Rapid advancements in genome sequencing have led to the collection of vast amounts of genomics data. Researchers may be interested in using machine learning models on such data to predict the pathogenicity or clinical significance of a genetic mutation. However, many genetic datasets contain imbalanced target variables that pose challenges to machine learning models: observations are skewed/imbalanced in regression tasks or class-imbalanced in classification tasks. Genetic datasets are also often high-cardinal and contain skewed predictor variables, which poses further challenges. We aimed to investigate the effects of data preprocessing, feature selection techniques, and model selection on the performance of models trained on these datasets. We measured performance with 5-fold cross-validation and compared averaged r-squared and accuracy metrics across different combinations of techniques. We found that outliers/skew in predictor or target variables did not pose a challenge to regression models. We also found that class-imbalanced target variables and skewed predictors had little to no impact on classification performance. Random forest was the best model to use for imbalanced regression tasks. While our study uses a genetic dataset as an example of a real-world application, our findings can be generalized to any similar datasets.

Many existing two-phase kernel-based hypothesis transfer learning algorithms employ the same kernel regularization across phases and rely on the known smoothness of functions to obtain optimality. Therefore, they fail to adapt to the varying and unknown smoothness between the target/source and their offset in practice. In this paper, we address these problems by proposing Smoothness Adaptive Transfer Learning (SATL), a two-phase kernel ridge regression(KRR)-based algorithm. We first prove that employing the misspecified fixed bandwidth Gaussian kernel in target-only KRR learning can achieve minimax optimality and derive an adaptive procedure to the unknown Sobolev smoothness. Leveraging these results, SATL employs Gaussian kernels in both phases so that the estimators can adapt to the unknown smoothness of the target/source and their offset function. We derive the minimax lower bound of the learning problem in excess risk and show that SATL enjoys a matching upper bound up to a logarithmic factor. The minimax convergence rate sheds light on the factors influencing transfer dynamics and demonstrates the superiority of SATL compared to non-transfer learning settings. While our main objective is a theoretical analysis, we also conduct several experiments to confirm our results.

W e study the in-context learning (ICL) ability of a Linear Transformer Block (L TB) that combines a linear attention component and a linear multi-layer perceptron (MLP) component. For ICL of linear regression with a Gaussian prior and a nonzero mean, we show that L TB can achieve nearly Bayes optimal ICL risk. In contrast, using only linear attention must incur an irreducible additive approximation error. Furthermore, we establish a correspondence between L TB and one-step gradient descent estimators with learnable initialization ( GD- β), in the sense that every GD- β estimator can be implemented by an L TB estimator and every optimal L TB estimator that minimizes the in-class ICL risk is effectively a GD- β estimator. Finally, we show that GD- β estimators can be efficiently optimized with gradient flow, despite a non-convex training objective. Our results reveal that L TB achieves ICL by implementing GD- β, and they highlight the role of MLP layers in reducing approximation error.

Most leading implementations of black-box variational inference (BBVI) are based on optimizing a stochastic evidence lower bound (ELBO). But such approaches to BBVI often converge slowly due to the high variance of their gradient estimates. In this work, we propose batch and match (BaM), an alternative approach to BBVI based on a score-based divergence. Notably, this score-based divergence can be optimized by a closed-form proximal update for Gaussian variational families with full covariance matrices. We analyze the convergence of BaM when the target distribution is Gaussian, and we prove that in the limit of infinite batch size the variational parameter updates converge exponentially quickly to the target mean and covariance. We also evaluate the performance of BaM on Gaussian and non-Gaussian target distributions that arise from posterior inference in hierarchical and deep generative models. In these experiments, we find that BaM typically converges in fewer (and sometimes significantly fewer) gradient evaluations than leading implementations of BBVI based on ELBO maximization.

The incredible success of transformers on sequence modeling tasks can be largely attributed to the self-attention mechanism, which allows information to be transferred between different parts of a sequence. Self-attention allows transformers to encode causal structure which makes them particularly suitable for sequence modeling. However, the process by which transformers learn such causal structure via gradient-based training algorithms remains poorly understood. To better understand this process, we introduce an in-context learning task that requires learning latent causal structure. We prove that gradient descent on a simplified two-layer transformer learns to solve this task by encoding the latent causal graph in the first attention layer. The key insight of our proof is that the gradient of the attention matrix encodes the mutual information between tokens. As a consequence of the data processing inequality, the largest entries of this gradient correspond to edges in the latent causal graph. As a special case, when the sequences are generated from in-context Markov chains, we prove that transformers learn an induction head (Olsson et al., 2022). We confirm our theoretical findings by showing that transformers trained on our in-context learning task are able to recover a wide variety of causal structures.

Adaptive time series forecasting is essential for prediction under regime changes. Several classical methods assume linear Gaussian state space model (LGSSM) with variances constant in time. However, there are many real-world processes that cannot be captured by such models. We consider a state-space model with Markov switching variances. Such dynamical systems are usually intractable because of their computational complexity increasing exponentially with time; Variational Bayes (VB) techniques have been applied to this problem. In this paper, we propose a new way of estimating variances based on online learning theory; we adapt expert aggregation methods to learn the variances over time. We apply the proposed method to synthetic data and to the problem of electricity load forecasting. We show that this method is robust to misspecification and outperforms traditional expert aggregation.

Sparse linear regression (SLR) is a well-studied problem in statistics where one is given a design matrix $X\in\mathbb{R}^{m\times n}$ and a response vector $y=X\theta^*+w$ for a $k$-sparse vector $\theta^*$ (that is, $\|\theta^*\|_0\leq k$) and small, arbitrary noise $w$, and the goal is to find a $k$-sparse $\widehat{\theta} \in \mathbb{R}^n$ that minimizes the mean squared prediction error $\frac{1}{m}\|X\widehat{\theta}-X\theta^*\|^2_2$. While $\ell_1$-relaxation methods such as basis pursuit, Lasso, and the Dantzig selector solve SLR when the design matrix is well-conditioned, no general algorithm is known, nor is there any formal evidence of hardness in an average-case setting with respect to all efficient algorithms. We give evidence of average-case hardness of SLR w.r.t. all efficient algorithms assuming the worst-case hardness of lattice problems. Specifically, we give an instance-by-instance reduction from a variant of the bounded distance decoding (BDD) problem on lattices to SLR, where the condition number of the lattice basis that defines the BDD instance is directly related to the restricted eigenvalue condition of the design matrix, which characterizes some of the classical statistical-computational gaps for sparse linear regression. Also, by appealing to worst-case to average-case reductions from the world of lattices, this shows hardness for a distribution of SLR instances; while the design matrices are ill-conditioned, the resulting SLR instances are in the identifiable regime. Furthermore, for well-conditioned (essentially) isotropic Gaussian design matrices, where Lasso is known to behave well in the identifiable regime, we show hardness of outputting any good solution in the unidentifiable regime where there are many solutions, assuming the worst-case hardness of standard and well-studied lattice problems.

Clustering of longitudinal data is used to explore common trends among subjects over time for a numeric measurement of interest. Various R packages have been introduced throughout the years for identifying clusters of longitudinal patterns, summarizing the variability in trajectories between subject in terms of one or more trends. We introduce the R package "latrend" as a framework for the unified application of methods for longitudinal clustering, enabling comparisons between methods with minimal coding. The package also serves as an interface to commonly used packages for clustering longitudinal data, including "dtwclust", "flexmix", "kml", "lcmm", "mclust", "mixAK", and "mixtools". This enables researchers to easily compare different approaches, implementations, and method specifications. Furthermore, researchers can build upon the standard tools provided by the framework to quickly implement new cluster methods, enabling rapid prototyping. We demonstrate the functionality and application of the latrend package on a synthetic dataset based on the therapy adherence patterns of patients with sleep apnea.

We study the classic problem of prediction with expert advice under bandit feedback. Our model assumes that one action, corresponding to the learner's abstention from play, has no reward or loss on every trial. We propose the CBA algorithm, which exploits this assumption to obtain reward bounds that can significantly improve those of the classical Exp4 algorithm. We can view our problem as the aggregation of confidence-rated predictors when the learner has the option of abstention from play. Importantly, we are the first to achieve bounds on the expected cumulative reward for general confidence-rated predictors. In the special case of specialists we achieve a novel reward bound, significantly improving previous bounds of SpecialistExp (treating abstention as another action). As an example application, we discuss learning unions of balls in a finite metric space. In this contextual setting, we devise an efficient implementation of CBA, reducing the runtime from quadratic to almost linear in the number of contexts. Preliminary experiments show that CBA improves over existing bandit algorithms.

In this paper, we consider a deterministic online linear regression model where we allow the responses to be multivariate. To address this problem, we introduce MultiVAW, a method that extends the well-known Vovk-Azoury-Warmuth algorithm to the multivariate setting, and show that it also enjoys logarithmic regret in time. We apply our results to the online hierarchical forecasting problem and recover an algorithm from this literature as a special case, allowing us to relax the hypotheses usually made for its analysis.