Efficient mining gapped sequential patterns for motifs in biological sequences

Finding Possible Promoter Binding Sites in DNA Sequences by Sequential Patterns Mining With Specific Numbers of Gaps

Identifying motifs in promoter regions is crucial to our understanding of transcription regulation. Researchers commonly use known promoter features in a variety of species to predict promoter motifs. However the results are not particularly useful. Different species rarely have similar features in promoter binding sites. In this study, we adopt sequence analysis techniques to find the possible promoter binding sites among different species. We sought to improve the existing algorithm to suit the task of mining sequential patterns with specific number of gaps. Moreover, we discuss the implementation of proposed method in a distributed environment. The proposed method finds the transcription start sites (TSS) and extracts possible promoter regions from DNA sequences according to TSS. We derived the motifs in the possible promoter regions, while taking into account the number of gaps in the motifs to deal with unimportant nucleotides. The motifs generated from promoter regions using the proposed methodology were shown to tolerate unimportant nucleotides. A comparison with known promoter motifs verified the efficacy of the proposed method.

Robotic Process Mining: Vision and Challenges

Robotic process automation (RPA) is an emerging technology that allows organizations automating repetitive clerical tasks by executing scripts that encode sequences of fine-grained interactions with Web and desktop applications. Examples of clerical tasks include opening a file, selecting a field in a Web form or a cell in a spreadsheet, and copy-pasting data across fields or cells. Given that RPA can automate a wide range of routines, this raises the question of which routines should be automated in the first place. This paper presents a vision towards a family of techniques, termed robotic process mining (RPM), aimed at filling this gap. The core idea of RPM is that repetitive routines amenable for automation can be discovered from logs of interactions between workers and Web and desktop applications, also known as user interactions (UI) logs. The paper defines a set of basic concepts underpinning RPM and presents a pipeline of processing steps that would allow an RPM tool to generate RPA scripts from UI logs. The paper also discusses research challenges to realize the envisioned pipeline.

Mining frequent biological sequences based on bitmap without candidate sequence generation

Biological sequences carry a lot of important genetic information of organisms. Furthermore, there is an inheritance law related to protein function and structure which is useful for applications such as disease prediction. Frequent sequence mining is a core technique for association rule discovery, but existing algorithms suffer from low efficiency or poor error rate because biological sequences differ from general sequences with more characteristics. In this paper, an algorithm for mining Frequent Biological Sequence based on Bitmap, FBSB, is proposed. FBSB uses bitmaps as the simple data structure and transforms each row into a quicksort list QS-list for sequence growth. For the continuity and accuracy requirement of biological sequence mining, tested sequences used during the mining process of FBSB are real ones instead of generated candidates, and all the frequent sequences can be mined without any errors. Comparing with other algorithms, the experimental results show that FBSB can achieve a better performance on both run time and scalability.

Motif mining based on network space compression

A network motif is a recurring subnetwork within a network, and it takes on certain functions in practical biological macromolecule applications. Previous algorithms have focused on the computational efficiency of network motif detection, but some problems in storage space and searching time manifested during earlier studies. The considerable computational and spacial complexity also presents a significant challenge. In this paper, we provide a new approach for motif mining based on compressing the searching space. According to the characteristic of the parity nodes, we cut down the searching space and storage space in real graphs and random graphs, thereby reducing the computational cost of verifying the isomorphism of sub-graphs. We obtain a new network with smaller size after removing parity nodes and the “repeated edges” connected with the parity nodes. Random graph structure and sub-graph searching are based on the Back Tracking Method; all sub-graphs can be searched for by adding edges progressively. Experimental results show that this algorithm has higher speed and better stability than its alternatives.