Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

RDF-TR: Exploiting structural redundancies to boost RDF compression

The number and volume of semantic data have grown impressively over the last decade, promoting compression as an essential tool for RDF preservation, sharing and management. In contrast to universal compressors, RDF compression techniques are able to detect and exploit specific forms of redundancy in RDF data. Thus, state-of-the-art RDF compressors excel at exploiting syntactic and semantic redundancies, i.e., repetitions in the serialization format and information that can be inferred implicitly. However, little attention has been paid to the existence of structural patterns within the RDF dataset; i.e. structural redundancy. In this paper, we analyze structural regularities in real-world datasets, and show three schema-based sources of redundancies that underpin the schema-relaxed nature of RDF. Then, we propose RDF-Tr (RDF Triples Reorganizer), a preprocessing technique that discovers and removes this kind of redundancy before the RDF dataset is effectively compressed. In particular, RDF-Tr groups subjects that are described by the same predicates, and locally re-codes the objects related to these predicates. Finally, we integrate RDF-Tr with two RDF compressors, HDT and k2-triples. Our experiments show that using RDF-Tr with these compressors improves by up to 2.3 times their original effectiveness, outperforming the most prominent state-of-the-art techniques

Finding relational redescriptions

We introduce relational redescription mining, that is, the task of finding two structurally different patterns that describe nearly the same set of object pairs in a relational dataset. By extending redescription mining beyond propositional and real-valued attributes, it provides a powerful tool to match different relational descriptions of the same concept. We propose an alternating scheme for solving this problem. Its core consists of a novel relational query miner that efficiently identifies discriminative connection patterns between pairs of objects. Compared to a baseline Inductive Logic Programming (ILP) approach, our query miner is able to mine more complex queries, much faster. We performed extensive experiments on three real world relational datasets, and present examples of redescriptions found, exhibiting the power of the method to expressively capture relations present in these networks

Structural advances for pattern discovery in multi-relational databases

With ever-growing storage needs and drift towards very large relational storage settings, multi-relational data mining has become a prominent and pertinent field for discovering unique and interesting relational patterns. As a consequence, a whole suite of multi-relational data mining techniques is being developed. These techniques may either be extensions to the already existing single-table mining techniques or may be developed from scratch. For the traditionalists, single-table mining algorithms can be used to work on multi-relational settings by making inelegant and time consuming joins of all target relations. However, complex relational patterns cannot be expressed in a single-table format and thus, cannot be discovered. This work presents a new multi-relational frequent pattern mining algorithm termed Multi-Relational Frequent Pattern Growth (MRFP Growth). MRFP Growth is capable of mining multiple relations, linked with referential integrity, for frequent patterns that satisfy a user specified support threshold. Empirical results on MRFP Growth performance and its comparison with the state-of-the-art multirelational data mining algorithms like WARMR and Decentralized Apriori are discussed at length. MRFP Growth scores over the latter two techniques in number of patterns generated and speed. The realm of multi-relational clustering is also explored in this thesis. A multi-Relational Item Clustering approach based on Hypergraphs (RICH) is proposed. Experimentally RICH combined with MRFP Growth proves to be a competitive approach for clustering multi-relational data. The performance and iii quality of clusters generated by RICH are compared with other clustering algorithms. Finally, the thesis demonstrates the applied utility of the theoretical implications of the above mentioned algorithms in an application framework for auto-annotation of images in an image database. The system is called CoMMA which stands for Combining Multi-relational Multimedia for Associations

Are Code Examples on an Online Q&A Forum Reliable?

Programmers often consult an online Q&A forum such as Stack Overflow to learn new APIs. This paper presents an empirical study on the prevalence and severity of API misuse on Stack Overflow. To reduce manual assessment effort, we design ExampleCheck, an API usage mining framework that extracts patterns from over 380K Java repositories on GitHub and subsequently reports potential API usage violations in Stack Overflow posts. We analyze 217,818 Stack Overflow posts using ExampleCheck and find that 31% may have potential API usage violations that could produce unexpected behavior such as program crashes and resource leaks. Such API misuse is caused by three main reasons---missing control constructs, missing or incorrect order of API calls, and incorrect guard conditions. Even the posts that are accepted as correct answers or upvoted by other programmers are not necessarily more reliable than other posts in terms of API misuse. This study result calls for a new approach to augment Stack Overflow with alternative API usage details that are not typically shown in curated examples