We consider the problem of learning a realization of a partially observed bilinear dynamical system (BLDS) from noisy input-output data. Given a single trajectory of input-output samples, we provide a finite time analysis for learning the system's Markov-like parameters, from which a balanced realization of the bilinear system can be obtained. Our bilinear system identification algorithm learns the system's Markov-like parameters by regressing the outputs to highly correlated, nonlinear, and heavy-tailed covariates. Moreover, the stability of BLDS depends on the sequence of inputs used to excite the system. These properties, unique to partially observed bilinear dynamical systems, pose significant challenges to the analysis of our algorithm for learning the unknown dynamics. We address these challenges and provide high probability error bounds on our identification algorithm under a uniform stability assumption. Our analysis provides insights into system theoretic quantities that affect learning accuracy and sample complexity. Lastly, we perform numerical experiments with synthetic data to reinforce these insights.

We propose a novel deep clustering method that integrates Variational Autoencoders (VAEs) into the Expectation-Maximization (EM) framework. Our approach models the probability distribution of each cluster with a VAE and alternates between updating model parameters by maximizing the Evidence Lower Bound (ELBO) of the log-likelihood and refining cluster assignments based on the learned distributions. This enables effective clustering and generation of new samples from each cluster. Unlike existing VAE-based methods, our approach eliminates the need for a Gaussian Mixture Model (GMM) prior or additional regularization techniques. Experiments on MNIST and FashionMNIST demonstrate superior clustering performance compared to state-of-the-art methods.

Detecting and classifying abnormal system states is critical for condition monitoring, but supervised methods often fall short due to the rarity of anomalies and the lack of labeled data. Therefore, clustering is often used to group similar abnormal behavior. However, evaluating cluster quality without ground truth is challenging, as existing measures such as the Silhouette Score (SSC) only evaluate the cohesion and separation of clusters and ignore possible prior knowledge about the data. To address this challenge, we introduce the Synchronized Anomaly Agreement Index (SAAI), which exploits the synchronicity of anomalies across multivariate time series to assess cluster quality. We demonstrate the effectiveness of SAAI by showing that maximizing SAAI improves accuracy on the task of finding the true number of anomaly classes K in correlated time series by 0.23 compared to SSC and by 0.32 compared to X-Means. We also show that clusters obtained by maximizing SAAI are easier to interpret compared to SSC.

The seminal work of Jordan, Kinderlehrer, and Otto [33] developed what is now widely known as the JKO scheme, a foundational method for generating iterative algorithms to compute distributions and reshaping our understanding of sampling algorithms. The JKO scheme can be interpreted as a gradient flow of the free energy with respect to the Wasserstein metric, often referred to as the Wasserstein gradient flow. This interpretation has led to significant advancements in machine learning, including applications in reinforcement learning to solve policy-distribution optimization problems [55]. While the JKO scheme traditionally assumes that the underlying model is fully known, in this paper, we relax this assumption by allowing models with unknown parameters. We develop statistical approaches to estimate these parameters and adapt the JKO scheme to work with the estimated values. Specifically, Langevin equations--stochastic differential equations--play a key role in describing the evolution of physical systems, facilitating stochastic gradient descent in machine learning, and enabling Markov chain Monte Carlo (MCMC) simulations in numerical computing. For examples and detailed discussions, see [11, 8, 51, 22, 19, 39, 43]. Solutions to Langevin equations, known as Langevin diffusions, are stochastic processes whose distributions evolve according to the Fokker-Planck equations [27, 48].

Measurement-constrained datasets, often encountered in semi-supervised learning, arise when data labeling is costly, time-intensive, or hindered by confidentiality or ethical concerns, resulting in a scarcity of labeled data. In certain cases, surrogate variables are accessible across the entire dataset and can serve as approximations to the true response variable; however, these surrogates often contain measurement errors and thus cannot be directly used for accurate prediction. We propose an optimal sampling strategy that effectively harnesses the available information from surrogate variables. This approach provides consistent estimators under the assumption of a generalized linear model, achieving theoretically lower asymptotic variance than existing optimal sampling algorithms that do not use surrogate data information. By employing the A-optimality criterion from optimal experimental design, our strategy maximizes statistical efficiency. Numerical studies demonstrate that our approach surpasses existing optimal sampling methods, exhibiting reduced empirical mean squared error and enhanced robustness in algorithmic performance. These findings highlight the practical advantages of our strategy in scenarios where measurement constraints exist and surrogates are available.

Estimating causal quantities from observational data is crucial for understanding the safety and effectiveness of medical treatments. However, to make reliable inferences, medical practitioners require not only estimating averaged causal quantities, such as the conditional average treatment effect, but also understanding the randomness of the treatment effect as a random variable. This randomness is referred to as aleatoric uncertainty and is necessary for understanding the probability of benefit from treatment or quantiles of the treatment effect. Yet, the aleatoric uncertainty of the treatment effect has received surprisingly little attention in the causal machine learning community. To fill this gap, we aim to quantify the aleatoric uncertainty of the treatment effect at the covariate-conditional level, namely, the conditional distribution of the treatment effect (CDTE). Unlike average causal quantities, the CDTE is not point identifiable without strong additional assumptions. As a remedy, we employ partial identification to obtain sharp bounds on the CDTE and thereby quantify the aleatoric uncertainty of the treatment effect. We then develop a novel, orthogonal learner for the bounds on the CDTE, which we call AU-learner. We further show that our AU-learner has several strengths in that it satisfies Neyman-orthogonality and, thus, quasi-oracle efficiency. Finally, we propose a fully-parametric deep learning instantiation of our AU-learner.

Handling anomalies is a critical preprocessing step in multivariate time series prediction. However, existing approaches that separate anomaly preprocessing from model training for multivariate time series prediction encounter significant limitations. Specifically, these methods fail to utilize auxiliary information crucial for identifying latent anomalies associated with spatiotemporal factors during the preprocessing stage. Instead, they rely solely on data distribution for anomaly detection, which can result in the incorrect processing of numerous samples that could otherwise contribute positively to model training. To address this, we propose STTS-EAD, an end-to-end method that seamlessly integrates anomaly detection into the training process of multivariate time series forecasting and aims to improve Spatio-Temporal learning based Time Series prediction via Embedded Anomaly Detection. Our proposed STTS-EAD leverages spatio-temporal information for forecasting and anomaly detection, with the two parts alternately executed and optimized for each other. To the best of our knowledge, STTS-EAD is the first to integrate anomaly detection and forecasting tasks in the training phase for improving the accuracy of multivariate time series forecasting. Extensive experiments on a public stock dataset and two real-world sales datasets from a renowned coffee chain enterprise show that our proposed method can effectively process detected anomalies in the training stage to improve forecasting performance in the inference stage and significantly outperform baselines.

Learning in the reproducing kernel Hilbert space (RKHS) such as the support vector machine has been recognized as a promising technique. It continues to be highly effective and competitive in numerous prediction tasks, particularly in settings where there is a shortage of training data or computational limitations exist. These methods are especially valued for their ability to work with small datasets and their interpretability. To address the issue of limited training data, mixup data augmentation, widely used in deep learning, has remained challenging to apply to learning in RKHS due to the generation of intermediate class labels. Although gradient descent methods handle these labels effectively, dual optimization approaches are typically not directly applicable. In this study, we present two novel algorithms that extend to a broader range of binary classification models. Unlike gradient-based approaches, our algorithms do not require hyperparameters like learning rates, simplifying their implementation and optimization. Both the number of iterations to converge and the computational cost per iteration scale linearly with respect to the dataset size. The numerical experiments demonstrate that our algorithms achieve faster convergence to the optimal solution compared to gradient descent approaches, and that mixup data augmentation consistently improves the predictive performance across various loss functions.

Understanding how molecular changes caused by genetic variation drive disease risk is crucial for deciphering disease mechanisms. However, interpreting genome sequences is challenging because of the vast size of the human genome, and because its consequences manifest across a wide range of cells, tissues and scales -- spanning from molecular to whole organism level. Here, we present Phenformer, a multi-scale genetic language model that learns to generate mechanistic hypotheses as to how differences in genome sequence lead to disease-relevant changes in expression across cell types and tissues directly from DNA sequences of up to 88 million base pairs. Using whole genome sequencing data from more than 150 000 individuals, we show that Phenformer generates mechanistic hypotheses about disease-relevant cell and tissue types that match literature better than existing state-of-the-art methods, while using only sequence data. Furthermore, disease risk predictors enriched by Phenformer show improved prediction performance and generalisation to diverse populations. Accurate multi-megabase scale interpretation of whole genomes without additional experimental data enables both a deeper understanding of molecular mechanisms involved in disease and improved disease risk prediction at the level of individuals.

Groups with complex set intersection relations are a natural way to model a wide array of data, from the formation of social groups to the complex protein interactions which form the basis of biological life. One approach to representing such "higher order" relationships is as a hypergraph. However, efforts to apply machine learning techniques to hypergraph structured datasets have been limited thus far. In this paper, we address the problem of link prediction in knowledge hypergraphs as well as simple hypergraphs and develop a novel, simple, and effective optimization architecture that addresses both tasks. Additionally, we introduce a novel feature extraction technique using node level clustering and we show how integrating data from node-level labels can improve system performance. Our self-supervised approach achieves significant improvement over state of the art baselines on several hyperedge prediction and knowledge hypergraph completion benchmarks.