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Applications of temporal graph learning for predicting the dynamics of biological systems

arXiv

arXiv:2605.28659v1 Announce Type: new Abstract: Biological foundation models have shown strong performance in single-cell representation learning by applying transformer architectures directly to gene-expression matrices. However, these approaches predominantly operate in static settings and do not explicitly model the temporal evolution of developmental programs in the cell. Modeling such dynamics is important for understanding how cellular states progressively emerge, differentiate, and reorganize during development or disease progression. In this work-in-progress paper, we investigate an alternative temporal graph-based perspective in which cellular states are represented through pseudotime-resolved gene regulatory networks and modeled as evolving graph structures over persistent gene identities. Starting from single-cell transcriptomic data, we infer pseudotime trajectories, discretize cells into developmental snapshots, reconstruct one gene regulatory network per snapshot, and app

Beyond External Monitors: Enhancing Transparency of Large Language Models for Easier Monitoring

arXiv

arXiv:2502.05242v3 Announce Type: replace-cross Abstract: Large language models (LLMs) are becoming increasingly capable, but the mechanisms of their thinking and decision-making processes remain unclear. Chain-of-thoughts (CoTs) have been commonly utilized to externalize LLMs' thinking, but this strategy fails to accurately reflect LLMs' thinking process. Techniques based on LLMs' hidden representations provide an inner perspective to improve the monitorability of their latent thinking. However, previous methods only try to develop external modules instead of making LLMs themselves easier to monitor. In this paper, we propose a novel method, TELLME, improving the transparency of LLMs and helping monitors identify unsuitable and sensitive behaviors. Furthermore, we showcase the effectiveness of TELLME on detoxification tasks, where LLMs achieve consistent improvement among multimodal test sets, distinct architectures, and varying parameter scales. We further analyze TELLME's improvemen

Short-Term Gain, Long-Term Fragility: AI Labor Substitution and the Erosion of Sustainable Capability

arXiv

arXiv:2605.27399v1 Announce Type: cross Abstract: What looks like acceleration can be a quiet transfer of burden from the present to the future. Attempts to replace human labor with AI systems are often presented as rational responses to technological progress, but that view is often structurally short-sighted. Across software development and adjacent knowledge industries, AI is increasingly attractive because it appears to reduce labor costs, speed output, and improve short-term metrics. Yet those gains may be achieved by drawing down human capabilities that are slow to build and difficult to restore. This paper develops a mechanism of capability masking and capability erosion under AI labor substitution. AI-generated output can create the appearance that organizational capability has been replaced, even when dependence on skilled human labor remains. That appearance can support hiring restraint while slower costs accumulate in the background. Evidence from AI-assisted coding shows th

Quality-constrained Entropy Maximization Policy Optimization for LLM Diversity

arXiv

arXiv:2602.15894v2 Announce Type: replace-cross Abstract: In many large language model (LLM) alignment applications, users expect not only high-quality outputs but also substantial diversity. However, existing methods often face a fundamental trade-off between these objectives: approaches that improve output quality tend to reduce diversity, while methods that increase diversity often do so at the expense of quality. In this work, we propose Quality-constrained Entropy Maximization Policy Optimization (QEMPO), a novel framework that enhances the diversity of LLM outputs while explicitly preserving output quality. QEMPO is grounded in a strong theoretical foundation: we derive a closed-form analytical solution that provably maximizes entropy-a principled measure of diversity-subject to a quality constraint, with guarantees on optimality under the defined objective. Leveraging this solution, QEMPO naturally supports both online and offline training settings. Empirical results demonstrate

CogVLA: Cognition-Aligned Vision-Language-Action Model via Instruction-Driven Routing & Sparsification

arXiv

arXiv:2508.21046v3 Announce Type: replace-cross Abstract: Recent Vision-Language-Action (VLA) models built on pre-trained Vision-Language Models (VLMs) require extensive post-training, resulting in high computational overhead that limits scalability and deployment.We propose CogVLA, a Cognition-Aligned Vision-Language-Action framework that leverages instruction-driven routing and sparsification to improve both efficiency and performance. CogVLA draws inspiration from human multimodal coordination and introduces a 3-stage progressive architecture. 1) Encoder-FiLM based Aggregation Routing (EFA-Routing) injects instruction information into the vision encoder to selectively aggregate and compress dual-stream visual tokens, forming a instruction-aware latent representation. 2) Building upon this compact visual encoding, LLM-FiLM based Pruning Routing (LFP-Routing) introduces action intent into the language model by pruning instruction-irrelevant visually grounded tokens, thereby achieving

Particle-Guided Diffusion Models for Partial Differential Equations

arXiv

arXiv:2601.23262v2 Announce Type: replace Abstract: We introduce a guided stochastic sampling method that augments sampling from diffusion models with physics-based guidance derived from partial differential equation (PDE) residuals and observational constraints, ensuring generated samples remain physically admissible. We embed this sampling procedure within a new Sequential Monte Carlo (SMC) framework, yielding a scalable generative PDE solver. Across multiple benchmark PDE systems as well as multiphysics and interacting PDE systems, our method produces solution fields with lower numerical error than existing state-of-the-art generative methods.

PrimitiveVLA: Learning Reusable Motion Primitives for Efficient and Generalizable Robotic Manipulation

arXiv

arXiv:2605.28634v2 Announce Type: replace Abstract: Vision-Language-Action (VLA) models offer a promising paradigm for generalist robotic policies, yet their adaptation is hindered by data inefficiency and poor generalization. We argue that these bottlenecks stem from the prevailing Direct Instruction-to-Control Mapping, which forces models to memorize monolithic trajectories rather than reusable motion patterns, i.e., primitives. We propose PrimitiveVLA, a framework that shifts this paradigm toward a Primitive-Centric Disassemble & Assemble paradigm. Supported by a shared Multimodal Canonical Representation (MCR), PrimitiveVLA unifies two phases: (1) Fine-tuning-phase Disassembly, which uses an automated pipeline to disassemble demonstrations into reusable primitives; and (2) Inference-phase Assembly, which employs a VLM-based planner and an LLM-generated switch module for robust closed-loop execution. By disassembling tasks into reusable primitives, PrimitiveVLA enables VLA models to

manipulationcontrol

RL Squeezes, SFT Expands: A Comparative Study of Reasoning LLMs

arXiv

arXiv:2509.21128v2 Announce Type: replace Abstract: Large language models (LLMs) are typically trained by reinforcement learning (RL) with verifiable rewards (RLVR) and supervised fine-tuning (SFT) on reasoning traces to improve their reasoning abilities. However, how these methods shape reasoning capabilities remains largely elusive. Going beyond an accuracy-based investigation of how these two components sculpt the reasoning process, this paper introduces a novel analysis framework that quantifies reasoning paths and captures their qualitative changes under each training process (with models of 1.5B, 7B, and 14B parameters on mathematical domains). Specifically, we investigate the reasoning process at two levels of granularity: the trajectory-level, which examines complete reasoning outputs, and the step-level, which analyzes reasoning graphs whose nodes correspond to individual reasoning steps. Notably, clustering of unique reasoning trajectories shows complementary effects: RL comp

reinforcement-learning

Dark Quest II: A Wide-Coverage Neural Network Emulator of the Nonlinear Matter Power Spectrum Across Extended Cosmologies

arXiv

arXiv:2605.28596v1 Announce Type: cross Abstract: \textsc{DarkEmulator2} is a neural network emulator of the nonlinear matter power spectrum in a nine-dimensional $w_0 w_a \nu o \mathrm{CDM}$ parameter space, developed as the emulator component of the \textsc{Dark Quest II} (DQ2) program. It is trained on simulations generated with the \textsc{Ginkaku} code, whose numerical implementation, accuracy tests, and post-processing pipeline are described in the companion paper. The design follows a unified strategy: in addition to the cosmological parameter vector, we supplement the neural network's inputs with three families of physically motivated auxiliary quantities -- the linear matter power spectrum, descriptors of the simulation resolution, and a low-dimensional summary of the initial Gaussian random field -- that are expected to improve generalization across the parameter space. Training a single network jointly across three simulation resolution tiers allows the emulator to exploit a

DataClawBench: An Agent Benchmark for Exploratory Real-World Financial Data Analysis

arXiv

arXiv:2605.02503v3 Announce Type: replace Abstract: Autonomous data analysis agents are increasingly expected to conduct exploratory analysis with limited human guidance about data. However, existing benchmarks typically evaluate such agents in prior-guided settings, providing selected data sources, explicit data schemas, or cleaned data, thereby understating the exploratory burden. To evaluate this realistic exploratory data analysis task, we introduce DataClawBench, a benchmark built from financial think-tank consulting scenarios where agents must independently explore unfamiliar, noisy, cross-domain data and produce verifiable conclusions. DataClawBench provides a unified real-world data environment with approximately 2.06 million records across enterprise, industry, and policy domains, with native data noise preserved. On top of this data environment, it defines 492 multi-step cross-domain tasks, each annotated with intermediate milestones that diagnose exploration and reasoning fa

autonomous

Latent Diffusion for Missing Data

arXiv

arXiv:2605.28427v1 Announce Type: new Abstract: Diffusion models have emerged as powerful generative approaches for missing-data imputation, yet most existing methods operate directly in data space and degrade when training data are heavily incomplete. We investigate whether shifting diffusion to a learned latent representation improves robustness under missing-completely-at-random (MCAR) corruption. To this end, we propose a two-stage framework: a robust VAE-based imputer first learns compact semantic features from incomplete observations, and a diffusion model is then trained in the resulting latent space. Across training missing rates, we perform a controlled comparison against pixel-space diffusion models under the same incomplete-data setting. The latent diffusion model maintains high sample quality and remains stable up to 50\% missingness, while pixel-space diffusion degrades progressively as missingness increases. For downstream imputation, latent diffusion also achieves consis

control

Beyond Model Ranking: Predictability-Aligned Evaluation for Time Series Forecasting

arXiv

arXiv:2509.23074v3 Announce Type: replace-cross Abstract: In the era of increasingly complex AI models for time series forecasting, progress is often measured by marginal improvements on benchmark leaderboards. However, this approach suffers from a fundamental flaw: standard evaluation metrics conflate a model's performance with the data's intrinsic unpredictability. To address this pressing challenge, we introduce a novel, predictability-aligned diagnostic framework grounded in spectral coherence. Our framework makes two primary contributions: the Spectral Coherence Predictability (SCP), a computationally efficient ($O(N\log N)$) and task-aligned score that quantifies the inherent difficulty of a given forecasting instance, and the Linear Utilization Ratio (LUR), a frequency-resolved diagnostic tool that precisely measures how effectively a model exploits the linearly predictable information within the data. We validate our framework's effectiveness and leverage it to reveal two core

HarmoVid: Relightful Video Portrait Harmonization

arXiv

arXiv:2605.28811v1 Announce Type: new Abstract: We present a method for harmonizing the lighting of a foreground video to match a target background scene, adjusting shadows, color tone, and illumination intensity (relightful harmonization). Unlike images, acquiring labeled data for videos, where identical motions are recorded under different lighting conditions, is practically infeasible and non-scalable. While one way to create such paired data is to apply existing image-based harmonization models frame by frame to a video, the resulting outputs often suffer from significant temporal jitters. We overcome this problem by introducing a novel lighting deflickering model that can stabilize the global and local lighting flickering artifacts. Our video diffusion model learns from these upgraded deflickered data with a volume of real and synthetic videos to generate high-quality video harmonization results. We further propose an asymmetric alpha mask conditioning technique to learn the clean

Provably Guaranteed Polytopic Uncertainty Quantification for SLAM

arXiv

arXiv:2605.28172v1 Announce Type: new Abstract: In safety-critical robotics applications, guaranteed and practical uncertainty quantification (UQ) in perception is vital. Many existing works either offer no formal containment guarantee, rely on restrictive modeling assumptions, or focus only on pose estimation rather than a complete SLAM pipeline. This paper presents provably guaranteed UQ algorithms for 3D-3D landmark-based SLAM. The algorithms consist of three basic UQ modules: forward UQ for mapping, backward UQ for pose tracking, and pose compound. Each module produces a certified uncertainty set; when the input uncertainty bounds are deterministic, the output sets inherit deterministic guarantees, i.e., they provably contain the true poses and landmarks. Specifically, we use polytopes to represent uncertainty sets, enabling tractable computations and a unified treatment of pose uncertainty. To enhance algorithms' practical usability, we incorporate conformal prediction to calibrat

slamperception

The Computational Boundary of Inference: Capability Internalization, Training, and the Turing Jump

arXiv

arXiv:2605.27381v1 Announce Type: cross Abstract: Claims about recursive self-improvement in AI often slide from repeated internal revision to the possibility of qualitatively stronger capability without clearly distinguishing the underlying computational regimes. This paper gives a formal separation result in classical computability theory that blocks that move under a precise modeling assumption. For an oracle $A$, let $\mathcal{C}(A)=\{B : B \leq_T A\}$ be the corresponding computational layer. We prove that finite internal self-modification remains inside $\mathcal{C}(A)$, while stabilized revision is governed instead by the jump $A'$ via the relativized limit lemma. Together with a local closure versus escape theorem, this yields a clean formal separation between within-layer iteration and ascent to a stronger relative level. The point is not that stronger layers never arise, but that they are not explained by finite repetition inside one already settled layer. The resulting separ

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