SIFTER search: a web server for accurate phylogeny-based protein function prediction.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded

Exact and efficient top-K inference for multi-target prediction by querying separable linear relational models

Many complex multi-target prediction problems that concern large target spaces are characterised by a need for efficient prediction strategies that avoid the computation of predictions for all targets explicitly. Examples of such problems emerge in several subfields of machine learning, such as collaborative filtering, multi-label classification, dyadic prediction and biological network inference. In this article we analyse efficient and exact algorithms for computing the top-$K$ predictions in the above problem settings, using a general class of models that we refer to as separable linear relational models. We show how to use those inference algorithms, which are modifications of well-known information retrieval methods, in a variety of machine learning settings. Furthermore, we study the possibility of scoring items incompletely, while still retaining an exact top-K retrieval. Experimental results in several application domains reveal that the so-called threshold algorithm is very scalable, performing often many orders of magnitude more efficiently than the naive approach

Efficient & Effective Selective Query Rewriting with Efficiency Predictions

To enhance effectiveness, a user's query can be rewritten internally by the search engine in many ways, for example by applying proximity, or by expanding the query with related terms. However, approaches that benefit effectiveness often have a negative impact on efficiency, which has impacts upon the user satisfaction, if the query is excessively slow. In this paper, we propose a novel framework for using the predicted execution time of various query rewritings to select between alternatives on a per-query basis, in a manner that ensures both effectiveness and efficiency. In particular, we propose the prediction of the execution time of ephemeral (e.g., proximity) posting lists generated from uni-gram inverted index posting lists, which are used in establishing the permissible query rewriting alternatives that may execute in the allowed time. Experiments examining both the effectiveness and efficiency of the proposed approach demonstrate that a 49% decrease in mean response time (and 62% decrease in 95th-percentile response time) can be attained without significantly hindering the effectiveness of the search engine

TarO : a target optimisation system for structural biology

This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative.Publisher PDFPeer reviewe

Deep Character-Level Click-Through Rate Prediction for Sponsored Search

Predicting the click-through rate of an advertisement is a critical component of online advertising platforms. In sponsored search, the click-through rate estimates the probability that a displayed advertisement is clicked by a user after she submits a query to the search engine. Commercial search engines typically rely on machine learning models trained with a large number of features to make such predictions. This is inevitably requires a lot of engineering efforts to define, compute, and select the appropriate features. In this paper, we propose two novel approaches (one working at character level and the other working at word level) that use deep convolutional neural networks to predict the click-through rate of a query-advertisement pair. Specially, the proposed architectures only consider the textual content appearing in a query-advertisement pair as input, and produce as output a click-through rate prediction. By comparing the character-level model with the word-level model, we show that language representation can be learnt from scratch at character level when trained on enough data. Through extensive experiments using billions of query-advertisement pairs of a popular commercial search engine, we demonstrate that both approaches significantly outperform a baseline model built on well-selected text features and a state-of-the-art word2vec-based approach. Finally, by combining the predictions of the deep models introduced in this study with the prediction of the model in production of the same commercial search engine, we significantly improve the accuracy and the calibration of the click-through rate prediction of the production system.Comment: SIGIR2017, 10 page

TimeTrader: Exploiting Latency Tail to Save Datacenter Energy for On-line Data-Intensive Applications

Datacenters running on-line, data-intensive applications (OLDIs) consume significant amounts of energy. However, reducing their energy is challenging due to their tight response time requirements. A key aspect of OLDIs is that each user query goes to all or many of the nodes in the cluster, so that the overall time budget is dictated by the tail of the replies' latency distribution; replies see latency variations both in the network and compute. Previous work proposes to achieve load-proportional energy by slowing down the computation at lower datacenter loads based directly on response times (i.e., at lower loads, the proposal exploits the average slack in the time budget provisioned for the peak load). In contrast, we propose TimeTrader to reduce energy by exploiting the latency slack in the sub- critical replies which arrive before the deadline (e.g., 80% of replies are 3-4x faster than the tail). This slack is present at all loads and subsumes the previous work's load-related slack. While the previous work shifts the leaves' response time distribution to consume the slack at lower loads, TimeTrader reshapes the distribution at all loads by slowing down individual sub-critical nodes without increasing missed deadlines. TimeTrader exploits slack in both the network and compute budgets. Further, TimeTrader leverages Earliest Deadline First scheduling to largely decouple critical requests from the queuing delays of sub- critical requests which can then be slowed down without hurting critical requests. A combination of real-system measurements and at-scale simulations shows that without adding to missed deadlines, TimeTrader saves 15-19% and 41-49% energy at 90% and 30% loading, respectively, in a datacenter with 512 nodes, whereas previous work saves 0% and 31-37%.Comment: 13 page

A Utility-Theoretic Approach to Privacy in Online Services

Online offerings such as web search, news portals, and e-commerce applications face the challenge of providing high-quality service to a large, heterogeneous user base. Recent efforts have highlighted the potential to improve performance by introducing methods to personalize services based on special knowledge about users and their context. For example, a user's demographics, location, and past search and browsing may be useful in enhancing the results offered in response to web search queries. However, reasonable concerns about privacy by both users, providers, and government agencies acting on behalf of citizens, may limit access by services to such information. We introduce and explore an economics of privacy in personalization, where people can opt to share personal information, in a standing or on-demand manner, in return for expected enhancements in the quality of an online service. We focus on the example of web search and formulate realistic objective functions for search efficacy and privacy. We demonstrate how we can find a provably near-optimal optimization of the utility-privacy tradeoff in an efficient manner. We evaluate our methodology on data drawn from a log of the search activity of volunteer participants. We separately assess users’ preferences about privacy and utility via a large-scale survey, aimed at eliciting preferences about peoples’ willingness to trade the sharing of personal data in returns for gains in search efficiency. We show that a significant level of personalization can be achieved using a relatively small amount of information about users