28,991 research outputs found
An Introduction to Recursive Partitioning: Rationale, Application and Characteristics of Classification and Regression Trees, Bagging and Random Forests
Recursive partitioning methods have become popular and widely used tools for nonparametric regression and classification in many scientific fields. Especially random forests, that can deal with large numbers of predictor variables even in the presence of complex interactions, have been applied successfully in genetics, clinical medicine and bioinformatics within the past few years.
High dimensional problems are common not only in genetics, but also in some areas of psychological research, where only few subjects can be measured due to time or cost constraints, yet a large amount of data is generated for each subject. Random forests have been shown to achieve a high prediction accuracy in such applications, and provide descriptive variable importance measures reflecting the impact of each variable in both main effects and interactions.
The aim of this work is to introduce the principles of the standard recursive partitioning methods as well as recent methodological improvements, to illustrate their usage for low and high dimensional data exploration, but also to point out limitations of the methods and potential pitfalls in their practical application.
Application of the methods is illustrated using freely available implementations in the R system for statistical computing
Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa
This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.\ud
•We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.\ud
•Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.\ud
•Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed
A hybrid algorithm for Bayesian network structure learning with application to multi-label learning
We present a novel hybrid algorithm for Bayesian network structure learning,
called H2PC. It first reconstructs the skeleton of a Bayesian network and then
performs a Bayesian-scoring greedy hill-climbing search to orient the edges.
The algorithm is based on divide-and-conquer constraint-based subroutines to
learn the local structure around a target variable. We conduct two series of
experimental comparisons of H2PC against Max-Min Hill-Climbing (MMHC), which is
currently the most powerful state-of-the-art algorithm for Bayesian network
structure learning. First, we use eight well-known Bayesian network benchmarks
with various data sizes to assess the quality of the learned structure returned
by the algorithms. Our extensive experiments show that H2PC outperforms MMHC in
terms of goodness of fit to new data and quality of the network structure with
respect to the true dependence structure of the data. Second, we investigate
H2PC's ability to solve the multi-label learning problem. We provide
theoretical results to characterize and identify graphically the so-called
minimal label powersets that appear as irreducible factors in the joint
distribution under the faithfulness condition. The multi-label learning problem
is then decomposed into a series of multi-class classification problems, where
each multi-class variable encodes a label powerset. H2PC is shown to compare
favorably to MMHC in terms of global classification accuracy over ten
multi-label data sets covering different application domains. Overall, our
experiments support the conclusions that local structural learning with H2PC in
the form of local neighborhood induction is a theoretically well-motivated and
empirically effective learning framework that is well suited to multi-label
learning. The source code (in R) of H2PC as well as all data sets used for the
empirical tests are publicly available.Comment: arXiv admin note: text overlap with arXiv:1101.5184 by other author
Evaluation of Surgical Skill Using Machine Learning with Optimal Wearable Sensor Locations
Evaluation of surgical skills during minimally invasive surgeries is needed when recruiting new surgeons. Although surgeons’ differentiation by skill level is highly complex, performance in specific clinical tasks such as pegboard transfer and knot tying could be determined using wearable EMG and accelerometer sensors. A wireless wearable platform has made it feasible to collect movement and muscle activation signals for quick skill evaluation during surgical tasks. However, it is challenging since the placement of multiple wireless wearable sensors may interfere with their performance in the assessment. This study utilizes machine learning techniques to identify optimal muscles and features critical for accurate skill evaluation. This study enrolled a total of twenty-six surgeons of different skill levels: novice (n = 11), intermediaries (n = 12), and experts (n = 3). Twelve wireless wearable sensors consisting of surface EMGs and accelerometers were placed bilaterally on bicep brachii, tricep brachii, anterior deltoid, flexor carpi ulnaris (FCU), extensor carpi ulnaris (ECU), and thenar eminence (TE) muscles to assess muscle activations and movement variability profiles. We found features related to movement complexity such as approximate entropy, sample entropy, and multiscale entropy played a critical role in skill level identification. We found that skill level was classified with highest accuracy by i) ECU for Random Forest Classifier (RFC), ii) deltoid for Support Vector Machines (SVM) and iii) biceps for Naïve Bayes Classifier with classification accuracies 61%, 57% and 47%. We found RFC classifier performed best with highest classification accuracy when muscles are combined i) ECU and deltoid (58%), ii) ECU and biceps (53%), and iii) ECU, biceps and deltoid (52%). Our findings suggest that quick surgical skill evaluation is possible using wearables sensors, and features from ECU, deltoid, and biceps muscles contribute an important role in surgical skill evaluation
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