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Using machine learning has proven effective at choosing the right set of optimizations for a particular program. For machine learning techniques to be most effective, compiler writers have to develop expressive means of characterizing the program being optimized. The current state-of-the-art techniques for characterizing programs include using a fixed-length feature vector of either source code features extracted during compile time or performance counters collected when running the program. For the problem of identifying optimizations to apply, models constructed using performance counter characterizations of a program have been shown to outperform models constructed using source code features. However, collecting performance counters requires running the program multiple times, and this "dynamic" method of characterizing programs can be specific to inputs of the program. It would be preferable to have a method of characterizing programs that is as expressive as performance counter features, but that is "static" like source code features and therefore does not require running the program.In this paper, we introduce a novel way of characterizing programs using a graph-based characterization, which uses the program's intermediate representation and an adapted learning algorithm to predict good optimization sequences. To evaluate different characterization techniques, we focus on loop-intensive programs and construct prediction models that drive polyhedral optimizations, such as auto-parallelism and various loop transformation.We show that our graph-based characterization technique outperforms three current state-of-the-art characterization techniques found in the literature. By using the sequences predicted to be the best by our graph-based model, we achieved up to 73% of the speedup achievable in our search space for a particular platform, whereas we could only achieve up to 59% by other state-of-the-art techniques we evaluated.

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BackgroundExisting methods for calculating semantic similarity between gene products using the Gene Ontology (GO) often rely on external resources, which are not part of the ontology. Consequently, changes in these external resources like biased term distribution caused by shifting of hot research topics, will affect the calculation of semantic similarity. One way to avoid this problem is to use semantic methods that are "intrinsic" to the ontology, i.e. independent of external knowledge.ResultsWe present a shortest-path graph kernel (spgk) method that relies exclusively on the GO and its structure. In spgk, a gene product is represented by an induced subgraph of the GO, which consists of all the GO terms annotating it. Then a shortest-path graph kernel is used to compute the similarity between two graphs. In a comprehensive evaluation using a benchmark dataset, spgk compares favorably with other methods that depend on external resources. Compared with simUI, a method that is also intrinsic to GO, spgk achieves slightly better results on the benchmark dataset. Statistical tests show that the improvement is significant when the resolution and EC similarity correlation coefficient are used to measure the performance, but is insignificant when the Pfam similarity correlation coefficient is used.ConclusionsSpgk uses a graph kernel method in polynomial time to exploit the structure of the GO to calculate semantic similarity between gene products. It provides an alternative to both methods that use external resources and "intrinsic" methods with comparable performance.

Deep learning is a powerful approach for distinguishing classes of images, and there is a growing interest in applying these methods to delimit species, particularly in the identification of mosquito vectors. Visual identification of mosquito species is the foundation of mosquito-borne disease surveillance and management, but can be hindered by cryptic morphological variation in mosquito vector species complexes such as the malaria-transmitting Anopheles gambiae complex. We sought to apply Convolutional Neural Networks (CNNs) to images of mosquitoes as a proof-of-concept to determine the feasibility of automatic classification of mosquito sex, genus, species, and strains using whole-body, 2D images of mosquitoes. We introduce a library of 1, 709 images of adult mosquitoes collected from 16 colonies of mosquito vector species and strains originating from five geographic regions, with 4 cryptic species not readily distinguishable morphologically even by trained medical entomologists. We present a methodology for image processing, data augmentation, and training and validation of a CNN. Our best CNN configuration achieved high prediction accuracies of 96.96% for species identification and 98.48% for sex. Our results demonstrate that CNNs can delimit species with cryptic morphological variation, 2 strains of a single species, and specimens from a single colony stored using two different methods. We present visualizations of the CNN feature space and predictions for interpretation of our results, and we further discuss applications of our findings for future applications in malaria mosquito surveillance.

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