Structure-based Virtual Screening (VS)1,2 aims at identifying compounds with previously unknown affinity for a target from its three-dimensional (3D) structure. Docking techniques are typically used to carry out this in silico prediction using their embedded scoring functions (SFs). When applied to VS, SFs seek to rank compounds based on their predicted affinity for the target as a way to discriminate between binders and non-binders. Despite the well-known limitations of SFs1,3,4,5, their application has been beneficial in many VS projects and successful applications have been reported3,6,7,8,9. Although the classical SFs used in VS experiments have often proven useful, improved accuracy requires novel approaches.

The data are usually recorded in rows and columns. A column represents a variable,whereas a row represents an observation, which is a set of p 1 values for a single subject i.e. one value for the response variable and one value for each of the p predictors. Each of the variables can be classified as either quantitative or qualitative. A technique used in cases where the response variable is binary is called logistic regression. In regression analysis, the predictor variables can be either quantitative and or qualitative. For the purpose of computations, however, the qualitative variables, if any, have to be coded into a set of indicator or dummy variables.

We present a semi-parametric approach to photographic image synthesis from semantic layouts. The approach combines the complementary strengths of parametric and nonparametric techniques. The nonparametric component is a memory bank of image segments constructed from a training set of images. Given a novel semantic layout at test time, the memory bank is used to retrieve photographic references that are provided as source material to a deep network. The synthesis is performed by a deep network that draws on the provided photographic material. Experiments on multiple semantic segmentation datasets show that the presented approach yields considerably more realistic images than recent purely parametric techniques. The results are shown in the supplementary video at https://youtu.be/U4Q98lenGLQ

We consider multi-response and multitask regression models, where the parameter matrix to be estimated is expected to have an unknown grouping structure. The groupings can be along tasks, or features, or both, the last one indicating a bi-cluster or "checkerboard" structure. Discovering this grouping structure along with parameter inference makes sense in several applications, such as multi-response Genome-Wide Association Studies. This additional structure can not only can be leveraged for more accurate parameter estimation, but it also provides valuable information on the underlying data mechanisms (e.g. relationships among genotypes and phenotypes in GWAS). In this paper, we propose two formulations to simultaneously learn the parameter matrix and its group structures, based on convex regularization penalties. We present optimization approaches to solve the resulting problems and provide numerical convergence guarantees. Our approaches are validated on extensive simulations and real datasets concerning phenotypes and genotypes of plant varieties.

Recent research has shown that deep ensemble for forest can achieve a huge increase in classification accuracy compared with the general ensemble learning method. Especially when there are only few training data. In this paper, we decide to take full advantage of this observation and introduce the Dense Adaptive Cascade Forest (daForest), which has better performance than the original one named Cascade Forest. And it is particularly noteworthy that daForest has a powerful ability to handle high-dimensional sparse data without any preprocessing on raw data like PCA or any other dimensional reduction methods. Our model is distinguished by three major features: the first feature is the combination of the SAMME.R boosting algorithm in the model, boosting gives the model the ability to continuously improve as the number of layer increases, which is not possible in stacking model or plain cascade forest. The second feature is our model connects each layer to its subsequent layers in a feed-forward fashion, to some extent this structure enhances the ability of the model to resist degeneration. When number of layers goes up, accuracy of model goes up a little in the first few layers then drop down quickly, we call this phenomenon degeneration in training stacking model. The third feature is that we add a hyper-parameter optimization layer before the first classification layer in the proposed deep model, which can search for the optimal hyper-parameter and set up the model in a brief period and nearly halve the training time without having too much impact on the final performance. Experimental results show that daForest performs particularly well on both high-dimensional low-order features and low-dimensional high-order features, and in some cases, even better than neural networks and achieves state-of-the-art results.

This paper introduces a new property of estimators of the strength of statistical association, which helps characterize how well an estimator will perform in scenarios where dependencies between continuous and discrete random variables need to be rank ordered. The new property, termed the estimator response curve, is easily computable and provides a marginal distribution agnostic way to assess an estimator's performance. It overcomes notable drawbacks of current metrics of assessment, including statistical power, bias, and consistency. We utilize the estimator response curve to test various measures of the strength of association that satisfy the data processing inequality (DPI), and show that the CIM estimator's performance compares favorably to kNN, vME, AP, and H_{MI} estimators of mutual information. The estimators which were identified to be suboptimal, according to the estimator response curve, perform worse than the more optimal estimators when tested with real-world data from four different areas of science, all with varying dimensionalities and sizes.

An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the throughput of in-silico simulation-based observations become similarly intractable for thorough analysis. This is especially the case in molecular biology, which served as a subject for this study. In this project, we aimed to test some approaches developed to deal with the curse of dimensionality. Among these we found dimension reduction techniques especially appealing. They can be used to identify irrelevant variability and help to understand critical processes underlying high-dimensional datasets. Additionally, we subjected our data sets to nonlinear time series analysis, as those are well established methods for results comparison. To investigate the usefulness of dimension reduction methods, we decided to base our study on a concrete sample set. The example was taken from the domain of systems biology concerning dynamic evolution of sub-cellular signaling. Particularly, the dataset relates to the yeast pheromone pathway and is studied in-silico with a stochastic model. The model reconstructs signal propagation stimulated by a mating pheromone. In the paper, we elaborate on the reason of multidimensional analysis problem in the context of molecular signaling, and next, we introduce the model of choice, simulation details and obtained time series dynamics. A description of used methods followed by a discussion of results and their biological interpretation finalize the paper.

Clustering is a complex process in finding the relevant hidden patterns in unlabeled datasets, broadly known as unsupervised learning. Support vector clustering algorithm is a well-known clustering algorithm based on support vector machines and Gaussian kernels. In this paper, we have investigated the support vector clustering algorithm in quantum paradigm. We have developed a quantum algorithm which is based on quantum support vector machine and the quantum kernel (Gaussian kernel and polynomial kernel) formulation. The investigation exhibits approximately exponential speed up in the quantum version with respect to the classical counterpart.

Data Science is quite a large and diverse field. As a result, it is really difficult to be a jack of all trades. Traditionally, Data Science would focus on mathematics, computer science and domain expertise. While I will briefly cover some computer science fundamentals, the bulk of this blog will mostly cover the mathematical basics one might either need to brush up on (or even take an entire course). In most data science workplaces, software skills are a must.

In machine learning, there are many ways to build a product or solution and each way assumes something different. Many times, it's not obvious how to navigate and identify which assumptions are reasonable. People new to machine learning make mistakes, which in hindsight will often feel silly. I've created a list of the top mistakes that novice machine learning engineers make. Hopefully, you can learn from these common errors and create more robust solutions that bring real value.