned memory admission is an effective strategy for improving the efficiency of parallel agentic systems. Project page: https://joefioresi718.github.io/LTS_webpage/

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

GenAutoML: An Agentic Framework for Dynamic Architecture Generation and Optimization in Time-Series Analysis

arXiv:2606.05860v2 Announce Type: replace Abstract: Designing neural architectures for time-series forecasting and anomaly detection remains a resource-intensive task that often requires substantial domain expertise. Traditional Automated Machine Learning (AutoML) systems typically rely on static, predefined search spaces, limiting their ability to adapt to diverse data characteristics. We present GenAutoML, an agentic framework that leverages Large Language Models (LLMs) as neural architects to bridge natural-language requirements and executable PyTorch implementations. The framework incorporates a Sandboxed Reflection Loop for autonomous code refinement and a Signature-Aware Runtime that enforces architectural consistency and execution safety. To improve robustness under non-stationary conditions, we further introduce a Dynamic Reversible Instance Normalization (Dyn-RevIN) wrapper. Experiments on the ETTh1, ETTm1, and Weather benchmarks demonstrate that GenAutoML can dynamically generate task-specific neural architectures tailored to dataset characteristics. Among the generated models, WaveInterferenceNet achieves inference latency below 0.01 ms per sample while maintaining competitive predictive performance. By emphasizing computational efficiency, architectural adaptability, and stable optimization behavior, GenAutoML enables the creation of ultra-lightweight neural networks suitable for resource-constrained and latency-sensitive Edge AI deployments.

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

Loss-Shift Transfer via Bayes Quotients

arXiv:2606.13178v1 Announce Type: new Abstract: Transfer learning is usually studied as a consequence of distribution shift. This paper identifies an orthogonal failure mode in which the data distribution is fixed and the loss changes. This setting is called loss shift. A loss determines which information in \(X\) is Bayes-relevant, and two losses may therefore require different representations even under the same joint law \(P(X,Y)\). The idea is formalized using Bayes quotients, which allow losses to be ordered by refinement. In the Bayes-quotient formulation, strict refinement gives an immediate qualitative obstruction. A source-minimal representation for a coarser loss is insufficient for a strictly finer target loss. For finite-output log loss, this obstruction becomes an exact quantitative identity. The excess risk is the conditional information about \(Y\) discarded by the representation. Experiments in controlled, learned, synthetic-image, and real-image settings show the predicted effect, i.e., classification-equivalent representations can have different optimal log-loss performance under a fixed data distribution.

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

Simulation of Language Evolution under Regulated Social Media Platforms: A Synergistic Approach of Large Language Models and Genetic Algorithms

arXiv:2502.19193v2 Announce Type: replace-cross Abstract: Social media platforms frequently impose restrictive policies to moderate user content, prompting the emergence of creative evasion language strategies. This paper presents a multi-agent framework based on Large Language Models (LLMs) to simulate the iterative evolution of language strategies under regulatory constraints. In this framework, participant agents, as social media users, continuously evolve their language expression, while supervisory agents emulate platform-level regulation by assessing policy violations. To achieve a more faithful simulation, we employ a dual design of language strategies (constraint and expression) to differentiate conflicting goals and utilize an LLM-driven GA (Genetic Algorithm) for the selection, mutation, and crossover of language strategies. The framework is evaluated using two distinct scenarios: an abstract password game and a realistic simulated illegal pet trade scenario. Experimental results demonstrate that as the number of dialogue rounds increases, both the number of uninterrupted dialogue turns and the accuracy of information transmission improve significantly. Furthermore, a user study with 40 participants validates the real-world relevance of the generated dialogues and strategies. Moreover, ablation studies validate the importance of the GA, emphasizing its contribution to long-term adaptability and improved overall results.

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

Gaussian Mixture Attention: Linear-Time Sequence Mixing via Probabilistic Latent Routing

arXiv:2606.18283v1 Announce Type: new Abstract: The dense token-to-token interaction pattern of standard dot-product attention remains a central bottleneck in scaling Transformer architectures to long contexts. We introduce Gaussian Mixture Attention (GMA), a probabilistic attention-style sequence mixer that replaces explicit pairwise query–key comparison with routing through $K$ learned Gaussian mixture components. Queries and keys are mapped to posterior responsibility vectors over a shared latent routing space; their overlap defines an implicit responsibility-space affinity, while values are written into and read from a $K$-slot latent memory. By exploiting the associativity of matrix multiplication, GMA avoids materializing the induced $N\times N$ affinity matrix and instead uses two responsibility matrices whose dominant activation storage scales as $\mathcal{O}(NK)$ rather than $\mathcal{O}(N^2)$ for fixed $K$. We formulate bidirectional and causal variants of GMA, provide an end-to-end differentiable parameterization of the Gaussian mixture components, and analyze its responsibility-modulated gradient structure, constrained non-negative low-rank affinity interpretation, and local routing stability. Empirically, GMA exhibits the intended fixed-$K$ linear memory scaling and is competitive with attention-style baselines on long-context classification, while causal GMA improves over tested linear/random-feature attention variants on WikiText-103 but remains behind optimized causal SDPA and Mamba in the current implementation. Analysis of learned responsibilities further shows broad component usage and moderate alignment with surface-form token categories, supporting GMA as a probabilistic, interpretable, fixed-$K$ linear-time attention-style alternative rather than a universal replacement for optimized softmax attention or state-space models.

20.
arXiv (quant-ph) 2026-06-16

Noise-induced shallow circuits and absence of barren plateaus

arXiv:2403.13927v3 Announce Type: replace Abstract: Motivated by realistic hardware considerations of the pre-fault-tolerant era, we comprehensively study the impact of uncorrected noise on quantum circuits. We first show that in the task of estimating observable expectation values any noise truncates most quantum circuits to effectively logarithmic depth. We then prove that quantum circuits under any non-unital noise do not exhibit barren plateaus for cost functions composed of local observables. However, by using the effective shallowness, we also design an efficient classical algorithm to estimate observable expectation values within any constant additive accuracy, with high probability over the choice of the circuit, in any circuit architecture. Taken together, our results establish that, unless we carefully engineer quantum circuits to take advantage of the noise, noisy quantum circuits are unlikely to offer an advantage over shallow ones for algorithms that output observable expectation value estimates, such as many variational quantum machine learning proposals.

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

Deep Reinforcement Learning for Minimum Zero-Forcing Sets

arXiv:2606.18106v1 Announce Type: new Abstract: This paper explores the problem of finding the minimum zero-forcing set on undirected graphs and proposes an adapted machine-learning framework to solve the problem. The minimum zero-forcing set problem is a graph coloring problem where the color of an initial set of nodes propagates throughout a network. The set of nodes is zero-forcing if it forces all uncolored nodes to change color under the constraint of the color-change rule. There are several applications to this problem across different domains such as network science, network control, and designing logical circuits. Finding the minimum zero-forcing set is shown to be NP-hard. We propose a reinforcement learning framework, SD-ZFS, that adapts the S2V-DQN architecture to the ZFS problem. We train several models on this adapted framework and analyze the performance across graph datasets that have varying structures. We evaluate how the models trained on the framework generalize, scale, and transfer to different network types. The results demonstrate the effectiveness of the framework when compared against the optimal solution and greedy heuristic. We provide further insight into how the ZFS problem can be solved through machine-learning and the influence of network structure on the problem.

22.
arXiv (CS.AI) 2026-06-11

StatefulDiscovery: Evidence-Calibrated Claim Formation in Open-Ended Scientific Discovery

arXiv:2606.11851v1 Announce Type: new Abstract: Open-ended scientific discovery asks agents to move beyond executing analyses for predefined questions. Across multiple rounds of exploration, a discovery agent must decide which phenomena warrant investigation while avoiding overinterpretation, where emerging claims exceed the evidential scope of the analyses supporting them. This creates an evidence-calibration problem: the exploration trajectory must be coupled with claim status so that evidence can guide both what to investigate next and what can be claimed. We introduce StatefulDiscovery, a discovery framework that externalizes investigation state and uses it to coordinate frontier selection, evidence acquisition, and claim adjudication. We evaluate StatefulDiscovery across 40 real-data discovery tasks. Compared with several baselines, StatefulDiscovery produces more claims overall judged to be both well-supported and high-value. Ablations indicate that structured hypotheses, local adjudication, and frontier control contribute to performance. Together, these results suggest that explicit discovery state can couple exploration with evidence-calibrated claim formation.

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

Rethinking the Pointer Loss in Table Structure Recognition: Geometry-Aware Pointer Loss for Spatial Locality

Table Structure Recognition (TSR) using a pointer network achieves impressive results by predicting HTML sequences while aligning tags to detected text (or cell) regions. However, our analysis reveals that when pointer networks fail, 79.6% of errors occur between spatially adjacent cells (Manhattan distance

24.
medRxiv (Medicine) 2026-06-17

Identifying anaphylaxis using weakly-supervised prediction models and natural language processing

Objectives Scalable computable phenotyping algorithms are critical for conducting high-throughput disease-outcome research in large, distributed-data electronic health record (EHR) and claims data settings. We developed and evaluated a claims- and EHR-based computable phenotyping algorithm for anaphylaxis, a rare acute condition that is challenging to accurately identify using claims data alone. Materials and Methods Potential anaphylaxis events came from two healthcare systems (Kaiser Permanente Washington [KPWA] and Vanderbilt University Medical Center [VUMC]). We engineered features from clinical text using automated natural language processing (NLP) methods. We then developed a phenotyping algorithm using four NLP- and diagnosis code-based silver labels (proxies for the gold-standard labels). Gold-standard abstracted outcomes were used to evaluate algorithm performance. Results The largest area under the receiver operating characteristic curve (AUC) was 0.931 for an NLP-based silver-label model at KPWA. Depending on the model and healthcare system site, positive predictive value (PPV) and sensitivity at the threshold of predicted probability that maximized F1 score ranged from 0.52 to 0.77 (PPV) and 0.78 to 1 (sensitivity). Discussion NLP-based silver-label models had large AUC at KPWA but not at VUMC. This may be because clinical text at KPWA is only available for outpatient encounters and secure messaging. High sensitivity for identifying anaphylaxis can be obtained using our best-performing models. Conclusion The best-performing models had better PPV and sensitivity tradeoffs than prior bespoke anaphylaxis models with costly, manually curated features. The simplicity of the approach compared to traditional phenotyping methods allows it to be deployed easily at multiple health care systems.

25.
PLOS Computational Biology 2026-06-01

Supervised deep learning with gene functional annotation for cell classification

作者:

by Zhexiao Lin, Yuanyuan Gao, Wei Sun Gene-by-gene differential expression analysis is a widely used supervised approach for interpreting single-cell RNA-sequencing (scRNA-seq) data. However, modern scRNA-seq datasets often contain large numbers of cells, leading to the identification of many differentially expressed genes with extremely small p-values but negligible effect sizes, thus making biological interpretation difficult. To overcome this challenge, we developed Supervised Deep learning with gene functional ANnotation (SDAN), a method that integrates gene functional annotation information (e.g., protein-protein interaction) with gene-expression profiles through a graph neural network. SDAN identifies functionally coherent gene sets that optimally classify cells, and the resulting cell-level classification scores can be aggregated to make individual-level predictions. We evaluated SDAN alongside three representative existing methods in three real-data applications aimed at identifying gene sets associated with severe COVID-19, dementia, and cancer immunotherapy response. Across all applications, SDAN consistently outperformed the alternative approaches by achieving two objectives simultaneously: accurate outcome classification and clear assignment of genes to functionally related gene sets.