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01.
arXiv (CS.CV) 2026-06-18

Confidence is Not Reliability: Rethinking MC Dropout in Brain Tumour Segmentation

Glioma segmentation in multiparametric MRI is a critical component of treatment planning. A segmentation model that fails silently on treatment-critical sub-regions represents a patient safety risk that overlap-based metrics such as Dice scores cannot expose. We ask whether voxel-level uncertainty estimation via Monte Carlo (MC) Dropout can reliably identify segmentation errors in clinically critical sub-regions, and whether calibration failure modes are detectable from standard reporting metrics alone. In an empirical two-model case study on 126 BraTS21 patients, we evaluate a high-performance pretrained SegResNet and a locally trained UNet with residual units (UNet-Res). MC dropout preserved segmentation accuracy ($|\Delta Dice|$ $

02.
arXiv (CS.AI) 2026-06-12

Intelligence as Managed Autonomy: Failure, Escalation, and Governance for Agentic AI Systems

arXiv:2605.27628v2 Announce Type: replace Abstract: As autonomous and agentic AI systems scale in robotic and human-machine environments, managing hallucination and persistent but unjustified action remains an open challenge. Rather than attributing these failures solely to model or alignment limitations, this paper explores the architectural vulnerability of unbounded autonomy - the presumption that an agent should continue operating regardless of rising uncertainty. It introduces a theory of managed autonomy that defines intelligent behavior through the formal capacity to detect epistemic drift, suspend reasoning, attempt recovery, and ultimately surrender control when reliability diminishes. We instantiate this theory via the SMARt (Self-Managing Multi-tier Autonomous Reasoning with Regulated/Revoked transitions) model, a four-layer framework featuring Stable, Meta-cognitive, Assisted, and Regulated states. By developing a timed, guarded Petri net formulation, we establish theoretically bounded properties for the system, demonstrating how architecture can formally mandate escalation, constrain invalid outputs, and ensure governance reachability under specified conditions. We further analyze how incorporating domain-specific trigger sets across varied operational settings (e.g., healthcare, robotics, etc.) can systematically preserve safety, assuming completeness and soundness criteria are met. Because these triggers are designed to be adaptive, the SMARt model accommodates the safe, controlled expansion of an agent's operational scope over time. We conclude that formalizing failure management within the autonomy lifecycle is a crucial step toward realizing reliable and governed artificial intelligence.

03.
arXiv (CS.CL) 2026-06-15

EmoMind: Decoding Affective Captions from Human Brain fMRI

Decoding visual experience from brain activity has advanced substantially, but current brain-to-text systems largely recover semantic content while discarding affect. Additionally, language models can generate emotional text when prompted with categorical labels, but such labels collapse rich inter-subject variability into coarse discrete bins. We present EmoMind, the first end-to-end pipeline for decoding affective captions directly from fMRI signals. EmoMind first retrieves a semantically grounded neutral scene description from brain-decoded visual features, then rewrites it using a continuous 34-dimensional emotion vector decoded from the same fMRI recording. To control the balance between content preservation and affective expression, we train the rewriter with classifier-free guidance against an identity-preserving null branch, enabling smooth interpolation between semantic fidelity and affective expressivity. We evaluate affective caption generation with a three-axis validation framework spanning subject-specificity, structural geometry, and causal control. We further augment this framework with a synthetic-brain substitution test that probes robustness to the measurement apparatus, and we benchmark each axis against GPT-4 prompted with brain-decoded top-5 emotion labels as a strong discrete baseline. Across two independent emotion fMRI datasets, EmoMind significantly outperforms label-prompted GPT-4 on all three axes, with the largest gains on metrics that require person-specific affective structure rather than population-level emotion aggregation. These results establish continuous brain-decoded affect as a viable control signal for individualized affective caption generation and open new directions for studying individual affective brain organisation.

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

S-Agent: Spatial Tool-Use Elicits Reasoning for Spatial Intelligence

Real-world spatial intelligence requires reasoning over a continuous and evolving 3D world, yet existing VLMs and tool-augmented agents largely remain tied to static, stateless inference from isolated visual observations. We introduce \textsc{S-Agent}, a spatial tool-use agentic paradigm for understanding and reasoning over continuous multi-view images and videos. By formulating spatial reasoning as spatio-temporal evidence accumulation rather than isolated frame-level prediction, \textsc{S-Agent} reshapes spatial perception into scene-centric understanding beyond frame-centric recognition. Specifically, \textsc{S-Agent} casts the VLM as a semantic planner that decides what evidence is needed, while a hierarchy of spatial tools and experts grounds objects in 2D, lifts them into 3D geometric evidence, and aggregates this evidence into high-level spatial knowledge (e.g., counting, measurement, orientation, and relative position). Additionally, a temporal memory mechanism, including Scene Memory for maintaining the evolving scene state and Agent Memory for accumulating reasoning context, enables evidence integration across frames and reasoning steps. Comprehensive experiments on multi-view and video spatial reasoning benchmarks show that \textsc{S-Agent} consistently improves both open-source and closed-source VLMs in a training-free manner. Beyond inference-time augmentation, supervised fine-tuning (SFT) on \textsc{S-Agent}-generated spatial trajectories \textsc{S-300K} yields \textsc{S-Agent-8B}, a compact spatial agent that significantly surpasses similar-scale baselines (e.g., Qwen3-VL-8B) and performs comparably to advanced closed-source models (e.g., GPT-5.4 and Gemini 3).

05.
arXiv (CS.CV) 2026-06-16

BRDFusion: Physics Meets Generation for Urban Scene Inverse Rendering

Inverse rendering of urban scenes from captured videos enables numerous applications, including content creation and autonomous driving simulation. Physically-based rendering methods follow and control lighting physics, but suffer from reconstruction and rendering artifacts. While generative models produce realistic videos, they offer limited consistency and controllability. We present BRDFusion, a unified framework that combines two complementary models for inverse and forward rendering. Specifically, BRDFusion recovers explicit, consistent scene properties with physical modeling and alleviates optimization ambiguity with generative priors. During forward rendering, the physical model provides controllable rendering from the scene configuration, and the generative model denoises and fixes artifacts. Therefore, our method produces high-quality videos while allowing precise control, outperforming baselines in real and synthetic scenes. Moreover, BRDFusion supports novel-view relighting, night simulation, and dynamic object insertion/editing. Project page: https://shigon255.github.io/brdfusion-page/

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

Fixed-Point Reasoners: Stable and Adaptive Deep Looped Transformers

arXiv:2606.18206v1 Announce Type: new Abstract: Looped architectures provide an inductive bias toward learning step-by-step procedures for tasks that require compositional reasoning. The number of effective layers reached by looping determines the quality of the solution these models find. Like deep architectures, looped architectures are prone to a signal propagation problem induced by depth as the halting decision is postponed. In this paper, we address this signal propagation issue using pre-norm layers and residual scaling. Building on these architectural modifications, we propose FPRM, a Transformer-based Fixed-Point Reasoning Model that uses fixed-point convergence as an end-to-end halting mechanism in a looped architecture. We show that fixed-point halting allows FPRM to adapt its compute to task difficulty. FPRM is effective on common reasoning benchmarks, namely Sudoku, Maze, state-tracking, and ARC-AGI.

07.
medRxiv (Medicine) 2026-06-12

Estimating the effectiveness of syndromic screening at airports for Bundibugyo ebolavirus disease

Authors:

We used a stochastic simulation model to estimate the effectiveness of combined exit and entry airport screening for Bundibugyo ebolavirus disease (BVD), using natural-history parameters from a Bayesian re-analysis of the 2012 Isiro outbreak. For a 12-hour international flight from DRC or Uganda at 86% screening sensitivity, we estimate 65% of infected travellers would arrive undetected (95% CrI: 38 - 76%). The main driver of this outcome is the relative duration of the the incubation period (approximately 7.7 days) and the onset-to-severe-disease interval (approximately 4 days): most infected travellers board before symptom onset and are undetectable by any syndromic screen, whilst those who are symptomatic progress rapidly to illness severe enough to preclude travel. This is compounded during active epidemic growth, when recently exposed (and therefore pre-symptomatic) cases are overrepresented among travellers. Syndromic airport screening offers limited protection against BVD spread via air travel, and should be complemented by outbreak control at source and strengthened clinical surveillance in receiving countries with high travel connectivity to affected areas.

08.
bioRxiv (Bioinfo) 2026-06-16

Evidence for recombination in dengue virus genomes

Recombination is a key driver of RNA virus evolution, yet its extent and evolutionary implications in dengue virus (DENV) remain incompletely understood. We conducted a comprehensive, genome-wide recombination screen across 6,905 complete DENV genomes representing all four serotypes, 82 countries, and eight decades of sampling (1944-2023) retrieved from the Bacterial and Viral Bioinformatics Resource Center. Using seven complementary recombination detection methods implemented in RDP5, we identified 66 recombination events across 53 unique recombinant sequences, of which 29 are newly described. Events included intra-genotypic (n = 18), inter-genotypic (n = 32), and inter-serotypic (n = 16) exchanges spanning 14 genotypes and four continents, with no meaningful serotype-level enrichment (Cramer's V = 0.054). Recombination was concentrated in non-structural genes, most frequently NS3 (19 events), NS5 (17), and NS2 (12), while the capsid gene contained no recombination events, consistent with strong functional constraint. Single-nucleotide polymorphism analyses confirmed low divergence between recombinants and their inferred parents in both recombinant and non-recombinant regions. Phylogenomic analysis of 6,642 sequences revealed that recombinants cluster significantly closer to their major parents (p = 8.9 x 10-6 ) and that their removal does not significantly alter tree topology (p = 0.898), suggesting that the short length of recombinant regions limits phylogenetic conflict. We also introduce RECOSIM, an unsupervised machine-learning tool for recombination detection that achieved higher precision than RDP5 on both simulated (93.4% vs. 80.0%) and empirical (98.1% vs. 39.3%) datasets. Collectively, these results establish recombination as a widespread, pan-serotypic phenomenon in DENV with implications for genomic surveillance, vaccine evaluation, and evolutionary inference.

09.
arXiv (quant-ph) 2026-06-15

Spin disorder competing with positional symmetry breaking governs the metal-insulator behavior in oxide paramagnets

arXiv:2606.14624v1 Announce Type: cross Abstract: Numerous transition-metal oxides have low-temperature antiferromagnetic (AFM) states and high-temperature paramagnetic (PM) phases, where the AFM state is usually insulating while the PM phase can be either insulating or metallic. Without involving strong correlation, we use symmetry-broken density-functional theory (DFT) to obtain the PM phases of insulating NaFeO3 vs the recently discovered metallic NaOsO3. We develop the understanding of insulating and metallic behaviors in paramagnetic oxides by analyzing the interactions between magnetic and positional symmetry breaking: The insulating gap is governed by the competition between the spin disorder that induces a distribution of different magnitudes of local magnetic moments and the polymorphous distribution of off-center atomic displacements. NaFeO3, on the other hand, has large positional displacement with small spin-disorder-induced moments distribution, leading to insulating PM phase, whereas NaOsO3 has a pronounced spin-disorder-induced moments distribution that forces the PM phase to become metallic. Our work identifies this symmetry-breaking competition as a general framework to bridge seemingly disparate metal-insulator behaviors in transition-metal oxides paramagnets without invoking strong correlation.

10.
arXiv (math.PR) 2026-06-18

First to reach $n$ game

arXiv:2506.08782v4 Announce Type: replace Abstract: We consider a game with two players, consisting of a number of rounds, where the first player to win $n$ rounds becomes the overall winner. Who wins each individual round is governed by a certain urn having two types of balls (type 1 and type 2). At each round, we randomly pick a ball from the urn, and its type determines which of the two players wins. We study the game under three regimes. In the first and the third regimes, a ball is taken without replacement, whilst in the second regime, it is returned to the urn with one more ball of the same colour. We study the properties of the random variables equal to the properly defined overall net profits of the players, and the results are drastically different in all three regimes.

11.
arXiv (CS.CV) 2026-06-12

An Improved Generative Adversarial Network for Micro-Resistivity Imaging Logging Restoration

An improved GAN-based imaging logging image restoration method is presented in this paper for solving the problem of partially missing micro-resistivity imaging logging images. The method uses FCN as the generative network infrastructure and adds a depth-separable convolutional residual block to learn and retain more effective pixel and semantic information; an Inception module is added to increase the multi-scale perceptual field of the network and reduce the number of parameters in the network; and a multi-scale feature extraction module and a spatial attention residual block are added to combine the channel attention. The multi-scale module adds a multi-scale feature extraction module and a spatial attention residual block, which combine the channel attention mechanism and the residual block to achieve multi-scale feature extraction. The global discriminative network and the local discriminative network are designed to gradually improve the content and semantic structure coherence between the restored parts and the whole image by playing off each other and the generative network. According to the experimental results, the average structural similarity measure of the five sets of imaged logging images with different sizes of missing regions in the test set is 0.903, which is an improvement of about 0.3 compared with other similar methods. It is shown that the method in this study can be used for the restoration of micro-resistivity imaging log images with good improvement in semantic structural coherence and texture details, thus providing a new deep learning method to ensure the smooth advancement of the subsequent interpretation of micro-resistivity imaging log images.

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

TMR-GGNN: Credit Card Fraud Detection based on Time-Aware Multi-Relational Guided Graph Neural Network

arXiv:2606.18444v1 Announce Type: cross Abstract: In recent years, credit card fraud detection has faced significant challenges due to highly imbalanced data, evolving fraud patterns, and complex relational structures among transaction entities. To address these issues, this research proposes a novel framework called Timeaware Multi Relational Guided Graph Neural Network (TMR GGNN). Particularly, the proposed TMR GGNN extends the encoder decoder Graph Neural Network GNN architecture by modeling heterogeneous interactions across customers, merchants, devices, and IPs over temporal windows. Subsequently, the proposed TMR GGNN approach constructs a dynamic, multi relational graph and incorporates a time aware relational attention mechanism within the encoder to adaptively weigh the transaction relevance based on temporal proximity and semantic context. Consequently, the decoder employs a contrastive learning module to distinguish between real and synthesized transaction patterns, while improving the models generalization of rare fraud cases. Additionally, to effectively manage severe class imbalances and emphasize discriminative learning, a composite loss function combining Information Noise Contrastive Estimation (InfoNCE) based contrastive loss with Focal Loss is introduced. This integration assists in improving fraud identification while mitigating false negatives.

13.
bioRxiv (Bioinfo) 2026-06-11

Pillbox: A Leakage-Aware Foundation-Model Predictor and Lineage-Ceiling Diagnostic for Cancer Drug Response

We present Pillbox, a predictor whose pipeline is audited against the six Asiaee leakage modes with the one residual pathway shown by per-fold ablation to be non-load-bearing on hard splits. Our model combines CpGPT methylation embeddings, CLAMP drug embeddings, and per-fold-fit gene-expression principal components which are fused by Feature-wise Linear Modulation (FiLM)-conditioned graph attention on the STRING v12 protein-protein interaction graph. Then we alpha-ensemble the model against a histogram-based gradient boosting regressor baseline. On GDSC GSE68379 (987 cell lines, 375 drugs) across seeds 42, 7, and 123, the ensemble reaches test R-Squared of 0.78, 0.77, and 0.76 on random, histology-blind, and site-blind splits respectively, with cell-aware lifts above the drug-mean floor of +0.054, +0.060, and +0.037. As a quantitative diagnostic for feature-stack saturation we propose the cross-architecture residual correlation, calibrated against a same-architecture-different-initialization control. On histology-blind splits the cross-architecture value of 0.939 falls short of the same-architecture ceiling of 0.974 by approximately 0.03 in residual correlation, a gap we interpret as the headroom available to architecture choice on top of the current foundation-model representation and consistent with the long-established observation that tissue lineage dominates cell-line drug response. We integrated curated mutation, methylation, and drug-target-expression channels, but these do not improve prediction once foundation-model embeddings are in place. Cross-screen validation against PRISM matches the GDSC-to-PRISM measurement reproducibility ceiling within 0.01 Spearman.

14.
arXiv (CS.CL) 2026-06-18

Compact Geometric Representations of Hierarchies

Computing geometric representations of data is a cornerstone of modern machine learning, typically achieved by training dual encoders which map queries and documents into a shared embedding space. Recent work of You et al. [NeurIPS '25] has extended this approach to hierarchical retrieval, where relevance is determined by the ancestor-descendant relationships in a Directed Acyclic Graph (DAG). While previous work has shown that valid embeddings exist when the number of descendants is small, these bounds degrade significantly for deep hierarchies, requiring dimensions as large as the total number of nodes. In this paper, we investigate compact reachability embeddings for more general graph classes and provide theoretical guarantees for representing hierarchies using embeddings whose dimension depends on structural graph parameters. We prove that for any directed tree, there exists a reachability embedding in constant dimension 3, independent of the tree's size or depth. We generalize this result to graphs characterized by treewidth $t$, constructing embeddings of dimension $O(t \log n)$, where $n$ is the number of nodes. Complementing these upper bounds, we provide matching or near-matching lower bounds, showing that dimension $\Omega(n)$ is necessary for general DAGs and $\Omega(t/\log(n/t))$ is required for graphs of treewidth $t$. We also obtain upper and lower bounds parameterized by the number of cross-edges in the DAG. We additionally show that our embeddings can be constructed on real world datasets, and that they give much smaller dimensions in high recall regimes compared to prior embeddings with theoretical guarantees.

15.
PLOS Medicine 2026-05-06

Pathways of emergency care for severely ill children in Nigerian and Ugandan hospitals: A process mapping study

Authors:

by Rami Subhi, Abiodun Sogbesan, Dan Muramuzi, Mikael Burhin, Ayobami A. Bakare, Adegoke G. Falade, Freddy E. Kitutu, Freddie Ssengooba, Carina King, Sumit Kane, Belinda Dawson-McClaren, Hamish R. Graham, the MOXY-Implementation Research Collaboration Background Child mortality remains high in countries with weak emergency care systems. Facility organisation for paediatric emergency care is heterogeneous and under-described. We examined how hospitals in Uganda and Nigeria are organised to deliver emergency care for neonates and children. Methods and findings We conducted a qualitative, multi-method study in 26 purposively selected secondary and tertiary facilities in Uganda and Nigeria from October 2023 to December 2024. Embedded researchers documented patient pathways, resources for care, and care processes for severely ill children (

16.
arXiv (quant-ph) 2026-06-12

Efficient certification of intractable quantum states with few Pauli measurements

arXiv:2511.07300v2 Announce Type: replace Abstract: Efficient verification of quantum computational resources is crucial as experiments advance toward fault-tolerance. Universal quantum computation can be achieved by consuming resource states through simple Pauli measurements, yet a significant gap remains between states that are easy to certify and those required for universality. We focus on Clifford-enhanced Product States, a class of resource states obtained by applying Clifford circuits to a product of single-qubit, potentially magic, states. While essential for universal computation, the certification of such states has previously relied on query oracles that are \#P-hard to implement, leaving their efficient, oracle-free verification an open challenge. In this work, we demonstrate that such classically intractable resource states can be efficiently verified using only Pauli measurements. Our protocol achieves sample- and time-efficiency in both i.i.d.\ and adversarial settings. This work fills a gap in Pauli-based certification, providing a new practical pathway to verify resource states that drive universal Pauli-based quantum computation.

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

Attention is Just Another Name for Coupling?: A Fast-Slow ODE Perspective on Hierarchical Pretraining

Authors:

arXiv:2606.16730v1 Announce Type: cross Abstract: Causal self-attention is a coupling mechanism: each token's hidden state is updated by a learned mixture of preceding tokens at the same timescale. This paper asks whether a second, temporally slower coupling-a slow sub-system operating on a temporally-downsampled view of the sequence and fed back into the fast path through a zero-initialised gate-complements it. The question is framed in the language of singularly perturbed ordinary differential equations (ODEs), where the fast variable $x$ evolves at the token rate, the slow variable $y$ evolves at one update per $P$ tokens, and the timescale ratio $\varepsilon = 1/P$ is enforced structurally by causal block-mean pooling. The paper instantiates the fast-slow ODE formalism as a concrete neural network: a fast path of standard causal attention over $T$ tokens, a slow path of full attention over $T/P$ pooled tokens ($P^2 \times$ cheaper per layer), and a zero-initialised additive gate. In addition, under a linear-generator assumption on the fast dynamics, we prove that the equilibrium manifold $x = \phi(y)$ is exactly the master-equation (ME) stationary distribution $p_{\mathrm{st}}(y)$; in that regime a learned MLP $\phi_\theta(y)$ is a variational approximation of it (the trained block is not a generator, so this identity is the structured limit, not a claim about the network as trained). Empirically, at $500$k tokens the coupling is neutral – the gate stays closed and the coupled and frozen ablations are within run-to-run noise – at a wall-clock cost comparable to a dense baseline. The contribution is the precise, gap-marked mapping itself, not a performance gain.

18.
arXiv (CS.LG) 2026-06-16

A Conservation Law for Equilibrium Propagation and Coupled Learning

arXiv:2606.15444v1 Announce Type: cross Abstract: In this paper we show that the physical learning methods known as coupled learning (CL) and equilibrium propagation (EP) conserve a mass-like quantity in the trainable parameters in the continuous-time, small-nudging limit. We prove that this conservation holds in a broad range of physically relevant settings. We then show that the conservation law constrains the training dynamics in a way that makes convergence reliable in important settings for linear circuits. We conclude by discussing some practical implications of this conservation law.

19.
arXiv (CS.LG) 2026-06-16

Using Reinforcement Learning to Optimize the Global and Local Crossing Number

arXiv:2509.06108v2 Announce Type: replace-cross Abstract: Graph drawing concerns the algorithmic visualization of graphs. A good drawing of a graph is easy to read and facilitates solving tasks on the graph. Several properties have been identified to occur in good drawings of graphs. Such properties include a low number of crossings, large angles between edges, short edges, and depicting symmetries. Many of these properties are explicitly measurable metrics. This brings us to the insight that graph drawing can be seen as a game. In this paper, we study a single-player optimization game in which the player iteratively moves vertices of a straight-line graph drawing to reduce edge crossings. This game arose naturally from the automatic track of the Graph Drawing Challenge, where solutions are obtained by repeatedly performing local vertex movements. We formalize this process as a game with full information and investigate whether reinforcement learning can discover effective strategies for playing it. Our reinforcement-learning agent observes the local geometric and structural context of a vertex and selects a movement direction with the goal of reducing either the global or the local crossing number, that is, the total number of crossings or the maximum number of crossings per edge. We compare the resulting strategies to existing methods and established crossing-minimization heuristics on standard benchmark graphs. While our approach does not out-compete state-of-the-art methods for minimizing the global crossing number, it is competitive and often superior for minimizing the local crossing number.

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

Learning Topology-Aware Implicit Field for Unified Pulmonary Tree Modeling with Incomplete Topological Supervision

Pulmonary trees extracted from CT images frequently exhibit topological incompleteness, such as missing or disconnected branches, which substantially degrades downstream anatomical analysis and limits the applicability of existing pulmonary tree modeling pipelines. Current approaches typically rely on dense volumetric processing, explicit graph reasoning, or generic point cloud completion priors, leading to limited efficiency, weak structural awareness, and reduced robustness under realistic structural corruption. We propose TopoField, a topology-aware implicit modeling framework that treats topology repair as a first-class modeling problem and enables unified multi-task inference for pulmonary tree analysis. TopoField represents pulmonary anatomy using sparse surface and skeleton point clouds and learns a continuous implicit field that supports topology repair without relying on complete or explicit disconnection annotations, by training on synthetically introduced structural disruptions over already incomplete trees. Building upon the repaired implicit representation, anatomical labeling and lung segment reconstruction are jointly inferred through task-specific implicit functions within a single forward pass. Extensive experiments on the Lung3D+ dataset demonstrate that TopoField consistently improves topological completeness and achieves accurate anatomical labeling and lung segment reconstruction under challenging incomplete scenarios. We further validate TopoField on real incomplete outputs from an external segmentation model, demonstrating its applicability to realistic segmentation pipelines. Owing to its implicit formulation, TopoField attains high computational efficiency, completing all tasks in just over one second per case, highlighting its practicality for large-scale and time-sensitive clinical applications.

21.
arXiv (CS.LG) 2026-06-11

SpaTeoGL: Spatiotemporal Graph Learning for Interpretable Seizure Onset Zone Analysis from Intracranial EEG

arXiv:2602.11801v2 Announce Type: replace Abstract: Accurate localization of the seizure onset zone (SOZ) from intracranial EEG (iEEG) is essential for epilepsy surgery but is challenged by complex spatiotemporal seizure dynamics. We propose SpaTeoGL, a spatiotemporal graph learning framework for interpretable seizure network analysis. SpaTeoGL jointly learns window-level spatial graphs capturing interactions among iEEG electrodes and a temporal graph linking time windows based on similarity of their spatial structure. The method is formulated within a smooth graph signal processing framework and solved via an alternating block coordinate descent algorithm with convergence guarantees. Experiments on a multicenter iEEG dataset with successful surgical outcomes show that SpaTeoGL is competitive with a baseline based on horizontal visibility graphs and logistic regression, while improving non-SOZ identification and providing interpretable insights into seizure onset and propagation dynamics.

22.
bioRxiv (Bioinfo) 2026-06-13

Reinforcement learning-driven unified generative framework for multi-objective RNA codon design

Current RNA codon design methods are limited by inefficient long-sequence processing and poor generalizability, often relying on a decoupled "generate-or-optimize" paradigm. We introduce RNARL, a reinforcement learning-driven framework that unifies sequence generation with multi-objective optimization. RNARL directly learns to generate high-performance sequences, effectively optimizing sequences over 3,900 nucleotides and demonstrating superior performance and universality across six species and five RNA types. RNARL thus establishes an effective and generalizable framework for RNA codon design. Finally, a user-friendly web platform is freely available to facilitate its application for RNA therapeutic design.

23.
arXiv (CS.LG) 2026-06-16

When Does q-error Predict Plan Regret? Three Regimes of Cardinality-Estimation Error

arXiv:2606.15600v1 Announce Type: cross Abstract: Cardinality-estimation (CE) research ranks estimators by q-error, yet it is well known that q-error is an imperfect proxy for query-plan quality. We give a measurement-driven account of when it is a good proxy and when it is not, and why. Modeling plan selection as an argmin over a piecewise-linear cost landscape, we find that plan regret (the cost of the chosen plan relative to the optimal, under true cardinalities) is governed by plan-cost geometry in a regime-dependent way. (i) For small errors, a true-point condition number kappa predicts regret and out-predicts q-error; its predictive power decays to zero as error grows, as a local linearization must. (ii) For large errors – where deployed learned estimators operate – an estimator-independent average-case sub-optimality measure ACS-infinity predicts which queries are regret-prone (Spearman rho ~ 0.54 on STATS-CEB), while q-error is nearly uninformative at the query level (rho ~ 0.05). (iii) The worst case is Haritsa's maximum sub-optimality (MSO). The three are one cost-ratio spectrum under three weightings. We prove a limit law ACS-infinity = sum_k r_k pi_k with cardinality-independent combinatorial weights, and validate every claim on STATS-CEB and JOB-light with four released estimators under pre-registered decision rules, and confirm on real PostgreSQL runtime that ACS-infinity predicts regret where q-error does not. The contribution is conceptual and empirical – an average-case companion to worst-case robust query optimization, and a characterization of when an accuracy metric tracks plan quality – rather than a new estimator. Code and the full pre-registration are public.

24.
arXiv (CS.AI) 2026-06-17

Multiple cyclicity and Wavelet Decomposition with Channel Correlation for Long-term Time Series Forecasting

arXiv:2606.17996v1 Announce Type: cross Abstract: Cyclicity and trend are important components of time series data and many studies based on cyclicity and trend have achieved good results in long-term time series forecasting. However, we believe that current work neglects the influence of real-world inter-channel correlations in time series data which leads to suboptimal predictions. Furthermore, these models rely on complex designs to capture diverse information so that resulting in low computational efficiency. To address this challenge, we propose McWC, a long-term time series forecasting model that separately models the cyclicity, trend, and inter-channel correlations. Specifically, McWC first decouples cyclical information from data using a multi-layer cyclicity construction module. Then, it extracts inter-channel correlations using multi-layer perceptron. Next, it models and fuses the multi-layer high-frequency and low-frequency information from data using a multi-level wavelet decomposition module. Finally, it aggregates the results of different components to obtain the output. Simultaneously, we decouple intra-channel autocorrelations by calculating a loss function in the frequency domain. Experiments on six real-world datasets demonstrate that McWC achieves state-of-the-art performance, exhibiting excellent computational efficiency and historical information extraction capabilities.

25.
arXiv (CS.LG) 2026-06-18

Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment

arXiv:2606.18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation. Yet these distributions are learned from broad unlabeled corpora and are not naturally conditioned on task-specific biological contexts such as interaction partners, cellular environments, or therapeutic interventions. Existing contextual matching methods often distort this interface through pooled embeddings, contrastive latent spaces, or task-specific prediction heads. We introduce LOGICA (Logit-space Contrastive Alignment), a framework for context-conditioned prediction that performs contrastive learning directly in output-logit space. Using gated cross-modal adapters compatible with each model's native token head, LOGICA preserves the pretrained likelihood interface and converts contextualized token log-likelihoods into matching scores. Alignment is defined through context-sensitive token probabilities rather than proximity in a shared embedding space, enabling learning from sparse paired data across models with distinct vocabularies, without a shared tokenizer or decoder. LOGICA is particularly effective for mutation-local variant ranking, where comparisons reduce to context-conditioned likelihoods of mutant tokens at perturbed sites. Across protein–ligand binding, TCR–peptide activity, and drug-conditioned resistance prediction, LOGICA improves over prior state-of-the-art methods, including matched latent-contrastive and conditional MLM baselines, while retaining a token-level interface for interpretation and generation. On held-out-gene single-mutation drug-resistance prediction, LOGICA improves AUC from near-random latent-space baselines of $\sim$0.55 to $\sim$0.65.