ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

BackgroundPeriodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.ResultsConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.ConclusionsThe ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org

A machine learning approach for layout inference in spreadsheets

Spreadsheet applications are one of the most used tools for content generation and presentation in industry and the Web. In spite of this success, there does not exist a comprehensive approach to automatically extract and reuse the richness of data maintained in this format. The biggest obstacle is the lack of awareness about the structure of the data in spreadsheets, which otherwise could provide the means to automatically understand and extract knowledge from these files. In this paper, we propose a classification approach to discover the layout of tables in spreadsheets. Therefore, we focus on the cell level, considering a wide range of features not covered before by related work. We evaluated the performance of our classifiers on a large dataset covering three different corpora from various domains. Finally, our work includes a novel technique for detecting and repairing incorrectly classified cells in a post-processing step. The experimental results show that our approach deliver s very high accuracy bringing us a crucial step closer towards automatic table extraction.Peer ReviewedPostprint (published version

A Multi-view Context-aware Approach to Android Malware Detection and Malicious Code Localization

Existing Android malware detection approaches use a variety of features such as security sensitive APIs, system calls, control-flow structures and information flows in conjunction with Machine Learning classifiers to achieve accurate detection. Each of these feature sets provides a unique semantic perspective (or view) of apps' behaviours with inherent strengths and limitations. Meaning, some views are more amenable to detect certain attacks but may not be suitable to characterise several other attacks. Most of the existing malware detection approaches use only one (or a selected few) of the aforementioned feature sets which prevent them from detecting a vast majority of attacks. Addressing this limitation, we propose MKLDroid, a unified framework that systematically integrates multiple views of apps for performing comprehensive malware detection and malicious code localisation. The rationale is that, while a malware app can disguise itself in some views, disguising in every view while maintaining malicious intent will be much harder. MKLDroid uses a graph kernel to capture structural and contextual information from apps' dependency graphs and identify malice code patterns in each view. Subsequently, it employs Multiple Kernel Learning (MKL) to find a weighted combination of the views which yields the best detection accuracy. Besides multi-view learning, MKLDroid's unique and salient trait is its ability to locate fine-grained malice code portions in dependency graphs (e.g., methods/classes). Through our large-scale experiments on several datasets (incl. wild apps), we demonstrate that MKLDroid outperforms three state-of-the-art techniques consistently, in terms of accuracy while maintaining comparable efficiency. In our malicious code localisation experiments on a dataset of repackaged malware, MKLDroid was able to identify all the malice classes with 94% average recall

Comparing the writing style of real and artificial papers

Recent years have witnessed the increase of competition in science. While promoting the quality of research in many cases, an intense competition among scientists can also trigger unethical scientific behaviors. To increase the total number of published papers, some authors even resort to software tools that are able to produce grammatical, but meaningless scientific manuscripts. Because automatically generated papers can be misunderstood as real papers, it becomes of paramount importance to develop means to identify these scientific frauds. In this paper, I devise a methodology to distinguish real manuscripts from those generated with SCIGen, an automatic paper generator. Upon modeling texts as complex networks (CN), it was possible to discriminate real from fake papers with at least 89\% of accuracy. A systematic analysis of features relevance revealed that the accessibility and betweenness were useful in particular cases, even though the relevance depended upon the dataset. The successful application of the methods described here show, as a proof of principle, that network features can be used to identify scientific gibberish papers. In addition, the CN-based approach can be combined in a straightforward fashion with traditional statistical language processing methods to improve the performance in identifying artificially generated papers.Comment: To appear in Scientometrics (2015