The average respondent used 7.7 tools/methods, similar to 2016 poll. Next, we compared the top 16 methods in this year's poll with their share last year - see Figure 1. We note a significant increase in Random Forests, Visualization, and Deep Learning share of usage, and decline in K-nn, PCA, and Boosting. Gradient Boosting Machines was a new entry in 2017. Deep Learning, despite its amazing successes, is reported used by only about 20% of KDnuggets readers.

The following problems are taken from the projects / assignments in the edX course Python for Data Science (UCSanDiagoX) and the coursera course Applied Machine Learning in Python (UMich). The IMDB Movie Dataset (MovieLens 20M) is used for the analysis. The dataset is downloaded from here . This dataset contains 20 million ratings and 465,000 tag applications applied to 27,000 movies by 138,000 users and was released in 4/2015. Understand the trend in average ratings for different movie genres over years (from 1995 to 2015) and Correlation between the trends for different genres (8 different genres are considered: Animation, Comedy, Romance, Thriller, Horror, Sci-Fi and Musical).

Engineering problems often involve data sources of variable fidelity with different costs of obtaining an observation. In particular, one can use both a cheap low fidelity function (e.g. a computational experiment with a CFD code) and an expensive high fidelity function (e.g. a wind tunnel experiment) to generate a data sample in order to construct a regression model of a high fidelity function. The key question in this setting is how the sizes of the high and low fidelity data samples should be selected in order to stay within a given computational budget and maximize accuracy of the regression model prior to committing resources on data acquisition. In this paper we obtain minimax interpolation errors for single and variable fidelity scenarios for a multivariate Gaussian process regression. Evaluation of the minimax errors allows us to identify cases when the variable fidelity data provides better interpolation accuracy than the exclusively high fidelity data for the same computational budget. These results allow us to calculate the optimal shares of variable fidelity data samples under the given computational budget constraint. Real and synthetic data experiments suggest that using the obtained optimal shares often outperforms natural heuristics in terms of the regression accuracy.

The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects. While recent models have relaxed this constraint to also account for pairwise interactions, these approaches do not provide a tractable path towards modeling higher-order dependencies. Here, we show how latent variable models with nonlinear dependencies can be applied to capture beyond-pairwise constraints in biomolecules. We present a new probabilistic model for sequence families, DeepSequence, that can predict the effects of mutations across a variety of deep mutational scanning experiments significantly better than site independent or pairwise models that are based on the same evolutionary data. The model, learned in an unsupervised manner solely from sequence information, is grounded with biologically motivated priors, reveals latent organization of sequence families, and can be used to extrapolate to new parts of sequence space.

Accurate diagnosis of psychiatric disorders plays a critical role in improving quality of life for patients and potentially supports the development of new treatments. Many studies have been conducted on machine learning techniques that seek brain imaging data for specific biomarkers of disorders. These studies have encountered the following dilemma: An end-to-end classification overfits to a small number of high-dimensional samples but unsupervised feature-extraction has the risk of extracting a signal of no interest. In addition, such studies often provided only diagnoses for patients without presenting the reasons for these diagnoses. This study proposed a deep neural generative model of resting-state functional magnetic resonance imaging (fMRI) data. The proposed model is conditioned by the assumption of the subject's state and estimates the posterior probability of the subject's state given the imaging data, using Bayes' rule. This study applied the proposed model to diagnose schizophrenia and bipolar disorders. Diagnosis accuracy was improved by a large margin over competitive approaches, namely a support vector machine, logistic regression, and multilayer perceptron with or without unsupervised feature-extractors in addition to a Gaussian mixture model. The proposed model visualizes brain regions largely related to the disorders, thus motivating further biological investigation.

The Morris Water Maze is commonly used in behavioural neuroscience for the study of spatial learning with rodents. Over the years, various methods of analysing rodent data collected in this task have been proposed. These methods span from classical performance measurements (e.g. escape latency, rodent speed, quadrant preference) to more sophisticated methods of categorisation which classify the animal swimming path into behavioural classes known as strategies. Classification techniques provide additional insight in relation to the actual animal behaviours but still only a limited amount of studies utilise them mainly because they highly depend on machine learning knowledge. We have previously demonstrated that the animals implement various strategies and by classifying whole trajectories can lead to the loss of important information. In this work, we developed a generalised and robust classification methodology which implements majority voting to boost the classification performance and successfully nullify the need of manual tuning. Based on this framework, we built a complete software, capable of performing the full analysis described in this paper. The software provides an easy to use graphical user interface (GUI) through which users can enter their trajectory data, segment and label them and finally generate reports and figures of the results.

The "least absolute shrinkage and selection operator" (Lasso) method has been adapted recently for networkstructured datasets. In particular, this network Lasso method allows to learn graph signals from a small number of noisy signal samples by using the total variation of a graph signal for regularization. While efficient and scalable implementations of the network Lasso are available, only little is known about the conditions on the underlying network structure which ensure network Lasso to be accurate. By leveraging concepts of compressed sensing, we address this gap and derive precise conditions on the underlying network topology and sampling set which guarantee the network Lasso for a particular loss function to deliver an accurate estimate of the entire underlying graph signal. We also quantify the error incurred by network Lasso in terms of two constants which reflect the connectivity of the sampled nodes.

Geometric variations of objects, which do not modify the object class, pose a major challenge for object recognition. These variations could be rigid as well as non-rigid transformations. In this paper, we design a framework for training deformable classifiers, where latent transformation variables are introduced, and a transformation of the object image to a reference instantiation is computed in terms of the classifier output, separately for each class. The classifier outputs for each class, after transformation, are compared to yield the final decision. As a by-product of the classification this yields a transformation of the input object to a reference pose, which can be used for downstream tasks such as the computation of object support. We apply a two-step training mechanism for our framework, which alternates between optimizing over the latent transformation variables and the classifier parameters to minimize the loss function. We show that multilayer perceptrons, also known as deep networks, are well suited for this approach and achieve state of the art results on the rotated MNIST and the Google Earth dataset, and produce competitive results on MNIST and CIFAR-10 when training on smaller subsets of training data.

Estimators computed from adaptively collected data do not behave like their non-adaptive brethren. Rather, the sequential dependence of the collection policy can lead to severe distributional biases that persist even in the infinite data limit. We develop a general method decorrelation procedure -- W-decorrelation -- for transforming the bias of adaptive linear regression estimators into variance. The method uses only coarse-grained information about the data collection policy and does not need access to propensity scores or exact knowledge of the policy. We bound the finite-sample bias and variance of the W-estimator and develop asymptotically correct confidence intervals based on a novel martingale central limit theorem. We then demonstrate the empirical benefits of the generic W-decorrelation procedure in two different adaptive data settings: the multi-armed bandits and autoregressive time series models.

Digital pathology is not only one of the most promising fields of diagnostic medicine, but at the same time a hot topic for fundamental research. Digital pathology is not just the transfer of histopathological slides into digital representations. The combination of different data sources (images, patient records, and *omics data) together with current advances in artificial intelligence/machine learning enable to make novel information accessible and quantifiable to a human expert, which is not yet available and not exploited in current medical settings. The grand goal is to reach a level of usable intelligence to understand the data in the context of an application task, thereby making machine decisions transparent, interpretable and explainable. The foundation of such an "augmented pathologist" needs an integrated approach: While machine learning algorithms require many thousands of training examples, a human expert is often confronted with only a few data points. Interestingly, humans can learn from such few examples and are able to instantly interpret complex patterns. Consequently, the grand goal is to combine the possibilities of artificial intelligence with human intelligence and to find a well-suited balance between them to enable what neither of them could do on their own. This can raise the quality of education, diagnosis, prognosis and prediction of cancer and other diseases. In this paper we describe some (incomplete) research issues which we believe should be addressed in an integrated and concerted effort for paving the way towards the augmented pathologist.