Decision-Theoretic Foundations for Causal Reasoning

We present a definition of cause and effect in terms of decision-theoretic primitives and thereby provide a principled foundation for causal reasoning. Our definition departs from the traditional view of causation in that causal assertions may vary with the set of decisions available. We argue that this approach provides added clarity to the notion of cause. Also in this paper, we examine the encoding of causal relationships in directed acyclic graphs. We describe a special class of influence diagrams, those in canonical form, and show its relationship to Pearl's representation of cause and effect. Finally, we show how canonical form facilitates counterfactual reasoning.Comment: See http://www.jair.org/ for any accompanying file

Quantifying the uncertainty in heritability

The use of mixed models to determine narrow-sense heritability and related quantities such as SNP heritability has received much recent attention. Less attention has been paid to the inherent variability in these estimates. One approach for quantifying variability in estimates of heritability is a frequentist approach, in which heritability is estimated using maximum likelihood and its variance is quantified through an asymptotic normal approximation. An alternative approach is to quantify the uncertainty in heritability through its Bayesian posterior distribution. In this paper, we develop the latter approach, make it computationally efficient and compare it to the frequentist approach. We show theoretically that, for a sufficiently large sample size and intermediate values of heritability, the two approaches provide similar results. Using the Atherosclerosis Risk in Communities cohort, we show empirically that the two approaches can give different results and that the variance/uncertainty can remain large

An automatic visual analysis system for tennis

This article presents a novel video analysis system for coaching tennis players of all levels, which uses computer vision algorithms to automatically edit and index tennis videos into meaningful annotations. Existing tennis coaching software lacks the ability to automatically index a tennis match into key events, and therefore, a coach who uses existing software is burdened with time-consuming manual video editing. This work aims to explore the effectiveness of a system to automatically detect tennis events. A secondary aim of this work is to explore the bene- fits coaches experience in using an event retrieval system to retrieve the automatically indexed events. It was found that automatic event detection can significantly improve the experience of using video feedback as part of an instructional coaching session. In addition to the automatic detection of key tennis events, player and ball movements are automati- cally tracked throughout an entire match and this wealth of data allows users to find interesting patterns in play. Player and ball movement information are integrated with the automatically detected tennis events, and coaches can query the data to retrieve relevant key points during a match or analyse player patterns that need attention. This coaching software system allows coaches to build advanced queries, which cannot be facilitated with existing video coaching solutions, without tedious manual indexing. This article proves that the event detection algorithms in this work can detect the main events in tennis with an average precision and recall of 0.84 and 0.86, respectively, and can typically eliminate man- ual indexing of key tennis events

(Semi-)Predictive Discretization During Model Selection

In this paper, we present an approach to discretizing multivariate continuous data while learning the structure of a graphical model. We derive the joint scoring function from the principle of predictive accuracy, which inherently ensures the optimal trade-off between goodness of fit and model complexity (including the number of discretization levels). Using the so-called finest grid implied by the data, our scoring function depends only on the number of data points in the various discretization levels. Not only can it be computed efficiently, but it is also independent of the metric used in the continuous space. Our experiments with gene expression data show that discretization plays a crucial role regarding the resulting network structure

Greater power and computational efficiency for kernel-based association testing of sets of genetic variants

Motivation: Set-based variance component tests have been identified as a way to increase power in association studies by aggregating weak individual effects. However, the choice of test statistic has been largely ignored even though it may play an important role in obtaining optimal power. We compared a standard statistical test-a score test-with a recently developed likelihood ratio (LR) test. Further, when correction for hidden structure is needed, or gene-gene interactions are sought, state-of-the art algorithms for both the score and LR tests can be computationally impractical. Thus we develop new computationally efficient methods. Results: After reviewing theoretical differences in performance between the score and LR tests, we find empirically on real data that the LR test generally has more power. In particular, on 15 of 17 real datasets, the LR test yielded at least as many associations as the score test-up to 23 more associations-whereas the score test yielded at most one more association than the LR test in the two remaining datasets. On synthetic data, we find that the LR test yielded up to 12% more associations, consistent with our results on real data, but also observe a regime of extremely small signal where the score test yielded up to 25% more associations than the LR test, consistent with theory. Finally, our computational speedups now enable (i) efficient LR testing when the background kernel is full rank, and (ii) efficient score testing when the background kernel changes with each test, as for gene-gene interaction tests. The latter yielded a factor of 2000 speedup on a cohort of size 13 500. Availability: Software available at http://research.microsoft.com/en-us/um/redmond/projects/MSCompBio/Fastlmm/. Contact: [email protected] Supplementary Information: Supplementary data are available at Bioinformatics online

PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees

Summary: Evolutionary biologists are often interested in finding correlations among biological traits across a number of species, as such correlations may lead to testable hypotheses about the underlying function. Because some species are more closely related than others, computing and visualizing these correlations must be done in the context of the evolutionary tree that relates species. In this note, we introduce PhyloDet (short for PhyloDetective), an evolutionary tree visualization tool that enables biologists to visualize multiple traits mapped to the tree

Intersected EMG heatmaps and deep learning based gesture recognition

Hand gesture recognition in myoelectric based prosthetic devices is a key challenge to offering effective solutions to hand/lower arm amputees. A novel hand gesture recognition methodology that employs the difference of EMG energy heatmaps as the input of a specific designed deep learning neural network is presented. Experimental results using data from real amputees indicate that the proposed design achieves 94.31% as average accuracy with best accuracy rate of 98.96%. A comparison of experimental results between the proposed novel hand gesture recognition methodology and other similar approaches indicates the superior effectiveness of the new design