Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here we present OhmNet, a hierarchy-aware unsupervised node feature learning approach for multi-layer networks. We build a multi-layer network, where each layer represents molecular interactions in a different human tissue. OhmNet then automatically learns a mapping of proteins, represented as nodes, to a neural embedding based low-dimensional space of features. OhmNet encourages sharing of similar features among proteins with similar network neighborhoods and among proteins activated in similar tissues. The algorithm generalizes prior work, which generally ignores relationships between tissues, by modeling tissue organization with a rich multiscale tissue hierarchy. We use OhmNet to study multicellular function in a multi-layer protein interaction network of 107 human tissues. In 48 tissues with known tissue-specific cellular functions, OhmNet provides more accurate predictions of cellular function than alternative approaches, and also generates more accurate hypotheses about tissue-specific protein actions. We show that taking into account the tissue hierarchy leads to improved predictive power. Remarkably, we also demonstrate that it is possible to leverage the tissue hierarchy in order to effectively transfer cellular functions to a functionally uncharacterized tissue. Overall, OhmNet moves from flat networks to multiscale models able to predict a range of phenotypes spanning cellular subsystems

Watson started as a follow-on project to IBM DeepBlue, the computer and AI program that defeated world chess champion Gary Kasparov. DeepBlue demonstrated that a computer could defeat a human in chess, a game with well-defined rules and limited, fully visible solutions. The real world, however, is much more complicated: information often is unstructured, problems ill defined, and solutions probabilistic at best. To equip AI to deal with the real world, IBM challenged its computer and data scientists to create a program that could defeat human contestants at Jeopardy!, a quiz show requiring answers to natural language questions over broad domains of knowledge otherwise known as unstructured data. As a quick refresher, artificial intelligence can be divided into three categories, as shown above.1The

The Word2Vec model has become a standard method for representing words as dense vectors. This is typically done as a preprocessing step, after which the learned vectors are fed into a discriminative model (typically an RNN) to generate predictions such as movie review sentiment, do machine translation, or even generate text, character by character. Previously, the bag of words model was commonly used to represent words and sentences as numerical vectors, which could then be fed into a classifier (for example Naive Bayes) to produce output predictions. Given a vocabulary of words and a document of words, a -dimensional vector would be created to represent the vector, where index denotes the number of times the th word in the vocabulary occured in the document. This model represented words as atomic units, assuming that all words were independent of each other.

Many articles have been written about the top machine learning algorithms: click here and here for instance. I received this morning and advertisement for a (self-published) book called Master Machine Learning Algorithms, and I could not resist to post the author's list of top 10 machine learning algorithms:: You can check the book here. You might have to attend classes taught by real practitioners (people who worked for big data solutions vendors) to learn modern tools that will give you a competitive edge on the job market. My upcoming book Data Science 2.0 will cover much of the topic, and my previous Wiley book is a good starting point.

In this study, we tested the interaction effect of multimodal datasets using a novel method called the kernel method for detecting higher order interactions among biologically relevant mulit-view data. Using a semiparametric method on a reproducing kernel Hilbert space (RKHS), we used a standard mixed-effects linear model and derived a score-based variance component statistic that tests for higher order interactions between multi-view data. The proposed method offers an intangible framework for the identification of higher order interaction effects (e.g., three way interaction) between genetics, brain imaging, and epigenetic data. Extensive numerical simulation studies were first conducted to evaluate the performance of this method. Finally, this method was evaluated using data from the Mind Clinical Imaging Consortium (MCIC) including single nucleotide polymorphism (SNP) data, functional magnetic resonance imaging (fMRI) scans, and deoxyribonucleic acid (DNA) methylation data, respectfully, in schizophrenia patients and healthy controls. We treated each gene-derived SNPs, region of interest (ROI) and gene-derived DNA methylation as a single testing unit, which are combined into triplets for evaluation. In addition, cardiovascular disease risk factors such as age, gender, and body mass index were assessed as covariates on hippocampal volume and compared between triplets. Our method identified $13$-triplets ($p$-values $\leq 0.001$) that included $6$ gene-derived SNPs, $10$ ROIs, and $6$ gene-derived DNA methylations that correlated with changes in hippocampal volume, suggesting that these triplets may be important in explaining schizophrenia-related neurodegeneration. With strong evidence ($p$-values $\leq 0.000001$), the triplet ({\bf MAGI2, CRBLCrus1.L, FBXO28}) has the potential to distinguish schizophrenia patients from the healthy control variations.

Submodular functions are a broad class of set functions, which naturally arise in diverse areas. Many algorithms have been suggested for the maximization of these functions. Unfortunately, once the function deviates from submodularity, the known algorithms may perform arbitrarily poorly. Amending this issue, by obtaining approximation results for set functions generalizing submodular functions, has been the focus of recent works. One such class, known as weakly submodular functions, has received a lot of attention. A key result proved by Das and Kempe (2011) showed that the approximation ratio of the greedy algorithm for weakly submodular maximization subject to a cardinality constraint degrades smoothly with the distance from submodularity. However, no results have been obtained for maximization subject to constraints beyond cardinality. In particular, it is not known whether the greedy algorithm achieves any non-trivial approximation ratio for such constraints. In this paper, we prove that a randomized version of the greedy algorithm (previously used by Buchbinder et al. (2014) for a different problem) achieves an approximation ratio of $(1 + 1/\gamma)^{-2}$ for the maximization of a weakly submodular function subject to a general matroid constraint, where $\gamma$ is a parameter measuring the distance of the function from submodularity. Moreover, we also experimentally compare the performance of this version of the greedy algorithm on real world problems against natural benchmarks, and show that the algorithm we study performs well also in practice. To the best of our knowledge, this is the first algorithm with a non-trivial approximation guarantee for maximizing a weakly submodular function subject to a constraint other than the simple cardinality constraint. In particular, it is the first algorithm with such a guarantee for the important and broad class of matroid constraints.

Kernel adaptive filters, a class of adaptive nonlinear time-series models, are known by their ability to learn expressive autoregressive patterns from sequential data. However, for trivial monotonic signals, they struggle to perform accurate predictions and at the same time keep computational complexity within desired boundaries. This is because new observations are incorporated to the dictionary when they are far from what the algorithm has seen in the past. We propose a novel approach to kernel adaptive filtering that compares new observations against dictionary samples in terms of their unit-norm (normalised) versions, meaning that new observations that look like previous samples but have a different magnitude are not added to the dictionary. We achieve this by proposing the unit-norm Gaussian kernel and define a sparsification criterion for this novel kernel. This new methodology is validated on two real-world datasets against standard KAF in terms of the normalised mean square error and the dictionary size.

This paper presents an approach for automation of interpretable feature selection for Internet Of Things Analytics (IoTA) using machine learning (ML) techniques. Authors have conducted a survey over different people involved in different IoTA based application development tasks. The survey reveals that feature selection is the most time consuming and niche skill demanding part of the entire workflow. This paper shows how feature selection is successfully automated without sacrificing the decision making accuracy and thereby reducing the project completion time and cost of hiring expensive resources. Several pattern recognition principles and state of art (SoA) ML techniques are followed to design the overall approach for the proposed automation. Three data sets are considered to establish the proof-of-concept. Experimental results show that the proposed automation is able to reduce the time for feature selection to $2$ days instead of $4-6$ months which would have been required in absence of the automation. This reduction in time is achieved without any sacrifice in the accuracy of the decision making process. Proposed method is also compared against Multi Layer Perceptron (MLP) model as most of the state of the art works on IoTA uses MLP based Deep Learning. Moreover the feature selection method is compared against SoA feature reduction technique namely Principal Component Analysis (PCA) and its variants. The results obtained show that the proposed method is effective.

The aim of semi-supervised learning is to improve supervised learners by exploiting potentially large amounts of, typically easier to obtain, unlabeled data [1]. Up to now, however, semi-supervised learners have reported mixed results when it comes to such improvements: it is not always the case that semi-supervision results in lower expected error rates. On the contrary, severely deteriorated performances have been observed in empirical studies and theory shows that improvement guarantees can often only be provided under rather stringent conditions [2-5]. Now, the principal suggestion put forward in this chapter is that, when dealing with semi-supervised learning, one may not only want to study the (expected) error rates these classifiers produce, but also to measure the classifiers' performances by means of the intrinsic loss they may be optimizing in the first place. That is, for classification routines that optimize a so-called surrogate loss at training time--which is what many machine learning and Bayesian decision theoretic approaches do [6, 7], we propose to also investigate how this loss behaves on the test set as this can provide us with an alternative view on the classifier's behavior that a mere error rate cannot capture. In fact, though the main example is concerned with semi-supervision, we would like to argue that in other learning scenarios, similar considerations might be beneficial. For instance in active learning [8], where rather than sampling randomly from ones input data to provide these instances with labels, one aims to do the sampling in a systematic way, trying to keep labeling cost as low as one can or, similarly, to learn from as few labeled examples as possible. Also here it may (or, we believe, it should) be of interest to not only compare the error rates that different approaches (e.g.

This paper proposes a novel approach for constructing effective personalized policies when the observed data lacks counter-factual information, is biased and possesses many features. The approach is applicable in a wide variety of settings from healthcare to advertising to education to finance. These settings have in common that the decision maker can observe, for each previous instance, an array of features of the instance, the action taken in that instance, and the reward realized -- but not the rewards of actions that were not taken: the counterfactual information. Learning in such settings is made even more difficult because the observed data is typically biased by the existing policy (that generated the data) and because the array of features that might affect the reward in a particular instance -- and hence should be taken into account in deciding on an action in each particular instance -- is often vast. The approach presented here estimates propensity scores for the observed data, infers counterfactuals, identifies a (relatively small) number of features that are (most) relevant for each possible action and instance, and prescribes a policy to be followed. Comparison of the proposed algorithm against the state-of-art algorithm on actual datasets demonstrates that the proposed algorithm achieves a significant improvement in performance.