Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.

Active deep learning method for the discovery of objects of interest in large spectroscopic surveys

Current archives of the LAMOST telescope contain millions of pipeline-processed spectra that have probably never been seen by human eyes. Most of the rare objects with interesting physical properties, however, can only be identified by visual analysis of their characteristic spectral features. A proper combination of interactive visualisation with modern machine learning techniques opens new ways to discover such objects. We apply active learning classification supported by deep convolutional networks to automatically identify complex emission-line shapes in multi-million spectra archives. We used the pool-based uncertainty sampling active learning driven by a custom-designed deep convolutional neural network with 12 layers inspired by VGGNet, AlexNet, and ZFNet, but adapted for one-dimensional feature vectors. The unlabelled pool set is represented by 4.1 million spectra from the LAMOST DR2 survey. The initial training of the network was performed on a labelled set of about 13000 spectra obtained in the region around H$\alpha$ by the 2m Perek telescope of the Ond\v{r}ejov observatory, which mostly contains spectra of Be and related early-type stars. The differences between the Ond\v{r}ejov intermediate-resolution and the LAMOST low-resolution spectrographs were compensated for by Gaussian blurring. After several iterations, the network was able to successfully identify emission-line stars with an error smaller than 6.5%. Using the technology of the Virtual Observatory to visualise the results, we discovered 1013 spectra of 948 new candidates of emission-line objects in addition to 664 spectra of 549 objects that are listed in SIMBAD and 2644 spectra of 2291 objects identified in an earlier paper of a Chinese group led by Wen Hou. The most interesting objects with unusual spectral properties are discussed in detail.