Bayesian Optimization for Mixed-Variable Problems in the Natural Sciences

Optimizing expensive black-box objectives over mixed search spaces is a common challenge across the natural sciences. Bayesian optimization (BO) offers sample-efficient strategies through probabilistic surrogate models and acquisition functions. However, its effectiveness diminishes in mixed or high-cardinality discrete spaces, where gradients are unavailable and optimizing the acquisition function becomes computationally demanding. In this work, we generalize the probabilistic reparameterization (PR) approach of Daulton et al. to handle non-equidistant discrete variables, enabling gradient-based optimization in fully mixed-variable settings with Gaussian process (GP) surrogates. With real-world scientific optimization tasks in mind, we conduct systematic benchmarks on synthetic and experimental objectives to obtain an optimized kernel formulations and demonstrate the robustness of our generalized PR method. We additionally show that, when combined with a modified BO workflow, our approach can efficiently optimize highly discontinuous and discretized objective landscapes. This work establishes a practical BO framework for addressing fully mixed optimization problems in the natural sciences, and is particularly well suited to autonomous laboratory settings where noise, discretization, and limited data are inherent.

EvA: An Evidence-First Audio Understanding Paradigm for LALMs

Large Audio Language Models (LALMs) still struggle in complex acoustic scenes because they often fail to preserve task-relevant acoustic evidence before reasoning begins. We call this failure the evidence bottleneck: state-of-the-art systems show larger deficits in evidence extraction than in downstream reasoning, suggesting that the main limitation lies in upstream perception rather than reasoning policy. To address this problem, we propose EvA (Evidence-First Audio), a dual-path architecture that combines Whisper and CED-Base through non-compressive, time-aligned fusion. EvA first aggregates intermediate CED layers to preserve multi-scale acoustic cues, then aligns the aggregated CED features to the Whisper timeline and adds the two streams without changing sequence length. We also build EvA-Perception, a large-scale open-source training set with about 54K event-ordered captions (150 h) and about 500K QA pairs. Under a unified zero-shot protocol, EvA achieves the best open-source Perception scores on MMAU, MMAR, and MMSU, and improves over Kimi-Audio-7B on all reported metrics, with the largest gains on perception-heavy splits. These results support the evidence-first hypothesis: stronger audio understanding depends on preserving acoustic evidence before reasoning.

R3DP: Real-Time 3D-Aware Policy for Embodied Manipulation

Embodied manipulation requires accurate 3D understanding of objects and their spatial relations to plan and execute contact-rich actions. While large-scale 3D vision models provide strong priors, their computational cost incurs prohibitive latency for real-time control. We propose Real-time 3D-aware Policy (R3DP), which integrates powerful 3D priors into manipulation policies without sacrificing real-time performance. A core innovation of R3DP is the asynchronous fast-slow collaboration module, which seamlessly integrates large-scale 3D priors into the policy without compromising real-time performance. The system maintains real-time efficiency by querying the pre-trained slow system (VGGT) only on sparse key frames, while simultaneously employing a lightweight Temporal Feature Prediction Network (TFPNet) to predict features for all intermediate frames. By leveraging historical data to exploit temporal correlations, TFPNet explicitly improves task success rates through consistent feature estimation. Additionally, to enable more effective multi-view fusion, we introduce a Multi-View Feature Fuser (MVFF) that aggregates features across views by explicitly incorporating camera intrinsics and extrinsics. R3DP offers a plug-and-play solution for integrating large models into real-time inference systems. We evaluate R3DP against multiple baselines across different visual configurations. R3DP effectively harnesses large-scale 3D priors to achieve superior results, outperforming single-view and multi-view DP by 32.9% and 51.4% in average success rate, respectively. Furthermore, by decoupling heavy 3D reasoning from policy execution, R3DP achieves a 44.8% reduction in inference time compared to a naive DP+VGGT integration.

OpaqueToolsBench: Learning Nuances of Tool Behavior Through Interaction

Tool-calling is essential for Large Language Model (LLM) agents to complete real-world tasks. While most existing benchmarks assume simple, perfectly documented tools, real-world tools (e.g., general "search" APIs) are often opaque, lacking clear best practices or failure modes. Can LLM agents improve their performance in environments with opaque tools by interacting and subsequently improving documentation? To study this, we create OpaqueToolsBench, a benchmark consisting of three distinct task-oriented environments: general function calling, interactive chess playing, and long-trajectory agentic search. Each environment provides underspecified tools that models must learn to use effectively to complete the task. Results on OpaqueToolsBench suggest existing methods for automatically documenting tools are expensive and unreliable when tools are opaque. To address this, we propose a simple framework, ToolObserver, that iteratively refines tool documentation by observing execution feedback from tool-calling trajectories. Our approach outperforms existing methods on OpaqueToolsBench across datasets, even in relatively hard settings. Furthermore, for test-time tool exploration settings, our method is also efficient, consuming 3.5-7.5x fewer total tokens than the best baseline.

Learning with Adaptive Prototype Manifolds for Out-of-Distribution Detection

Out-of-distribution (OOD) detection is a critical task for the safe deployment of machine learning models in the real world. Existing prototype-based representation learning methods have demonstrated exceptional performance. Specifically, we identify two fundamental flaws that universally constrain these methods: the Static Homogeneity Assumption (fixed representational resources for all classes) and the Learning-Inference Disconnect (discarding rich prototype quality knowledge at inference). These flaws fundamentally limit the model's capacity and performance. To address these issues, we propose APEX (Adaptive Prototype for eXtensive OOD Detection), a novel OOD detection framework designed via a Two-Stage Repair process to optimize the learned feature manifold. APEX introduces two key innovations to address these respective flaws: (1) an Adaptive Prototype Manifold (APM), which leverages the Minimum Description Length (MDL) principle to automatically determine the optimal prototype complexity $K_c^*$ for each class, thereby fundamentally resolving prototype collision; and (2) a Posterior-Aware OOD Scoring (PAOS) mechanism, which quantifies prototype quality (cohesion and separation) to bridge the learning-inference disconnect. Comprehensive experiments on benchmarks such as CIFAR-100 validate the superiority of our method, where APEX achieves new state-of-the-art performance.

VMF-GOS: Geometry-guided virtual Outlier Synthesis for Long-Tailed OOD Detection

Out-of-Distribution (OOD) detection under long-tailed distributions is a highly challenging task because the scarcity of samples in tail classes leads to blurred decision boundaries in the feature space. Current state-of-the-art (sota) methods typically employ Outlier Exposure (OE) strategies, relying on large-scale real external datasets (such as 80 Million Tiny Images) to regularize the feature space. However, this dependence on external data often becomes infeasible in practical deployment due to high data acquisition costs and privacy sensitivity. To this end, we propose a novel data-free framework aimed at completely eliminating reliance on external datasets while maintaining superior detection performance. We introduce a Geometry-guided virtual Outlier Synthesis (GOS) strategy that models statistical properties using the von Mises-Fisher (vMF) distribution on a hypersphere. Specifically, we locate a low-likelihood annulus in the feature space and perform directional sampling of virtual outliers in this region. Simultaneously, we introduce a new Dual-Granularity Semantic Loss (DGS) that utilizes contrastive learning to maximize the distinction between in-distribution (ID) features and these synthesized boundary outliers. Extensive experiments on benchmarks such as CIFAR-LT demonstrate that our method outperforms sota approaches that utilize external real images.

Breaking Semantic Hegemony: Decoupling Principal and Residual Subspaces for Generalized OOD Detection

While feature-based post-hoc methods have made significant strides in Out-of-Distribution (OOD) detection, we uncover a counter-intuitive Simplicity Paradox in existing state-of-the-art (SOTA) models: these models exhibit keen sensitivity in distinguishing semantically subtle OOD samples but suffer from severe Geometric Blindness when confronting structurally distinct yet semantically simple samples or high-frequency sensor noise. We attribute this phenomenon to Semantic Hegemony within the deep feature space and reveal its mathematical essence through the lens of Neural Collapse. Theoretical analysis demonstrates that the spectral concentration bias, induced by the high variance of the principal subspace, numerically masks the structural distribution shift signals that should be significant in the residual subspace. To address this issue, we propose D-KNN, a training-free, plug-and-play geometric decoupling framework. This method utilizes orthogonal decomposition to explicitly separate semantic components from structural residuals and introduces a dual-space calibration mechanism to reactivate the model's sensitivity to weak residual signals. Extensive experiments demonstrate that D-KNN effectively breaks Semantic Hegemony, establishing new SOTA performance on both CIFAR and ImageNet benchmarks. Notably, in resolving the Simplicity Paradox, it reduces the FPR95 from 31.3% to 2.3%; when addressing sensor failures such as Gaussian noise, it boosts the detection performance (AUROC) from a baseline of 79.7% to 94.9%.

Robust Uncertainty Quantification for Factual Generation of Large Language Models

The rapid advancement of large language model(LLM) technology has facilitated its integration into various domains of professional and daily life. However, the persistent challenge of LLM hallucination has emerged as a critical limitation, significantly compromising the reliability and trustworthiness of AI-generated content. This challenge has garnered significant attention within the scientific community, prompting extensive research efforts in hallucination detection and mitigation strategies. Current methodological frameworks reveal a critical limitation: traditional uncertainty quantification approaches demonstrate effectiveness primarily within conventional question-answering paradigms, yet exhibit notable deficiencies when confronted with non-canonical or adversarial questioning strategies. This performance gap raises substantial concerns regarding the dependability of LLM responses in real-world applications requiring robust critical thinking capabilities. This study aims to fill this gap by proposing an uncertainty quantification scenario in the task of generating with multiple facts. We have meticulously constructed a set of trap questions contained with fake names. Based on this scenario, we innovatively propose a novel and robust uncertainty quantification method(RU). A series of experiments have been conducted to verify its effectiveness. The results show that the constructed set of trap questions performs excellently. Moreover, when compared with the baseline methods on four different models, our proposed method has demonstrated great performance, with an average increase of 0.1-0.2 in ROCAUC values compared to the best performing baseline method, providing new sights and methods for addressing the hallucination issue of LLMs.

VLA-Arena: An Open-Source Framework for Benchmarking Vision-Language-Action Models

While Vision-Language-Action models (VLAs) are rapidly advancing towards generalist robot policies, it remains difficult to quantitatively understand their limits and failure modes. To address this, we introduce a comprehensive benchmark called VLA-Arena. We propose a novel structured task design framework to quantify difficulty across three orthogonal axes: (1) Task Structure, (2) Language Command, and (3) Visual Observation. This allows us to systematically design tasks with fine-grained difficulty levels, enabling a precise measurement of model capability frontiers. For Task Structure, VLA-Arena's 170 tasks are grouped into four dimensions: Safety, Distractor, Extrapolation, and Long Horizon. Each task is designed with three difficulty levels (L0-L2), with fine-tuning performed exclusively on L0 to assess general capability. Orthogonal to this, language (W0-W4) and visual (V0-V4) perturbations can be applied to any task to enable a decoupled analysis of robustness. Our extensive evaluation of state-of-the-art VLAs reveals several critical limitations, including a strong tendency toward memorization over generalization, asymmetric robustness, a lack of consideration for safety constraints, and an inability to compose learned skills for long-horizon tasks. To foster research addressing these challenges and ensure reproducibility, we provide the complete VLA-Arena framework, including an end-to-end toolchain from task definition to automated evaluation and the VLA-Arena-S/M/L datasets for fine-tuning. Our benchmark, data, models, and leaderboard are available at https://vla-arena.github.io.

LLM$^3$-DTI: A Large Language Model and Multi-modal data co-powered framework for Drug-Target Interaction prediction

Drug-target interaction (DTI) prediction is of great significance for drug discovery and drug repurposing. With the accumulation of a large volume of valuable data, data-driven methods have been increasingly harnessed to predict DTIs, reducing costs across various dimensions. Therefore, this paper proposes a $\textbf{L}$arge $\textbf{L}$anguage $\textbf{M}$odel and $\textbf{M}$ulti-$\textbf{M}$odel data co-powered $\textbf{D}$rug $\textbf{T}$arget $\textbf{I}$nteraction prediction framework, named LLM$^3$-DTI. LLM$^3$-DTI constructs multi-modal data embedding to enhance DTI prediction performance. In this framework, the text semantic embeddings of drugs and targets are encoded by a domain-specific LLM. To effectively align and fuse multi-modal embedding. We propose the dual cross-attention mechanism and the TSFusion module. Finally, these multi-modal data are utilized for the DTI task through an output network. The experimental results indicate that LLM$^3$-DTI can proficiently identify validated DTIs, surpassing the performance of the models employed for comparison across diverse scenarios. Consequently, LLM$^3$-DTI is adept at fulfilling the task of DTI prediction with excellence. The data and code are available at https://github.com/chaser-gua/LLM3DTI.