Large language model (LLM) agents are increasingly deployed in structured biomedical data environments, yet they often produce fluent but overconfident outputs when reasoning over complex multi-table data. We introduce an uncertainty-aware agent for query-conditioned multi-table summarization that leverages two complementary signals: (i) retrieval uncertainty--entropy over multiple table-selection rollouts--and (ii) summary uncertainty--combining self-consistency and perplexity. Summary uncertainty is incorporated into reinforcement learning (RL) with Group Relative Policy Optimization (GRPO), while both retrieval and summary uncertainty guide inference-time filtering and support the construction of higher-quality synthetic datasets. On multi-omics benchmarks, our approach improves factuality and calibration, nearly tripling correct and useful claims per summary (3.0\(\rightarrow\)8.4 internal; 3.6\(\rightarrow\)9.9 cancer multi-omics) and substantially improving downstream survival prediction (C-index 0.32\(\rightarrow\)0.63). These results demonstrate that uncertainty can serve as a control signal--enabling agents to abstain, communicate confidence, and become more reliable tools for complex structured-data environments.

We propose a scalable method for constructing a temporal opinion knowledge base with large language models (LLMs) as automated annotators. Despite the demonstrated utility of time-series opinion analysis of text for downstream applications such as forecasting and trend analysis, existing methodologies underexploit this potential due to the absence of temporally grounded fine-grained annotations. Our approach addresses this gap by integrating well-established opinion mining formulations into a declarative LLM annotation pipeline, enabling structured opinion extraction without manual prompt engineering. We define three data models grounded in sentiment and opinion mining literature, serving as schemas for structured representation. We perform rigorous quantitative evaluation of our pipeline using human-annotated test samples. We carry out the final annotations using two separate LLMs, and inter-annotator agreement is computed label-wise across the fine-grained opinion dimensions, analogous to human annotation protocols. The resulting knowledge base encapsulates time-aligned, structured opinions and is compatible with applications in Retrieval-Augmented Generation (RAG), temporal question answering, and timeline summarisation.

Optical microrobots actuated by optical tweezers (OT) offer great potential for biomedical applications such as cell manipulation and microscale assembly. These tasks demand accurate three-dimensional perception to ensure precise control in complex and dynamic biological environments. However, the transparent nature of microrobots and low-contrast microscopic imaging challenge conventional deep learning methods, which also require large annotated datasets that are costly to obtain. To address these challenges, we propose a physics-informed, data-efficient framework for depth estimation of optical microrobots. Our method augments convolutional feature extraction with physics-based focus metrics, such as entropy, Laplacian of Gaussian, and gradient sharpness, calculated using an adaptive grid strategy. This approach allocates finer grids over microrobot regions and coarser grids over background areas, enhancing depth sensitivity while reducing computational complexity. We evaluate our framework on multiple microrobot types and demonstrate significant improvements over baseline models. Specifically, our approach reduces mean squared error (MSE) by over 60% and improves the coefficient of determination (R^2) across all test cases. Notably, even when trained on only 20% of the available data, our model outperforms ResNet50 trained on the full dataset, highlighting its robustness under limited data conditions. Our code is available at: https://github.com/LannWei/CBS2025.

Probabilistic Time Series Forecasting (PTSF) plays a critical role in domains requiring accurate and uncertainty-aware predictions for decision-making. However, existing methods offer suboptimal distribution modeling and suffer from a mismatch between training and evaluation metrics. Surprisingly, we found that augmenting a strong point estimator with a zero-mean Gaussian, whose standard deviation matches its training error, can yield state-of-the-art performance in PTSF. In this work, we propose RDIT, a plug-and-play framework that combines point estimation and residual-based conditional diffusion with a bidirectional Mamba network. We theoretically prove that the Continuous Ranked Probability Score (CRPS) can be minimized by adjusting to an optimal standard deviation and then derive algorithms to achieve distribution matching. Evaluations on eight multivariate datasets across varied forecasting horizons demonstrate that RDIT achieves lower CRPS, rapid inference, and improved coverage compared to strong baselines.

Text classification is the task of automatically assigning text documents correct labels from a predefined set of categories. In real-life (text) classification tasks, observations and misclassification costs are often unevenly distributed between the classes - known as the problem of imbalanced data. Synthetic oversampling is a popular approach to imbalanced classification. The idea is to generate synthetic observations in the minority class to balance the classes in the training set. Many general-purpose oversampling methods can be applied to text data; however, imbalanced text data poses a number of distinctive difficulties that stem from the unique nature of text compared to other domains. One such factor is that when the sample size of text increases, the sample vocabulary (i.e., feature space) is likely to grow as well. We introduce a novel Markov chain based text oversampling method. The transition probabilities are estimated from the minority class but also partly from the majority class, thus allowing the minority feature space to expand in oversampling. We evaluate our approach against prominent oversampling methods and show that our approach is able to produce highly competitive results against the other methods in several real data examples, especially when the imbalance is severe.

Recent advances in large language models (LLMs) have demonstrated impressive capabilities in code-related tasks, such as code generation and automated program repair. Despite their promising performance, most existing approaches for code repair suffer from high training costs or computationally expensive inference. Retrieval-augmented generation (RAG), with its efficient in-context learning paradigm, offers a more scalable alternative. However, conventional retrieval strategies, which are often based on holistic code-text embeddings, fail to capture the structural intricacies of code, resulting in suboptimal retrieval quality. To address the above limitations, we propose ReCode, a fine-grained retrieval-augmented in-context learning framework designed for accurate and efficient code repair. Specifically, ReCode introduces two key innovations: (1) an algorithm-aware retrieval strategy that narrows the search space using preliminary algorithm type predictions; and (2) a modular dual-encoder architecture that separately processes code and textual inputs, enabling fine-grained semantic matching between input and retrieved contexts. Furthermore, we propose RACodeBench, a new benchmark constructed from real-world user-submitted buggy code, which addresses the limitations of synthetic benchmarks and supports realistic evaluation. Experimental results on RACodeBench and competitive programming datasets demonstrate that ReCode achieves higher repair accuracy with significantly reduced inference cost, highlighting its practical value for real-world code repair scenarios.

Language-guided long-horizon manipulation of deformable objects presents significant challenges due to high degrees of freedom, complex dynamics, and the need for accurate vision-language grounding. In this work, we focus on multi-step cloth folding, a representative deformable-object manipulation task that requires both structured long-horizon planning and fine-grained visual perception. To this end, we propose a unified framework that integrates a Large Language Model (LLM)-based planner, a Vision-Language Model (VLM)-based perception system, and a task execution module. Specifically, the LLM-based planner decomposes high-level language instructions into low-level action primitives, bridging the semantic-execution gap, aligning perception with action, and enhancing generalization. The VLM-based perception module employs a SigLIP2-driven architecture with a bidirectional cross-attention fusion mechanism and weight-decomposed low-rank adaptation (DoRA) fine-tuning to achieve language-conditioned fine-grained visual grounding. Experiments in both simulation and real-world settings demonstrate the method's effectiveness. In simulation, it outperforms state-of-the-art baselines by 2.23, 1.87, and 33.3 on seen instructions, unseen instructions, and unseen tasks, respectively. On a real robot, it robustly executes multi-step folding sequences from language instructions across diverse cloth materials and configurations, demonstrating strong generalization in practical scenarios. Project page: https://language-guided.netlify.app/

Singing-driven 3D head animation is a challenging yet promising task with applications in virtual avatars, entertainment, and education. Unlike speech, singing involves richer emotional nuance, dynamic prosody, and lyric-based semantics, requiring the synthesis of fine-grained, temporally coherent facial motion. Existing speech-driven approaches often produce oversimplified, emotionally flat, and semantically inconsistent results, which are insufficient for singing animation. To address this, we propose Think2Sing, a diffusion-based framework that leverages pretrained large language models to generate semantically coherent and temporally consistent 3D head animations, conditioned on both lyrics and acoustics. A key innovation is the introduction of motion subtitles, an auxiliary semantic representation derived through a novel Singing Chain-of-Thought reasoning process combined with acoustic-guided retrieval. These subtitles contain precise timestamps and region-specific motion descriptions, serving as interpretable motion priors. We frame the task as a motion intensity prediction problem, enabling finer control over facial regions and improving the modeling of expressive motion. To support this, we create a multimodal singing dataset with synchronized video, acoustic descriptors, and motion subtitles, enabling diverse and expressive motion learning. Extensive experiments show that Think2Sing outperforms state-of-the-art methods in realism, expressiveness, and emotional fidelity, while also offering flexible, user-controllable animation editing.

The rapid evolution of artificial intelligence (AI), together with the increased availability of social media and news for epidemiological surveillance, are marking a pivotal moment in epidemiology and public health research. Leveraging the power of generative AI, we use an ensemble approach which incorporates multiple Large Language Models (LLMs) to extract valuable actionable epidemiological information from the World Health Organization (WHO) Disease Outbreak News (DONs). DONs is a collection of regular reports on global outbreaks curated by the WHO and the adopted decision-making processes to respond to them. The extracted information is made available in a daily-updated dataset and a knowledge graph, referred to as eKG, derived to provide a nuanced representation of the public health domain knowledge. We provide an overview of this new dataset and describe the structure of eKG, along with the services and tools used to access and utilize the data that we are building on top. These innovative data resources open altogether new opportunities for epidemiological research, and the analysis and surveillance of disease outbreaks.

The large set of technical documentation of legacy accelerator systems, coupled with the retirement of experienced personnel, underscores the urgent need for efficient methods to preserve and transfer specialized knowledge. This paper explores the application of large language models (LLMs), to automate and enhance the extraction of information from particle accelerator technical documents. By exploiting LLMs, we aim to address the challenges of knowledge retention, enabling the retrieval of domain expertise embedded in legacy documentation. We present initial results of adapting LLMs to this specialized domain. Our evaluation demonstrates the effectiveness of LLMs in extracting, summarizing, and organizing knowledge, significantly reducing the risk of losing valuable insights as personnel retire. Furthermore, we discuss the limitations of current LLMs, such as interpretability and handling of rare domain-specific terms, and propose strategies for improvement. This work highlights the potential of LLMs to play a pivotal role in preserving institutional knowledge and ensuring continuity in highly specialized fields.