Accurate disease risk prediction based on genomic and clinical data can lead to more effective disease screening, early prevention, and personalized treatment strategies. However, despite the identifications of hundreds of disease-associated genomic and molecular features for many disease traits through genome-wide studies in the past two decades, drug resistance often causes the targeted therapies to fail in cancer patients, which is largely due to tumor heterogeneity (Zhang et al., 2022). For advanced cancers, tumor heterogeneity encompasses both the malignant cells and their microenvironment, which makes it challenging to develop accurate prediction models for personalized treatment strategies that account for intratumor heterogeneity. Single-cell technologies provide an unprecedented opportunity for dissecting the interplay between the cancer cells and the associated tumor microenvironment (TME), and the produced high-dimensional omics data should also augment existing survival modeling approaches for identifying tumor cell type-specific genes predictive of cancer patient survival.

Bayesian inference is useful to obtain a predictive distribution with a small generalization error. However, since posterior distributions are rarely evaluated analytically, we employ the variational Bayesian inference or sampling method to approximate posterior distributions. When we obtain samples from a posterior distribution, Hamiltonian Monte Carlo (HMC) has been widely used for the continuous variable part and Markov chain Monte Carlo (MCMC) for the discrete variable part. Another sampling method, the bouncy particle sampler (BPS), has been proposed, which combines uniform linear motion and stochastic reflection to perform sampling. BPS was reported to have the advantage of being easier to set simulation parameters than HMC. To accelerate the convergence to a posterior distribution, we introduced parallel tempering (PT) to BPS, and then proposed an algorithm when the inverse temperature exchange rate is set to infinity. We performed numerical simulations and demonstrated its effectiveness for multimodal distribution.

Langevin Monte Carlo (LMC) algorithms are popular Markov Chain Monte Carlo (MCMC) methods to sample a target probability distribution, which arises in many applications in machine learning. Inspired by regime-switching stochastic differential equations in the probability literature, we propose and study regime-switching Langevin dynamics (RS-LD) and regime-switching kinetic Langevin dynamics (RS-KLD). Based on their discretizations, we introduce regime-switching Langevin Monte Carlo (RS-LMC) and regime-switching kinetic Langevin Monte Carlo (RS-KLMC) algorithms, which can also be viewed as LMC and KLMC algorithms with random stepsizes. We also propose frictional-regime-switching kinetic Langevin dynamics (FRS-KLD) and its associated algorithm frictional-regime-switching kinetic Langevin Monte Carlo (FRS-KLMC), which can also be viewed as the KLMC algorithm with random frictional coefficients. We provide their 2-Wasserstein non-asymptotic convergence guarantees to the target distribution, and analyze the iteration complexities. Numerical experiments using both synthetic and real data are provided to illustrate the efficiency of our proposed algorithms.

Time Series Anomaly Detection metrics serve as crucial tools for model evaluation. However, existing metrics suffer from several limitations: insufficient discriminative power, strong hyperparameter dependency, sensitivity to perturbations, and high computational overhead. This paper introduces Confidence-Consistency Evaluation (CCE), a novel evaluation metric that simultaneously measures prediction confidence and uncertainty consistency. By employing Bayesian estimation to quantify the uncertainty of anomaly scores, we construct both global and event-level confidence and consistency scores for model predictions, resulting in a concise CCE metric. Theoretically and experimentally, we demonstrate that CCE possesses strict boundedness, Lipschitz robustness against score perturbations, and linear time complexity $\mathcal{O}(n)$. Furthermore, we establish RankEval, a benchmark for comparing the ranking capabilities of various metrics. RankEval represents the first standardized and reproducible evaluation pipeline that enables objective comparison of evaluation metrics. Both CCE and RankEval implementations are fully open-source.

This paper investigates the expected excess risk of In-Context Learning (ICL) for multi-class classification. We model each task as a sequence of labeled prompt samples and a query input, where a pre-trained model estimates the conditional class probabilities of the query. The expected excess risk is defined as the average truncated Kullback-Leibler (KL) divergence between the predicted and ground-truth conditional class distributions, averaged over a specified family of tasks. We establish a new oracle inequality for the expected excess risk based on KL divergence in multiclass classification. This allows us to derive tight upper and lower bounds for the expected excess risk in transformer-based models, demonstrating that the ICL estimator achieves the minimax optimal rate--up to a logarithmic factor--for conditional probability estimation. From a technical standpoint, our results introduce a novel method for controlling generalization error using the uniform empirical covering entropy of the log-likelihood function class. Furthermore, we show that multilayer perceptrons (MLPs) can also perform ICL and achieve this optimal rate under specific assumptions, suggesting that transformers may not be the exclusive architecture capable of effective ICL.

Gradient-based causal discovery shows great potential for deducing causal structure from data in an efficient and scalable way. Those approaches however can be susceptible to distributional biases in the data they are trained on. We identify two such biases: Marginal Distribution Asymmetry, where differences in entropy skew causal learning toward certain factorizations, and Marginal Distribution Shift Asymmetry, where repeated interventions cause faster shifts in some variables than in others. For the bivariate categorical setup with Dirichlet priors, we illustrate how these biases can occur even in controlled synthetic data. To examine their impact on gradient-based methods, we employ two simple models that derive causal factorizations by learning marginal or conditional data distributions - a common strategy in gradient-based causal discovery. We demonstrate how these models can be susceptible to both biases. We additionally show how the biases can be controlled. An empirical evaluation of two related, existing approaches indicates that eliminating competition between possible causal factorizations can make models robust to the presented biases.

We introduce bandit importance sampling (BIS), a new class of importance sampling methods designed for settings where the target density is expensive to evaluate. In contrast to adaptive importance sampling, which optimises a proposal distribution, BIS directly designs the samples through a sequential strategy that combines space-filling designs with multi-armed bandits. Our method leverages Gaussian process surrogates to guide sample selection, enabling efficient exploration of the parameter space with minimal target evaluations. We establish theoretical guarantees on convergence and demonstrate the effectiveness of the method across a broad range of sampling tasks. BIS delivers accurate approximations with fewer target evaluations, outperforming competing approaches across multimodal, heavy-tailed distributions, and real-world applications to Bayesian inference of computationally expensive models.

Intelligent control of Unmanned Aerial Vehicles (UAVs) swarms has emerged as a critical research focus, and it typically requires the swarm to navigate effectively while avoiding obstacles and achieving continuous coverage over multiple mission targets. Although traditional Multi-Agent Reinforcement Learning (MARL) approaches offer dynamic adaptability, they are hindered by the semantic gap in numerical communication and the rigidity of homogeneous role structures, resulting in poor generalization and limited task scalability. Recent advances in Large Language Model (LLM)-based control frameworks demonstrate strong semantic reasoning capabilities by leveraging extensive prior knowledge. However, due to the lack of online learning and over-reliance on static priors, these works often struggle with effective exploration, leading to reduced individual potential and overall system performance. To address these limitations, we propose a Role-Adaptive LLM-Driven Yoked navigation algorithm RALLY. Specifically, we first develop an LLM-driven semantic decision framework that uses structured natural language for efficient semantic communication and collaborative reasoning. Afterward, we introduce a dynamic role-heterogeneity mechanism for adaptive role switching and personalized decision-making. Furthermore, we propose a Role-value Mixing Network (RMIX)-based assignment strategy that integrates LLM offline priors with MARL online policies to enable semi-offline training of role selection strategies. Experiments in the Multi-Agent Particle Environment (MPE) environment and a Software-In-The-Loop (SITL) platform demonstrate that RALLY outperforms conventional approaches in terms of task coverage, convergence speed, and generalization, highlighting its strong potential for collaborative navigation in agentic multi-UAV systems.

Robot-assisted feeding requires reliable bite acquisition, a challenging task due to the complex interactions between utensils and food with diverse physical properties. These interactions are further complicated by the temporal variability of food properties-for example, steak becomes firm as it cools even during a meal. To address this, we propose SAVOR, a novel approach for learning skill affordances for bite acquisition-how suitable a manipulation skill (e.g., skewering, scooping) is for a given utensil-food interaction. In our formulation, skill affordances arise from the combination of tool affordances (what a utensil can do) and food affordances (what the food allows). Tool affordances are learned offline through calibration, where different utensils interact with a variety of foods to model their functional capabilities. Food affordances are characterized by physical properties such as softness, moisture, and viscosity, initially inferred through commonsense reasoning using a visually-conditioned language model and then dynamically refined through online multi-modal visuo-haptic perception using SAVOR-Net during interaction. Our method integrates these offline and online estimates to predict skill affordances in real time, enabling the robot to select the most appropriate skill for each food item. Evaluated on 20 single-item foods and 10 in-the-wild meals, our approach improves bite acquisition success rate by 13% over state-of-the-art (SOTA) category-based methods (e.g. use skewer for fruits). These results highlight the importance of modeling interaction-driven skill affordances for generalizable and effective robot-assisted bite acquisition. Website: https://emprise.cs.cornell.edu/savor/

Achieving coordinated teamwork among legged robots requires both fine-grained locomotion control and long-horizon strategic decision-making. Robot soccer offers a compelling testbed for this challenge, combining dynamic, competitive, and multi-agent interactions. In this work, we present a hierarchical multi-agent reinforcement learning (MARL) framework that enables fully autonomous and decentralized quadruped robot soccer. First, a set of highly dynamic low-level skills is trained for legged locomotion and ball manipulation, such as walking, dribbling, and kicking. On top of these, a high-level strategic planning policy is trained with Multi-Agent Proximal Policy Optimization (MAPPO) via Fictitious Self-Play (FSP). This learning framework allows agents to adapt to diverse opponent strategies and gives rise to sophisticated team behaviors, including coordinated passing, interception, and dynamic role allocation. With an extensive ablation study, the proposed learning method shows significant advantages in the cooperative and competitive multi-agent soccer game. We deploy the learned policies to real quadruped robots relying solely on onboard proprioception and decentralized localization, with the resulting system supporting autonomous robot-robot and robot-human soccer matches on indoor and outdoor soccer courts.