arXiv subjects

Matloob Khushi

Publications and source records attributed to Matloob Khushi.

21 records · Page 2Linked to original sources

arXiv2020

Benchmarking database performance for genomic data

Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene annotations are common research needs. The data can be saved in a database system for easy management, however, there is no comprehensive database built-in algorithm at present to identify overlapping regions. Therefore I have developed a region-mapping (RegMap) SQL-based algorithm to perform genomic operations and have benchmarked the performance of different databases. Benchmarking identified that PostgreSQL extracts overlapping regions much faster than MySQL. Insertion and data uploads in PostgreSQL were also better, although general searching capability of both databases was almost equivalent. In addition, using the algorithm pair-wise, overlaps of >1000 datasets of transcription factor binding sites and histone marks, collected from previous publications, were reported and it was found that HNF4G significantly co-locates with cohesin subunit STAG1 (SA1).

cs.DB↗

arXiv2020

Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information

Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is hampered by their large file sizes. We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large digital slide into a desired quality JPEG image. The image is linked to the patients clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website www.abctb.org.au using Deep Zoom open source technology. Using the ABCTB online search engine, digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of digital microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis.

eess.IV↗

arXiv2019

Mining Temporal Evolution of Knowledge Graph and Genealogical Features for Literature-based Discovery Prediction

Literature-based knowledge discovery process identifies the important but implicit relations among information embedded in published literature. Existing techniques from Information Retrieval and Natural Language Processing attempt to identify the hidden or unpublished connections between information concepts within published literature, however, these techniques undermine the concept of predicting the future and emerging relations among scientific knowledge components encapsulated within the literature. Keyword Co-occurrence Network (KCN), built upon author selected keywords (i.e., knowledge entities), is considered as a knowledge graph that focuses both on these knowledge components and knowledge structure of a scientific domain by examining the relationships between knowledge entities. Using data from two multidisciplinary research domains other than the medical domain, capitalizing on bibliometrics, the dynamicity of temporal KCNs, and a Long Short Term Memory recurrent neural network, this study proposed a framework to successfully predict the future literature-based discoveries - the emerging connections among knowledge units. Framing the problem as a dynamic supervised link prediction task, the proposed framework integrates some novel node and edge-level features. Temporal importance of keywords computed from both bipartite and unipartite networks, communities of keywords, built upon genealogical relations, and relative importance of temporal citation counts used in the feature construction process. Both node and edge-level features were input into an LSTM network to forecast the feature values for positive and negatively labeled non-connected keyword pairs and classify them accurately. High classification performance rates suggest that these features are supportive both in predicting the emerging connections between scientific knowledge units and emerging trend analysis.

cs.SI↗