Classification algorithms using RNA-Sequencing (RNA-Seq) data as input are used in a variety of biological applications. By nature, RNA-Seq data is subject to uncontrolled fluctuations both within and especially across datasets, which presents a major difficulty for a trained classifier to generalize to an external dataset. Replacing raw gene counts with the rank of gene counts inside an observation has proven effective to mitigate this problem. However, the rank of a feature is by definition relative to all other features, including highly variable features that introduce noise in the ranking. To address this problem and obtain more robust ranks, we propose a logistic regression model, optirank, which learns simultaneously the parameters of the model and the genes to use as a reference set in the ranking. We show the effectiveness of this method on simulated data. We also consider real classification tasks, which present different kinds of distribution shifts between train and test data. Those tasks concern a variety of applications, such as cancer of unknown primary classification, identification of specific gene signatures, and determination of cell type in single-cell RNA-Seq datasets. On those real tasks, optirank performs at least as well as the vanilla logistic regression on classical ranks, while producing sparser solutions. In addition, to increase the robustness against dataset shifts, we propose a multi-source learning scheme and demonstrate its effectiveness when used in combination with rank-based classifiers.

In data science, machine learning algorithms are used to automate a system. In practice, there are mainly two types of problems -- i. Supervised, and ii. In the supervised problem, the training dataset is labelled. That means the algorithm has a target value. The supervised learning algorithm tries to predict the values like target values and optimizes its parameters accordingly.

Originally published on Towards AI the World's Leading AI and Technology News and Media Company. If you are building an AI-related product or service, we invite you to consider becoming an AI sponsor. At Towards AI, we help scale AI and technology startups. Let us help you unleash your technology to the masses. Logistic regression is a supervised machine learning algorithm to create models used for binary classification problems conventionally.

Is this another spam email? How does your email spam filter tell? Perhaps it uses a simple machine learning technique. In this post, we're going to learn about what it is and how we can create a Python logistic regression program. Unlike linear regression, logistic regression is used for classification rather than prediction along a continuous range.

In multiple domains, statistical tasks are performed in distributed settings, with data split among several end machines that are connected to a fusion center. In various applications, the end machines have limited bandwidth and power, and thus a tight communication budget. In this work we focus on distributed learning of a sparse linear regression model, under severe communication constraints. We propose several two round distributed schemes, whose communication per machine is sublinear in the data dimension. In our schemes, individual machines compute debiased lasso estimators, but send to the fusion center only very few values. On the theoretical front, we analyze one of these schemes and prove that with high probability it achieves exact support recovery at low signal to noise ratios, where individual machines fail to recover the support. We show in simulations that our scheme works as well as, and in some cases better, than more communication intensive approaches.

Metallic glasses are one of the most interesting mechanical materials studied in the last years, but as amorphous solids, they differ strongly from their crystalline counterparts. This matter can be addressed with the development and application of predictive techniques capable to describe the plastic regime. Here, machine learning models were employed for the prediction of plastic properties in CuZr metallic glasses. To this aim, 100 different samples were subjected to tensile tests by means of molecular dynamics simulations. A total of 17 materials properties were calculated and explored using statistical analysis. Strong correlations were found for stoichiometry, temperature, structural, and elastic properties with plastic properties. Three regression models were employed for the prediction of six plastic properties. Linear and Ridge regressions delivered the better prediction capability, with coefficients of determination above $$\sim$$ 80% for three plastic properties, whereas Lasso regression rendered lower performance, with coefficients of determination above $$\sim$$ 60% for two plastic properties. Overall, our work shows that molecular dynamics simulations together with machine learning models can provide a framework for the prediction of plastic behavior of complex materials.

Identifying the mathematical relationships that best describe a dataset remains a very challenging problem in machine learning, and is known as Symbolic Regression (SR). In contrast to neural networks which are often treated as black boxes, SR attempts to gain insight into the underlying relationships between the independent variables and the target variable of a given dataset by assembling analytical functions. In this paper, we present GSR, a Generalized Symbolic Regression approach, by modifying the conventional SR optimization problem formulation, while keeping the main SR objective intact. In GSR, we infer mathematical relationships between the independent variables and some transformation of the target variable. We constrain our search space to a weighted sum of basis functions, and propose a genetic programming approach with a matrix-based encoding scheme. We show that our GSR method is competitive with strong SR benchmark methods, achieving promising experimental performance on the well-known SR benchmark problem sets. Finally, we highlight the strengths of GSR by introducing SymSet, a new SR benchmark set which is more challenging relative to the existing benchmarks.

The stochastic proximal point (SPP) methods have gained recent attention for stochastic optimization, with strong convergence guarantees and superior robustness to the classic stochastic gradient descent (SGD) methods showcased at little to no cost of computational overhead added. In this article, we study a minibatch variant of SPP, namely M-SPP, for solving convex composite risk minimization problems. The core contribution is a set of novel excess risk bounds of M-SPP derived through the lens of algorithmic stability theory. Particularly under smoothness and quadratic growth conditions, we show that M-SPP with minibatch-size $n$ and iteration count $T$ enjoys an in-expectation fast rate of convergence consisting of an $\mathcal{O}\left(\frac{1}{T^2}\right)$ bias decaying term and an $\mathcal{O}\left(\frac{1}{nT}\right)$ variance decaying term. In the small-$n$-large-$T$ setting, this result substantially improves the best known results of SPP-type approaches by revealing the impact of noise level of model on convergence rate. In the complementary small-$T$-large-$n$ regime, we provide a two-phase extension of M-SPP to achieve comparable convergence rates. Moreover, we derive a near-tight high probability (over the randomness of data) bound on the parameter estimation error of a sampling-without-replacement variant of M-SPP. Numerical evidences are provided to support our theoretical predictions when substantialized to Lasso and logistic regression models.

Because of the widespread existence of noise and data corruption, recovering the true regression parameters with a certain proportion of corrupted response variables is an essential task. Methods to overcome this problem often involve robust least-squares regression, but few methods perform well when confronted with severe adaptive adversarial attacks. In many applications, prior knowledge is often available from historical data or engineering experience, and by incorporating prior information into a robust regression method, we develop an effective robust regression method that can resist adaptive adversarial attacks. First, we propose the novel TRIP (hard Thresholding approach to Robust regression with sImple Prior) algorithm, which improves the breakdown point when facing adaptive adversarial attacks. Then, to improve the robustness and reduce the estimation error caused by the inclusion of priors, we use the idea of Bayesian reweighting to construct the more robust BRHT (robust Bayesian Reweighting regression via Hard Thresholding) algorithm. We prove the theoretical convergence of the proposed algorithms under mild conditions, and extensive experiments show that under different types of dataset attacks, our algorithms outperform other benchmark ones. Finally, we apply our methods to a data-recovery problem in a real-world application involving a space solar array, demonstrating their good applicability.

Linear/Logistic Regression: a statistical method for modeling the linear relationship between a dependent variable and one or more independent variables -- can be used to understand the relationships between variables based on the t-tests and coefficients. Decision Trees: a type of machine learning algorithm that creates a tree-like model of decisions and their possible consequences. They are useful for understanding the relationships between variables by looking at the rules that split the branches. Principal Component Analysis (PCA): a dimensionality reduction technique that projects the data onto a lower-dimensional space while retaining as much variance as possible. PCA can be used to simplify the data or to determine feature importance.