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01.
arXiv (CS.AI) 2026-06-16

A comparative and critical study of EEGNet for fNIRS-driven cognitive load classification

arXiv:2606.16160v1 Announce Type: cross Abstract: Accurately classifying cognitive load from functional near-infrared spectroscopy (fNIRS) signals remains a significant challenge due to temporal variability, inter-subject differences, and sensitivity to preprocessing choices. This study provides a comprehensive evaluation of EEGNet for fNIRS-based cognitive load classification by systematically examining the effects of temporal segmentation strategies (overlapping vs. non-overlapping), window lengths (10s, 20s, 30s), feature extraction methods (Analysis of Variance (ANOVA), Principal Component Analysis (PCA), Fast Independent Component Analysis (FastICA)), learning rate configurations (fixed and adaptive), and evaluation protocols (random split vs. subject-independent (SI)). Results from random-split experiments show that overlapping segmentation, combined with smaller fixed learning rates (0.01-0.001), yields the highest accuracies, due to temporal redundancy and dense sampling of hemodynamic transitions. However, SI evaluation reveals a substantial drop in accuracy, demonstrating limited generalization to unseen participants. Under SI evaluation, non-overlapping segmentation outperformed overlapping windows, with the best accuracy of 56.11% achieved using PCA features with a 20-second window and a 0.1 learning rate. These findings indicate that eliminating temporal redundancy helps the model learn more robust and generalizable representations of cognitive load across individuals. Although adaptive learning rate strategy improved training stability, it did not surpass the performance of optimally selected fixed learning rates. The study highlights the critical role of segmentation strategy and learning rate selection in improving model generalization and identifies methodological considerations essential for developing reliable, real-time, and SI cognitive load classification systems using fNIRS.

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

Whole-Brain Connectomic Graph Model Enables Whole-Body Locomotion Control in Fruit Fly

arXiv:2602.17997v3 Announce Type: replace Abstract: Animals perform coordinated whole-body movements under the control of neural systems shaped by brain-wide connectivity. The mapping of the whole-brain neural connections, or the connectomes, provides a natural graph for modeling sensorimotor information flow, yet its potential as a neural controller for embodied agents remains largely unexplored. Here, we introduce the Fly-connectomic Graph Model, which directly instantiates the whole-brain connectome of an adult Drosophila as a graph-structured neural controller for movements of a simulated biomechanical fruit fly via deep reinforcement learning. We achieve stable performance across diverse locomotion tasks, as well as better sample efficiency compared to both graph and non-graph baselines. Our results demonstrate a biologically informed way towards effective control policy design by translating whole-brain wiring principles into actionable architectural priors, while also improving the interpretability through dynamic information flow. This work also highlights the potential to bridge neuromechanics with embodied intelligence by providing a computational platform for investigating the sensorimotor transformation underlying animal behavior and a paradigm to advance the development of more nature-aligned intelligent systems.

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

MeshFlow: Efficient Artistic Mesh Generation via MeshVAE and Flow-based Diffusion Transformer

We present MeshFlow, a new method for generating artist-like 3D meshes. Current mesh generators often adopt Auto-Regressive (AR) next-token prediction, a natural choice given the discrete nature of mesh topology. However, AR methods scale poorly because the inference cost is quadratic in mesh size. They also require discretizing the vertex coordinates, which introduces quantization errors. To address these challenges, we introduce a Variational Autoencoder (VAE) that, supervised with a contrastive loss, represents both continuous vertex positions and discrete connectivity in a continuous latent space. This latent space is significantly more compact than prior token-based mesh representations. We then build a 3D generator based on a Rectified Flow transformer, generating all mesh vertices and edges in parallel. Our model generates meshes 18x faster than the fastest AR generator while also achieving excellent accuracy across standard mesh-generation metrics. Homepage: https://mesh-flow.github.io/, Code: https://github.com/facebookresearch/meshflow

04.
arXiv (CS.CL) 2026-06-11

Notes2Skills: From Lab Notebooks to Certainty-Aware Scientific Agent Skills

Scientific discovery workflows usually contain and rely heavily on lab notes, where researchers record observations, interpret uncertain results, and plan follow-up experiments. Such informative lab notes preserve evolving scientific reasoning and author uncertainty, rather than polished final results exhibited in publications, providing a valuable opportunity for AI to engage in scientific exploration at a more comprehensive and deeper level. However, most prior work on scientific text focuses on papers, protocols, or structured databases, leaving informal laboratory notes underexplored as inputs to AI agents for science. This gap matters because lab notes often intermingle validated observations, tentative judgments, and possible experimental next steps within the same passage. If these signals are conflated, an AI agent may mistake uncertain scientific judgments for confirmed conclusions or executable actions. To this end, we present Notes2Skills, a two-stage framework for turning lab notebooks into verifiable skills for scientific AI agents while preserving the author's certainty. Across seven conditions and three wet-lab sessions, Notes2Skills is the only configuration that neither mistakes uncertain notes for firm instructions nor discards firm ones. We show that certainty preservation is the missing piece between lab notebooks and reliable agent skills, opening a path toward safer AI co-scientist systems.

05.
arXiv (quant-ph) 2026-06-12

To Cool, or Not to Cool? Displacement Sensing with Hot Quantum States

arXiv:2606.13650v1 Announce Type: new Abstract: Quantum-enhanced displacement sensing with bosonic systems is typically formulated assuming that the oscillator is cooled close to its ground state before nonclassical probe preparation. We investigate whether such near-ground-state initialization is necessary, or whether sensitive probes can instead be generated directly from thermal states. We analyze hot quantum probes produced by squeezing, number-raising, and Schrödinger-cat-state generation applied to thermal inputs. We identify two distinct mechanisms by which thermal mixedness can remain compatible with enhanced displacement sensitivity. First, projecting a mixed probe onto a definite parity sector removes the usual thermal suppression of the displacement quantum Fisher information, which can then increase with initial thermal occupation. Second, coherent superpositions of opposite displacements can retain sensitivity through coherence between their displaced components, even when the underlying state is mixed. We use these two mechanisms to classify hot-state protocols according to whether their sensitivity comes from parity selection, coherence between displaced components, or both. Finally, we formulate an experimentally relevant optimization problem comparing initial cooling with direct hot-state preparation under realistic decoherence and show that complete cooling is not universally optimal. Our results establish hot-state engineering as a route to quantum-enhanced bosonic displacement sensing without mandatory ground-state initialization.

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

Fast Non-Episodic Finite-Horizon RL with K-Step Lookahead Thresholding

arXiv:2602.00781v2 Announce Type: replace Abstract: Online reinforcement learning in non-episodic, finite-horizon MDPs remains underexplored and is challenged by the need to estimate returns to a fixed terminal time. Existing infinite-horizon methods, which often rely on discounted contraction, do not naturally account for this fixed-horizon structure. We introduce a modified Q-function: rather than targeting the full-horizon, we learn a K-step lookahead Q-function that truncates planning to the next K steps. To further improve sample efficiency, we introduce a thresholding mechanism: actions are selected only when their estimated K-step lookahead value exceeds a time-varying threshold. We provide an efficient tabular learning algorithm for this novel objective, proving it achieves fast finite-sample convergence: it achieves minimax optimal constant regret for $K=1$ and $\mathcal{O}(\max((K-1),C_{K-1})\sqrt{SAT\log(T)})$ regret for any $K \geq 2$. We numerically evaluate the performance of our algorithm under the objective of maximizing reward. Our implementation adaptively increases K over time, balancing lookahead depth against estimation variance. Empirical results demonstrate superior cumulative rewards over state-of-the-art tabular RL methods across synthetic MDPs and RL environments: JumpRiverswim, FrozenLake and AnyTrading. Code is provided on \href{https://github.com/jamie01713/K-Step-Lookahead}{github}.

07.
arXiv (CS.CV) 2026-06-16

Latent Action Pretraining Through World Modeling

Vision-Language-Action (VLA) models have gained popularity for learning robotic manipulation tasks that follow language instructions. State-of-the-art VLAs, such as OpenVLA and $\pi_{0}$, were trained on large-scale, manually labeled action datasets collected through teleoperation. More recent approaches, including LAPA and villa-X, introduce latent action representations that enable unsupervised pretraining on unlabeled datasets by modeling abstract visual changes between frames. Although these methods have shown strong results, their large model sizes make deployment in real-world settings challenging. In this work, we propose LAWM, a model-agnostic framework to pretrain imitation learning models in a self-supervised way, by learning latent action representations from unlabeled video data through world modeling. These videos can be sourced from robot recordings or videos of humans performing actions with everyday objects. Our framework is able to transfer learned knowledge across tasks, environments, and embodiments. It outperforms models pretrained with ground-truth robot actions and other similar pretraining methods on the LIBERO benchmark and real-world setup, while being efficient and practical for real-world settings.

08.
arXiv (CS.AI) 2026-06-17

Transformer-Based Warm-Starting for Feasible and Optimal Terminal Approach to Tumbling Objects with Space Manipulators

arXiv:2606.17317v1 Announce Type: cross Abstract: Real-time trajectory generation for on-orbit robotic servicing is challenging due to the nonlinear coupling between spacecraft bus motion, manipulator dynamics, visibility cone, and trajectory-level safety constraints. This paper studies learning-based warm-starting for sequential convex programming (SCP) in the terminal approach of a space manipulator toward a tumbling target. The proposed framework decomposes the problem into a system center-of-mass translational planning stage and a coupled attitude–manipulator torque-allocation stage, and applies a causal transformer warm-start to the latter, which constitutes the dominant computational bottleneck. Linear and flow matching action decoders are compared under different action-chunking and training dataset sizes, and the resulting warm-starts are evaluated under both cost-optimal and feasibility projection using SCP. Across 300 held-out scenarios, the learned warm-start reduces the second-stage SCP iteration count by up to 28% and the runtime by 23% while preserving the final control-cost distribution. When the learned warm-starts are used for nonconvex feasibility projection, they nearly halve the runtime relative to cost-optimal SCP, while avoiding the catastrophic high-cost tail behavior observed when initialized heuristically. These results indicate that sequence-model warm-starts can improve both the computational efficiency and trajectory robustness of optimization-based terminal guidance for space manipulation.

09.
arXiv (CS.CV) 2026-06-15

$\mu_0$: A Scalable 3D Interaction-Trace World Model

World models that capture how actions induce physical change enable scalable robot learning without reliance on embodiment-specific action labels. Pixel-space video models provide broad visual priors but expend model capacity on dense appearance reconstruction, while direct action models require embodiment-specific labels that hinder scalability. We present $\mu_0$, a scalable world model based on 3D traces. Rather than predicting dense pixels or directly modeling actions, $\mu_0$ forecasts smooth 3D trajectories for salient interaction points such as objects, tools, hands, and contact regions, yielding a compact, embodiment-agnostic motion interface. To enable training from diverse video sources, our TraceExtract system automatically extracts 3D supervision by selecting keypoints, constructing globally aligned traces, and associating motion segments with hierarchical language captions. This TraceExtract supervision pretrains $\mu_0$ by combining a pretrained vision-language backbone with a modular trace expert, which represents each query via B-spline control points and predicts future traces. Experiments show that $\mu_0$ outperforms baselines in both 2D and 3D trace prediction, including trace prediction models and tokenized VLM methods. Because $\mu_0$ is frozen and reusable, it can be paired with action experts for downstream robot embodiments. Despite action-free pretraining, the resulting trace-conditioned policies achieve performance competitive with VLA models pretrained with action supervision, such as $\pi_0$. These results establish 3D traces as a scalable and transferable representation for cross-embodiment manipulation.

10.
arXiv (CS.AI) 2026-06-18

The Long Delay to Arithmetic Generalization: When Learned Representations Outrun Behavior

arXiv:2604.13082v2 Announce Type: replace-cross Abstract: Grokking in transformers trained on algorithmic tasks is characterized by a long delay between training-set fit and abrupt generalization, but the source of that delay remains poorly understood. In encoder-decoder arithmetic models, we argue that this delay reflects limited access to already learned structure rather than failure to acquire that structure in the first place. We study one-step Collatz prediction and find that the encoder organizes parity and residue structure within the first few thousand training steps, while output accuracy remains near chance for tens of thousands more. Causal interventions support the decoder bottleneck hypothesis. Transplanting a trained encoder into a fresh model accelerates grokking by 2.75 times, while transplanting a trained decoder actively hurts. Freezing a converged encoder and retraining only the decoder eliminates the plateau entirely and yields 97.6% accuracy, compared to 86.1% for joint training. What makes the decoder's job harder or easier depends on numeral representation. Across 15 bases, those whose factorization aligns with the Collatz map's arithmetic (e.g., base 24) reach 99.8% accuracy, while binary fails completely because its representations collapse and never recover. The choice of base acts as an inductive bias that controls how much local digit structure the decoder can exploit, producing large differences in learnability from the same underlying task.

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

Exploration Structure in LLM Agents for Multi-File Change Localization

arXiv:2606.11976v1 Announce Type: cross Abstract: Software engineering tools increasingly rely on LLM based agents to localize files to change to resolve a software issue. Most AI agents explore repositories linearly, that is, visiting one directory or file per step. We postulate that this is a structural mismatch for changes that span several subsystems. We compare linear sequential exploration against non-linear, domain-scoped parallel agentic exploration. Using SWE Bench Pro as initial benchmark, we focus on ansible as an exemplar. We construct an approach for persistent-session evaluation of GitHub issues anchored at a single base commit. We compare our non-linear domain-agent file traversal system against a base LLM without direct repository access, a single agent Recursive Language Model (RLM) baseline with a persistent Python REPL and an external CLI baseline using Codex 5.5 High. Domain scoped parallel agent spawning with a small Haiku-class model achieves the highest micro F1 among Haiku class models by a large margin. Domain-agents is the second highest behind only the much larger Codex 5.5 High on our own expanded benchmark including over more recent PRs from 2025 and 2026. On the original, curated, 2020 SWE-bench Pro benchmark, a larger Sonnet plain LLM baseline attains higher micro F1 by predicting few files, leading to higher precision, but at significantly lower all gold recall. We also present three additional findings. First, documentation evolution is a latent dependency unresolved by any approach. Second, naive file system access can degrade localization driven by test-file over prediction. Lastly, forced multi-agent consultation does not measurably help and raises token cost substantially.

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

Conformalized Quantum DeepONet Ensembles for Scalable Operator Learning with Distribution-Free Uncertainty

arXiv:2605.00330v2 Announce Type: replace Abstract: Operator learning enables fast surrogate modeling of high-dimensional dynamical systems, but existing approaches face two fundamental limitations: quadratic inference complexity and unreliable uncertainty quantification in safety-critical settings. We propose Conformalized Quantum DeepONet Ensembles, a framework that addresses both challenges simultaneously. By leveraging Quantum Orthogonal Neural Networks (QOrthoNNs), we reduce operator inference complexity from O(n^2) to O(n), enabling scalable evaluation over fine discretizations. To provide rigorous uncertainty quantification, we combine ensemble-based epistemic modeling with adaptive conformal prediction, yielding distribution-free coverage guarantees. A key challenge in ensembling is that naive parallelism scales hardware resources linearly with the number of models. We resolve this by using Superposed Parameterized Quantum Circuits (SPQCs), which compress multiple ensemble members into a single circuit and enable simultaneous multi-model execution. Experiments on synthetic partial differential equations and real-world power system dynamics demonstrate that our approach achieves accurate predictions while maintaining calibrated uncertainty under realistic quantum noise. These results establish a practical pathway toward scalable, uncertainty-aware operator learning in quantum machine learning.

13.
arXiv (math.PR) 2026-06-16

Structure preserving properties of higher order moment closures for TASEP

arXiv:2604.15925v2 Announce Type: replace-cross Abstract: The totally asymmetric simple exclusion process (TASEP) is a stochastic model for the unidirectional flow of interacting particles on a 1D-lattice that is much used in systems biology and statistical physics. Its master equation describes the evolution of the probability distribution on the configuration space. The size of the master equation grows exponentially with the length of the lattice. It is known that the complexity of the system may be reduced using mean-field approximations. We provide a rigorous definition of a family of such models using moments of any order and an extension to the pair approximation for obtaining closures for the system. The dimension of these models grows linearly with the lattice size and exponentially in the order of the approximation. Moreover, we show that the states of these models still have a probabilistic interpretation and that basic structural properties of the master equation are preserved. This extends known results on the Ribosome Flow Model which can be viewed as the first order approximation for TASEP.

14.
arXiv (CS.CV) 2026-06-11

PT-WNO: Point Transformer with Wavelet Neural Operator for 3D Point Cloud Semantic Segmentation

Point cloud semantic segmentation requires architectures that capture both fine-grained local geometry and broad global scene structure. Transformer-based networks have demonstrated strong performance by focusing on detailed local feature aggregation; however, global context is conveyed primarily through skip connections across encoder-decoder stages, which we argue is insufficient for full scene understanding. We hypothesize that augmenting skip connections with a learnable global feature extraction module allows the network to acquire scene-level knowledge before descending into local detail, leading to richer and more contextually grounded representations. To this end, we propose Point Transformer with Wavelet Neural Operato (PT-WNO), which integrates a shared Wavelet Neural Operator (WNO) branch alongside the skip connections of a point cloud transformer backbone. At each encoder-decoder transition, point features are projected onto a dense 3D volumetric grid where the WNO captures multi-scale global spectral context through learnable wavelet decomposition and reconstruction. These global features are fused back into the network via lightweight adapters, complementing rather than replacing the existing skip connections. Experiments on four large-scale 3D point cloud benchmarks demonstrate the effectiveness of PT-WNO. On S3DIS (Area 5), PT-WNO achieves 71.59% mIoU, outperforming the Point Transformer v3 (PTv3) baseline by +1.03 points. On DALES it achieves 81.05% mIoU (+1.47 over the baseline). On ScanNet~v2, PT-WNO obtains 76.19% mIoU, remaining competitive with the baseline (76.36%).

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

Gen-VCoT: Generative Visual Chain-of-Thought Reasoning via Diffusion-Based RGB Intermediate Representations

Multimodal large language models (MLLMs) excel at visual reasoning but rely on text-based chain-of-thought (CoT), lacking interpretable visual intermediates. Existing methods use opaque tokens or external tools, missing key properties. We propose Gen-VCoT, a framework using expert vision models to generate RGB images as reasoning intermediates. It has three stages: visual grounding (SAM segmentation), geometric reasoning (Marigold depth maps), and semantic reasoning (Qwen2-VL integration). An adaptive router selects reasoning depth. Evaluations show Gen-VCoT improves spatial (25% better) and depth (50% better) questions, but may hurt simple factual queries. Text CoT outperforms visual intermediates on CLEVR (91.2% vs 62.5%), showing task-dependent optimal representations. Gen-VCoT establishes a new paradigm for interpretable multimodal reasoning.

16.
arXiv (quant-ph) 2026-06-19

Resolving problems with the continuum limit in coherent-state path integrals

arXiv:2602.02466v2 Announce Type: replace Abstract: The paper solves the problem of continuum limit in bosonic thermal coherent-state path integrals. For this purpose, exact discrete versions of the path integral are constructed for three different orderings of the Hamiltonian: normal, anti-normal and symmetric (Weyl order). Subsequently, their different continuum versions are checked on the harmonic oscillator, to choose the symmetric ordering as a possibly correct choice for all polynomial Hamiltonians. Spotted mathematical subtleties in the simple case serve as a clue to the general solution. Finally, a general justification for the symmetric order is provided by deriving the continuum path integral starting from the exact discrete case using a renormalization procedure in the imaginary time frequency domain. While the role of Weyl order has already been found, the paper provides the missing proof of its suitability for every polynomial Hamiltonian and simplifies the previously established construction by referring only to creation and annihilation operators (without position and momentum operators).

17.
arXiv (CS.AI) 2026-06-11

Multi-Rate Mixture of Experts for Accelerating Liquid Neural Network Training

arXiv:2606.12240v1 Announce Type: cross Abstract: Multivariate time-series data often exhibit complex temporal dependencies, irregular sampling, and heterogeneous dynamics across multiple time scales, making accurate sequence modeling particularly challenging. Traditional recurrent neural networks (RNNs), such as Long Short-Term Memory (LSTM) networks, operate in discrete time and may struggle to effectively capture continuous and irregular temporal behaviors. Liquid Neural Networks (LNNs) address some of these limitations through continuous-time dynamics, but standard LNN architectures typically rely on a single dynamical system, limiting their ability to model heterogeneous temporal patterns. To address these challenges, we propose a Multi-Rate Mixture-of-Experts (MR-MoE) framework built on top of Liquid Neural Networks. In the proposed architecture, multiple LNN-based experts operate at distinct time scales, enabling the model to explicitly separate fast-changing dynamics from slow-evolving temporal trends. A gating network further enables adaptive expert specialization based on input conditions. In addition, we incorporate both feature-level and temporal attention mechanisms to improve robustness, interpretability, and long-range dependency modeling. Feature-level attention suppresses noisy or irrelevant variables, while temporal attention selectively focuses on informative historical states. We evaluate the proposed framework on a complex multivariate time-series prediction task and compare it against strong baselines, including LSTM, monolithic LNN, and standard MoE models. Experimental results demonstrate that the proposed MR-MoE framework consistently achieves improved AUROC and AUPRC performance while maintaining favorable computational efficiency. These results highlight the effectiveness of combining continuous-time dynamics, multi-scale expert decomposition, and adaptive attention mechanisms for time-series modeling.

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

Beyond Uniform Forgetting: A Study of Sequential Direct Preference Optimization Across Preference Settings

Aligning language models with human preferences often requires optimising multiple behavioural objectives. A practical approach is to apply these objectives sequentially using preference optimisation methods such as Direct Preference Optimisation (DPO), but it remains unclear whether later training uniformly degrades preferences learned earlier or whether the effect depends on the relationship between objectives. We study sequential DPO across four preference settings covering distributional conflict, multi-attribute interaction, strong safety signal, and compatible response-quality objectives. Using Llama-3.1-8B-Instruct with LoRA adapters, we evaluate all objectives after every stage with a fixed base-model reference. We find that sequential DPO does not produce a single forgetting pattern; preference change ranges from partial degradation to stability, pair-level redistribution, or positive transfer depending on objective relationship, signal strength, and training order. Pair-level analysis using length-normalised policy margins shows that aggregate metrics can mask heterogeneous changes across preference pairs, whereas quartile decomposition reveals that high-confidence pairs can either degrade or improve depending on the setting. Mechanistic diagnostics show that Stage~2 gradients and adapter updates are near-orthogonal to the previous objective across all settings, providing little evidence that direct gradient opposition is the primary driver. These findings suggest that future sequential alignment pipelines should account for objective compatibility and signal strength, rather than assuming that later objectives affect earlier preferences uniformly.

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

ShowFlow: From Robust Single Concept to Condition-Free Multi-Concept Generation

Customizing image generation remains a core challenge in controllable image synthesis. For single-concept generation, maintaining both identity preservation and prompt alignment is challenging. In multi-concept scenarios, relying solely on a prompt without additional conditions like layout boxes or semantic masks, often leads to identity loss and concept omission. In this paper, we introduce ShowFlow, a comprehensive framework designed to tackle these challenges. We propose ShowFlow-S for single-concept image generation, and ShowFlow-M for handling multiple concepts. ShowFlow-S introduces a KronA-WED adapter, which integrates a Kronecker adapter with weight and embedding decomposition, and together with a novel Semantic-Aware Attention Regularization (SAR) training objective to enhance single-concept generation. Building on this foundation, ShowFlow-M directly reuses robust models learned by ShowFlow-S to support multi-concept generation without extra conditions, incorporating a Subject-Adaptive Matching Attention (SAMA) and a Layout Consistency guidance as the plug-and-play module. Extensive experiments and user studies validate ShowFlow's effectiveness, highlighting its potential in real-world applications like advertising and virtual dressing. Our source code will be publicly available at: https://htrvu.github.io/showflow.

20.
arXiv (CS.AI) 2026-06-15

FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction

arXiv:2602.22822v3 Announce Type: replace Abstract: Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice. While novel architectures constantly claim state-of-the-art performance, inconsistent metadata conditioning and entangled preprocessing pipelines hinder fair architectural comparisons. Besides, existing evaluations are often restricted to curated datasets, failing to capture the heterogeneity and cross-domain shifts of real-world metabolomics. Furthermore, current benchmarks lack difficulty-aware diagnostics and leave blind to how models behave under specific compute or data constraints. To address this, we present FlexMS, a modular public-data benchmark framework that standardizes MS/MS prediction across public resources while keeping molecular encoders, metadata conditioning, predictor heads, and downstream retrieval under one protocol. FlexMS establishes a fair evaluation playground which significantly lowers the barrier for integrating new predictive tools. Rather than solely optimizing for average scores, FlexMS augments aggregate accuracy with difficulty-aware diagnostics, providing actionable guidance on model selection across different compute constraints, data scales, and downstream retrieval objectives. Ultimately, FlexMS provides the community with a reproducible standard to identify which algorithmic conclusions are stable and which operating points are most viable in practice.

21.
arXiv (CS.LG) 2026-06-19

Comparative Study of Neural Surrogate Architectures for Autoregressive Prediction of Internal Battery States

arXiv:2606.20053v1 Announce Type: new Abstract: The Doyle-Fuller-Newman (DFN) model resolves internal electrochemical states in lithium-ion batteries with high fidelity. However, the numerical solution of its governing equations is computationally prohibitive for real-time deployment, limiting scalability from individual cells to pack and fleet-scale applications. While machine learning surrogates can substantially reduce inference latency through GPU acceleration, most existing approaches learn solution approximations tied to specific operating conditions rather than learning generalizable state-evolution dynamics. This work presents a systematic comparison of four neural network architectures (MLP, ResNet, U-Net, FNO) formulated as autoregressive state-transition operators that predict full DFN internal states across a wide range of operating conditions. To ensure a controlled architectural comparison, all models are trained under a unified framework using multi-step unrolling and current-conditioning, isolating the impact of spatial inductive bias. Results demonstrate that the U-Net's multi-scale feature hierarchy achieves a mean final-step nRMSE of 3% averaged across all internal state variables after 300-step autoregressive rollouts, while providing a 5.38x speed-up over the numerical solver. These findings highlight spatial inductive bias as a critical determinant of surrogate performance, advancing the development of surrogates for internal state observability for next-generation battery management systems and digital twins.

22.
arXiv (CS.LG) 2026-06-19

Off-Policy Evaluation for Missingness-Aware Policies in MDPs with Rewards Missing Not at Random

arXiv:2606.20206v1 Announce Type: cross Abstract: In offline Reinforcement Learning, immediate rewards in logged batch data are often unobserved due to sparse or irregular record-keeping, or censored beyond certain reward values. This issue arises in practical settings, including health care and marketing. We investigate off-policy evaluation (OPE) in finite-horizon Markov decision processes when rewards are missing not at random (MNAR), which breaks ignorability and induces selection bias even after conditioning on states and actions. To address this, we formalize a reward-dependent propensity model and use future states as shadow variables to identify the full-data conditional mean reward. We further introduce a bridge function that recovers the conditional mean reward without explicitly modeling the MNAR mechanism, and estimate it via a min-max procedure to avoid double sampling. Building upon these identification results, we propose an Fitted-Q-Evaluation-style estimator that propagates the recovered rewards while allowing target policies to depend on past missingness indicators. Finally, we establish consistency and finite-sample error bounds for our OPE estimator, and show through experiments the strong performance of our method compared to existing methods on simulated and MIMIC-III Sepsis data.

23.
arXiv (CS.LG) 2026-06-17

Meta-classification of one-class classification models using ranking correlation and nearest neighbor

arXiv:2606.17858v1 Announce Type: new Abstract: Machine Learning (ML) techniques have been applied to various problems. However, applying ML to ML models is an unexplored direction. For this purpose, this paper considers a meta-classification of one-class classification (OCC) models, because all ML models could be approximated as OCC models. The proposal represents OCC models as normality rankings and classifies them using nearest-neighbor and ranking-correlation metrics. The experiment classifies OCC models, where classes correspond to training datasets, algorithms, and hyperparameters. The proposal achieves high accuracy when class labels are datasets. Moreover, it can classify algorithms when the training datasets contain the same class. In addition, the discussion highlights that the classification of OCC models is essentially the classification of datasets that treats multiple samples as a single input. The experiment demonstrates the classification of datasets using sleeping records. The proposed method can provide a unified solution for classifying OCC models, datasets, and rankings. Source code is uploaded to the public repository https://github.com/ToshiHayashi/ClassOCC.

24.
PLOS Computational Biology 2026-06-12

Stage-dependent role of NEK7 in the inactive-to-active conformational transition of NLRP3 monomer

Authors:

by Jin Peng, Wenjian Li, Hao Wang, Xiaohui Chen, Manjie Zhang, Bin Sun The NLRP3 inflammasome is a multiprotein complex that primes cytokine production in the innate immune system. The inflammasome activation involves the cage-to-disk transition of NLRP3 oligomers, facilitated by the co-factor NEK7 protein. While NEK7’s role in promoting cage disassembly has been reported, its involvement in the large conformational changes of the NLRP3 monomer during activation remains elusive. Here, by using multi-scale simulations, we uncovered a stage-dependent role of NEK7 in the inactive-to-active transition. In the early stage, NEK7 reshapes the dynamics of the highly unstable inactive NLRP3 monomer to resemble active state, priming the conformational transition. In the middle stage, NEK7 impedes progression by populating an intermediate state farther from the active conformation than the NEK7-free counterpart, and structures in this state exhibit reduced allosteric potential toward activation. In the late stage, NEK7 has negligible impact, as the active conformation remains inherently isolated by a high energy barrier regardless of NEK7 presence. This highlights the critical role of oligomeric assembly in enabling monomeric NLRP3 to complete its conformational transition, in agreement with experiment observations. Our work suggests a multilayered activation mechanism where oligomer-level assembly and monomeric conformational changes are coupled, providing new mechanistic insights into this physiologically essential macromolecular process.

25.
arXiv (CS.CL) 2026-06-16

From Affect Prediction to Affect Forecasting: Evidence for Distinct Information Sources in Longitudinal Text

Modeling dimensional affect in longitudinal text requires distinguishing current affect estimation from future affective change forecasting. Existing approaches often treat each text as an independent observation and apply similar assumptions to both tasks, without testing whether they rely on different information sources. This paper investigates that distinction using longitudinal self-reported ecological essays and feeling-word entries. We propose the Trait–State Affective Prediction (TSAP) framework and its temporal extension E-TSAP for per-text valence and arousal prediction, evaluated on a held-out prediction test set of 1,737 entries from 91 users. We further propose the Affective Change Forecaster Hybrid (ACF-Hybrid) for next-step affective change forecasting, evaluated on a held-out forecasting test set of 46 users. For prediction, E-TSAP achieves composite Pearson correlations of 0.670 for valence and 0.449 for arousal. For forecasting, textual representations perform worse than compact numeric trajectory baselines: the text-inclusive model achieves only r=0.316 for valence and r=0.284 for arousal, whereas a simple prior-state baseline reaches r=0.615 and r=0.670, respectively. ACF-Hybrid, using dimension-specific numeric trajectory features, achieves r=0.659 for valence and $r=0.658$ for arousal. These results show that textual semantics support current affect prediction, whereas future affective change is better captured through prior numeric trajectory dynamics.