Mappings from biological sequences (DNA, RNA, protein) to quantitative measures of sequence functionality play an important role in contemporary biology. We are interested in the related tasks of (i) inferring predictive sequence-to-function maps and (ii) decomposing sequence-function maps to elucidate the contributions of individual subsequences. Because each sequence-function map can be written as a weighted sum over subsequences in multiple ways, meaningfully interpreting these weights requires "gauge-fixing," i.e., defining a unique representation for each map. Recent work has established that most existing gauge-fixed representations arise as the unique solutions to $L_2$-regularized regression in an overparameterized "weight space" where the choice of regularizer defines the gauge. Here, we establish the relationship between regularized regression in overparameterized weight space and Gaussian process approaches that operate in "function space," i.e. the space of all real-valued functions on a finite set of sequences. We disentangle how weight space regularizers both impose an implicit prior on the learned function and restrict the optimal weights to a particular gauge. We also show how to construct regularizers that correspond to arbitrary explicit Gaussian process priors combined with a wide variety of gauges. Next, we derive the distribution of gauge-fixed weights implied by the Gaussian process posterior and demonstrate that even for long sequences this distribution can be efficiently computed for product-kernel priors using a kernel trick. Finally, we characterize the implicit function space priors associated with the most common weight space regularizers. Overall, our framework unifies and extends our ability to infer and interpret sequence-function relationships.

Regularized models are often sensitive to the scales of the features in the data and it has therefore become standard practice to normalize (center and scale) the features before fitting the model. But there are many different ways to normalize the features and the choice may have dramatic effects on the resulting model. In spite of this, there has so far been no research on this topic. In this paper, we begin to bridge this knowledge gap by studying normalization in the context of lasso, ridge, and elastic net regression. We focus on normal and binary features and show that the class balances of binary features directly influences the regression coefficients and that this effect depends on the combination of normalization and regularization methods used. We demonstrate that this effect can be mitigated by scaling binary features with their variance in the case of the lasso and standard deviation in the case of ridge regression, but that this comes at the cost of increased variance. For the elastic net, we show that scaling the penalty weights, rather than the features, can achieve the same effect. Finally, we also tackle mixes of binary and normal features as well as interactions and provide some initial results on how to normalize features in these cases.

We use transductive regression techniques to learn mappings between source and target features of given parallel corpora and use these mappings to generate machine translation outputs. We show the effectiveness of $L_1$ regularized regression (\textit{lasso}) to learn the mappings between sparsely observed feature sets versus $L_2$ regularized regression. Proper selection of training instances plays an important role to learn correct feature mappings within limited computational resources and at expected accuracy levels. We introduce \textit{dice} instance selection method for proper selection of training instances, which plays an important role to learn correct feature mappings for improving the source and target coverage of the training set. We show that $L_1$ regularized regression performs better than $L_2$ regularized regression both in regression measurements and in the translation experiments using graph decoding. We present encouraging results when translating from German to English and Spanish to English. We also demonstrate results when the phrase table of a phrase-based decoder is replaced with the mappings we find with the regression model.

We study the effect of norm based regularization on the size of coresets for regression problems. Specifically, given a matrix $ \mathbf{A} \in {\mathbb{R}}^{n \times d}$ with $n\gg d$ and a vector $\mathbf{b} \in \mathbb{R} ^ n $ and $\lambda > 0$, we analyze the size of coresets for regularized versions of regression of the form $\|\mathbf{Ax}-\mathbf{b}\|_p^r + \lambda\|{\mathbf{x}}\|_q^s$ . Prior work has shown that for ridge regression (where $p,q,r,s=2$) we can obtain a coreset that is smaller than the coreset for the unregularized counterpart i.e. least squares regression (Avron et al). We show that when $r \neq s$, no coreset for regularized regression can have size smaller than the optimal coreset of the unregularized version. The well known lasso problem falls under this category and hence does not allow a coreset smaller than the one for least squares regression. We propose a modified version of the lasso problem and obtain for it a coreset of size smaller than the least square regression. We empirically show that the modified version of lasso also induces sparsity in solution, similar to the original lasso. We also obtain smaller coresets for $\ell_p$ regression with $\ell_p$ regularization. We extend our methods to multi response regularized regression. Finally, we empirically demonstrate the coreset performance for the modified lasso and the $\ell_1$ regression with $\ell_1$ regularization.

Regularized regression problems are ubiquitous in statistical modeling, signal processing, and machine learning. Sparse regression in particular has been instrumental in scientific model discovery, including compressed sensing applications, variable selection, and high-dimensional analysis. We propose a broad framework for sparse relaxed regularized regression, called SR3. The key idea is to solve a relaxation of the regularized problem, which has three advantages over the state-of-the-art: (1) solutions of the relaxed problem are superior with respect to errors, false positives, and conditioning, (2) relaxation allows extremely fast algorithms for both convex and nonconvex formulations, and (3) the methods apply to composite regularizers such as total variation (TV) and its nonconvex variants. We demonstrate the advantages of SR3 (computational efficiency, higher accuracy, faster convergence rates, greater flexibility) across a range of regularized regression problems with synthetic and real data, including applications in compressed sensing, LASSO, matrix completion, TV regularization, and group sparsity. To promote reproducible research, we also provide a companion Matlab package that implements these examples.

Variable (feature, gene, model, which we use interchangeably) selections for regression with high-dimensional BIGDATA have found many applications in bioinformatics, computational biology, image processing, and engineering. One appealing approach is the L0 regularized regression which penalizes the number of nonzero features in the model directly. L0 is known as the most essential sparsity measure and has nice theoretical properties, while the popular L1 regularization is only a best convex relaxation of L0. Therefore, it is natural to expect that L0 regularized regression performs better than LASSO. However, it is well-known that L0 optimization is NP-hard and computationally challenging. Instead of solving the L0 problems directly, most publications so far have tried to solve an approximation problem that closely resembles L0 regularization. In this paper, we propose an efficient EM algorithm (L0EM) that directly solves the L0 optimization problem. $L_0$EM is efficient with high dimensional data. It also provides a natural solution to all Lp p in [0,2] problems. The regularized parameter can be either determined through cross-validation or AIC and BIC. Theoretical properties of the L0-regularized estimator are given under mild conditions that permit the number of variables to be much larger than the sample size. We demonstrate our methods through simulation and high-dimensional genomic data. The results indicate that L0 has better performance than LASSO and L0 with AIC or BIC has similar performance as computationally intensive cross-validation. The proposed algorithms are efficient in identifying the non-zero variables with less-bias and selecting biologically important genes and pathways with high dimensional BIGDATA.

In the quest to make Brain Computer Interfacing (BCI) more usable, dry electrodes have emerged that get rid of the initial 30 minutes required for placing an electrode cap. Another time consuming step is the required individualized adaptation to the BCI user, which involves another 30 minutes calibration for assessing a subjects brain signature. In this paper we aim to also remove this calibration proceedure from BCI setup time by means of machine learning. In particular, we harvest a large database of EEG BCI motor imagination recordings (83 subjects) for constructing a library of subject-specific spatio-temporal filters and derive a subject independent BCI classifier. Our offline results indicate that BCI-na\{i}ve users could start real-time BCI use with no prior calibration at only a very moderate performance loss."

In this paper we consider the problem of grouped variable selection in high-dimensional regression using $\ell_1-\ell_q$ regularization ($1\leq q \leq \infty$), which can be viewed as a natural generalization of the $\ell_1-\ell_2$ regularization (the group Lasso). The key condition is that the dimensionality $p_n$ can increase much faster than the sample size $n$, i.e. $p_n \gg n$ (in our case $p_n$ is the number of groups), but the number of relevant groups is small. The main conclusion is that many good properties from $\ell_1-$regularization (Lasso) naturally carry on to the $\ell_1-\ell_q$ cases ($1 \leq q \leq \infty$), even if the number of variables within each group also increases with the sample size. With fixed design, we show that the whole family of estimators are both estimation consistent and variable selection consistent under different conditions. We also show the persistency result with random design under a much weaker condition. These results provide a unified treatment for the whole family of estimators ranging from $q=1$ (Lasso) to $q=\infty$ (iCAP), with $q=2$ (group Lasso)as a special case. When there is no group structure available, all the analysis reduces to the current results of the Lasso estimator ($q=1$).