Learning the heterogeneous bibliographic information network for literature-based discovery

Leveraging spiking neural networks for topic modeling

This article investigates the application of spiking neural networks (SNNs) to the problem of topic modeling (TM): the identification of significant groups of words that represent human-understandable topics in large sets of documents. Our research is based on the hypothesis that an SNN that implements the Hebbian learning paradigm is capable of becoming specialized in the detection of statistically significant word patterns in the presence of adequately tailored sequential input. To support this hypothesis, we propose a novel spiking topic model (STM) that transforms text into a sequence of spikes and uses that sequence to train single-layer SNNs. In STM, each SNN neuron represents one topic, and each of the neuron's weights corresponds to one word. STM synaptic connections are modified according to spike-timing-dependent plasticity; after training, the neurons' strongest weights are interpreted as the words that represent topics. We compare the performance of STM with four other TM methods Latent Dirichlet Allocation (LDA), Biterm Topic Model (BTM), Embedding Topic Model (ETM) and BERTopic on three datasets: 20Newsgroups, BBC news, and AG news. The results demonstrate that STM can discover high-quality topics and successfully compete with comparative classical methods. This sheds new light on the possibility of the adaptation of SNN models in unsupervised natural language processing.

Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique

BACKGROUND

Automated hypothesis generation (HG) focuses on uncovering hidden connections within the extensive information that is publicly available. This domain has become increasingly popular, thanks to modern machine learning algorithms. However, the automated evaluation of HG systems is still an open problem, especially on a larger scale.

RESULTS

This paper presents a novel benchmarking framework Dyport for evaluating biomedical hypothesis generation systems. Utilizing curated datasets, our approach tests these systems under realistic conditions, enhancing the relevance of our evaluations. We integrate knowledge from the curated databases into a dynamic graph, accompanied by a method to quantify discovery importance. This not only assesses hypotheses accuracy but also their potential impact in biomedical research which significantly extends traditional link prediction benchmarks. Applicability of our benchmarking process is demonstrated on several link prediction systems applied on biomedical semantic knowledge graphs. Being flexible, our benchmarking system is designed for broad application in hypothesis generation quality verification, aiming to expand the scope of scientific discovery within the biomedical research community.

CONCLUSIONS

Dyport is an open-source benchmarking framework designed for biomedical hypothesis generation systems evaluation, which takes into account knowledge dynamics, semantics and impact. All code and datasets are available at: https://github.com/IlyaTyagin/Dyport .

Knowledge Graphs for Indication Expansion: An Explainable Target-Disease Prediction Method

Indication expansion aims to find new indications for existing targets in order to accelerate the process of launching a new drug for a disease on the market. The rapid increase in data types and data sources for computational drug discovery has fostered the use of semantic knowledge graphs (KGs) for indication expansion through target centric approaches, or in other words, target repositioning. Previously, we developed a novel method to construct a KG for indication expansion studies, with the aim of finding and justifying alternative indications for a target gene of interest. In contrast to other KGs, ours combines human-curated full-text literature and gene expression data from biomedical databases to encode relationships between genes, diseases, and tissues. Here, we assessed the suitability of our KG for explainable target-disease link prediction using a glass-box approach. To evaluate the predictive power of our KG, we applied shortest path with tissue information- and embedding-based prediction methods to a graph constructed with information published before or during 2010. We also obtained random baselines by applying the shortest path predictive methods to KGs with randomly shuffled node labels. Then, we evaluated the accuracy of the top predictions using gene-disease links reported after 2010. In addition, we investigated the contribution of the KG’s tissue expression entity to the prediction performance. Our experiments showed that shortest path-based methods significantly outperform the random baselines and embedding-based methods outperform the shortest path predictions. Importantly, removing the tissue expression entity from the KG severely impacts the quality of the predictions, especially those produced by the embedding approaches. Finally, since the interpretability of the predictions is crucial in indication expansion, we highlight the advantages of our glass-box model through the examination of example candidate target-disease predictions.

Application of graph theory in the library domain—Building a faceted framework based on a literature review

Based on a literature review, we present a framework for structuring the application of graph theory in the library domain. Our goal is to provide both researchers and libraries with a standard tool to classify scientific work, at the same time allowing for the identification of previously underrepresented areas where future research might be productive. To achieve this, we compile graph theoretical approaches from the literature to consolidate the components of our framework on a solid basis. The extendable framework consists of multiple facets grouped into five categories whose elements can be arbitrarily combined. Libraries can benefit from these facets by using them as a point of reference for the (meta)data they offer. Further work on formally defining the framework’s categories as well as on integration of other graph-related research areas not discussed in this article (e.g. knowledge graphs) would be desirable and helpful in the future.

Exploration of Shared Themes Between Food Security and Internet of Things Research Through Literature-Based Discovery

This paper applied a literature-based discovery methodology utilizing citation networks and text mining in order to extract and represent shared terminologies found in disjoint academic literature on food security and the Internet of Things. The topic of food security includes research on improvements in nutrition, sustainable agriculture, and a plurality of other social challenges, while the Internet of Things refers to a collection of technologies from which solutions can be drawn. Academic articles on both topics were classified into subclusters, and their text contents were compared against each other to find shared terms. These terms formed a network from which clusters of related keywords could be identified, potentially easing the exploration of common themes. Thirteen transversal themes, including blockchain, healthcare, and air quality, were found. This method can be applied by policymakers and other stakeholders to understand how a given technology could contribute to solving a pressing social issue.

Tracking and Mining the COVID-19 Research Literature

The unprecedented, explosive growth of the COVID-19 domain presents challenges to researchers to keep up with research knowledge within the domain. This article profiles this research to help make that knowledge more accessible via overviews and novel categorizations. We provide websites offering means for researchers to probe more deeply to address specific questions. We further probe and reassemble COVID-19 topical content to address research issues concerning topical evolution and emphases on tactical vs. strategic approaches to mitigate this pandemic and reduce future viral threats. Data suggest that heightened attention to strategic, immunological factors is warranted. Connecting with and transferring in research knowledge from outside the COVID-19 domain demand a viable COVID-19 knowledge model. This study provides complementary topical categorizations to facilitate such modeling to inform future Literature-Based Discovery endeavors.

Connecting the Dots: Hypotheses Generation by Leveraging Semantic Shifts

Literature-based Discovery (LBD) (a.k.a. Hypotheses Generation) is a systematic knowledge discovery process that elicit novel inferences about previously unknown scientific knowledge by rationally connecting complementary and non-interactive literature. Prompt identification of such novel knowledge is beneficial not only for researchers but also for various other stakeholders such as universities, funding bodies and academic publishers. Almost all the prior LBD research suffer from two major limitations. Firstly, the over-reliance of domain-dependent resources which restrict the models’ applicability to certain domains/problems. In this regard, we propose a generalisable LBD model that supports both cross-domain and cross-lingual knowledge discovery. The second persistent research deficiency is the mere focus of static snapshot of the corpus (i.e. ignoring the temporal evolution of topics) to detect the new knowledge. However, the knowledge in scientific literature changes dynamically and thus relying merely on static snapshot limits the model’s ability in capturing semantically meaningful connections. As a result, we propose a novel temporal model that captures semantic change of topics using diachronic word embeddings to unravel more accurate connections. The model was evaluated using the largest available literature repository to demonstrate the efficiency of the proposed cues towards recommending novel knowledge.

Relation path feature embedding based convolutional neural network method for drug discovery

BACKGROUND

Drug development is an expensive and time-consuming process. Literature-based discovery has played a critical role in drug development and may be a supplementary method to help scientists speed up the discovery of drugs.

METHODS

Here, we propose a relation path features embedding based convolutional neural network model with attention mechanism for drug discovery from literature, which we denote as PACNN. First, we use predications from biomedical abstracts to construct a biomedical knowledge graph, and then apply a path ranking algorithm to extract drug-disease relation path features on the biomedical knowledge graph. After that, we use these drug-disease relation features to train a convolutional neural network model which combined with the attention mechanism. Finally, we employ the trained models to mine drugs for treating diseases.

RESULTS

The experiment shows that the proposed model achieved promising results, comparing to several random walk algorithms.

CONCLUSIONS

In this paper, we propose a relation path features embedding based convolutional neural network with attention mechanism for discovering potential drugs from literature. Our method could be an auxiliary method for drug discovery, which can speed up the discovery of new drugs for the incurable diseases.

A survey on literature based discovery approaches in biomedical domain

Literature Based Discovery (LBD) refers to the problem of inferring new and interesting knowledge by logically connecting independent fragments of information units through explicit or implicit means. This area of research, which incorporates techniques from Natural Language Processing (NLP), Information Retrieval and Artificial Intelligence, has significant potential to reduce discovery time in biomedical research fields. Formally introduced in 1986, LBD has grown to be a significant and a core task for text mining practitioners in the biomedical domain. Together with its inter-disciplinary nature, this has led researchers across domains to contribute in advancing this field of study. This survey attempts to consolidate and present the evolution of techniques in this area. We cover a variety of techniques and provide a detailed description of the problem setting, the intuition, the advantages and limitations of various influential papers. We also list the current bottlenecks in this field and provide a general direction of research activities for the future. In an effort to be comprehensive and for ease of reference for off-the-shelf users, we also list many publicly available tools for LBD. We hope this survey will act as a guide to both academic and industry (bio)-informaticians, introduce the various methodologies currently employed and also the challenges yet to be tackled.

A systematic review on literature-based discovery workflow

As scientific publication rates increase, knowledge acquisition and the research development process have become more complex and time-consuming. Literature-Based Discovery (LBD), supporting automated knowledge discovery, helps facilitate this process by eliciting novel knowledge by analysing existing scientific literature. This systematic review provides a comprehensive overview of the LBD workflow by answering nine research questions related to the major components of the LBD workflow (i.e., input, process, output, and evaluation). With regards to the input component, we discuss the data types and data sources used in the literature. The process component presents filtering techniques, ranking/thresholding techniques, domains, generalisability levels, and resources. Subsequently, the output component focuses on the visualisation techniques used in LBD discipline. As for the evaluation component, we outline the evaluation techniques, their generalisability, and the quantitative measures used to validate results. To conclude, we summarise the findings of the review for each component by highlighting the possible future research directions.

SemaTyP: a knowledge graph based literature mining method for drug discovery

Background

Drug discovery is the process through which potential new medicines are identified. High-throughput screening and computer-aided drug discovery/design are the two main drug discovery methods for now, which have successfully discovered a series of drugs. However, development of new drugs is still an extremely time-consuming and expensive process. Biomedical literature contains important clues for the identification of potential treatments. It could support experts in biomedicine on their way towards new discoveries.

Methods

Here, we propose a biomedical knowledge graph-based drug discovery method called SemaTyP, which discovers candidate drugs for diseases by mining published biomedical literature. We first construct a biomedical knowledge graph with the relations extracted from biomedical abstracts, then a logistic regression model is trained by learning the semantic types of paths of known drug therapies’ existing in the biomedical knowledge graph, finally the learned model is used to discover drug therapies for new diseases.

Results

The experimental results show that our method could not only effectively discover new drug therapies for new diseases, but also could provide the potential mechanism of action of the candidate drugs.

Conclusions

In this paper we propose a novel knowledge graph based literature mining method for drug discovery. It could be a supplementary method for current drug discovery methods.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2167-5) contains supplementary material, which is available to authorized users.

Rediscovering Don Swanson: the Past, Present and Future of Literature-Based Discovery

The late Don R. Swanson was well appreciated during his lifetime as Dean of the Graduate Library School at University of Chicago, as winner of the American Society for Information Science Award of Merit for 2000, and as author of many seminal articles. In this informal essay, I will give my personal perspective on Don's contributions to science, and outline some current and future directions in literature-based discovery that are rooted in concepts that he developed.

Emerging approaches in literature-based discovery: techniques and performance review

Literature-based discovery systems aim at discovering valuable latent connections between previously disparate research areas. This is achieved by analyzing the contents of their respective literatures with the help of various intelligent computational techniques. In this paper, we review the progress of literature-based discovery research, focusing on understanding their technical features and evaluating their performance. The present literature-based discovery techniques can be divided into two general approaches: the traditional approach and the emerging approach. The traditional approach, which dominate the current research landscape, comprises mainly of techniques that rely on utilizing lexical statistics, knowledge-based and visualization methods in order to address literature-based discovery problems. On the other hand, we have also observed the births of new trends and unprecedented paradigm shifts among the recently emerging literature-based discovery approach. These trends are likely to shape the future trajectory of the next generation literature-based discovery systems.