Relationship extraction for knowledge graph creation from biomedical literature

Biomedical research is growing in such an exponential pace that scientists, researchers and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a ways that claims and hypothesis can be easily found, accessed and validated. Knowledge graphs can provide such framework for semantic knowledge representation from literature. However, in order to build knowledge graph, it is necessary to extract knowledge in form of relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and T5-based model as an example of modern deep learning) methods for scalable relationship extraction from biomedical literature for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets, showing that T5 model handles well both small datasets, due to its pre-training on large C4 dataset as well as unbalanced data. The best performing model was T5 model fine-tuned on balanced data, with reported F1-score of 0.88.

MASK: A flexible framework to facilitate de-identification of clinical texts

Medical health records and clinical summaries contain a vast amount of important information in textual form that can help advancing research on treatments, drugs and public health. However, the majority of these information is not shared because they contain private information about patients, their families, or medical staff treating them. Regulations such as HIPPA in the US, PHIPPA in Canada and GDPR regulate the protection, processing and distribution of this information. In case this information is de-identified and personal information are replaced or redacted, they could be distributed to the research community. In this paper, we present MASK, a software package that is designed to perform the de-identification task. The software is able to perform named entity recognition using some of the state-of-the-art techniques and then mask or redact recognized entities. The user is able to select named entity recognition algorithm (currently implemented are two versions of CRF-based techniques and BiLSTM-based neural network with pre-trained GLoVe and ELMo embedding) and masking algorithm (e.g. shift dates, replace names/locations, totally redact entity).

Deep learning guided Android malware and anomaly detection

In the past decade, the cyber-crime related to mobile devices has increased. Mobile devices, especially the ones running on Android operating system are particularly interesting to malware creators, as the users often keep the biggest amount of personal information on their mobile devices, such as their contacts, social media profiles, emails, and bank accounts. Both dynamic and static malware analysis is necessary to prevent and detect malware, as both techniques have their benefits and shortcomings. In this paper, we propose a deep learning technique that relies on LSTM and encoder-decoder neural network architectures for dynamic malware analysis based on CPU, memory and battery usage. The proposed system is able to detect and notify users about anomalies in system that is likely consequence of malware behaviour. The method was implemented as a part of OWASP Seraphimdroids anti-malware mechanism and notifies users about anomalies on their devices. The method proved to perform with an F1-score of 79.2%.

GNTeam at 2018 n2c2: Feature-augmented BiLSTM-CRF for drug-related entity recognition in hospital discharge summaries

Monitoring the administration of drugs and adverse drug reactions are key parts of pharmacovigilance. In this paper, we explore the extraction of drug mentions and drug-related information (reason for taking a drug, route, frequency, dosage, strength, form, duration, and adverse events) from hospital discharge summaries through deep learning that relies on various representations for clinical named entity recognition. This work was officially part of the 2018 n2c2 shared task, and we use the data supplied as part of the task. We developed two deep learning architecture based on recurrent neural networks and pre-trained language models. We also explore the effect of augmenting word representations with semantic features for clinical named entity recognition. Our feature-augmented BiLSTM-CRF model performed with F1-score of 92.67% and ranked 4th for entity extraction sub-task among submitted systems to n2c2 challenge. The recurrent neural networks that use the pre-trained domain-specific word embeddings and a CRF layer for label optimization perform drug, adverse event and related entities extraction with micro-averaged F1-score of over 91%. The augmentation of word vectors with semantic features extracted using available clinical NLP toolkits can further improve the performance. Word embeddings that are pre-trained on a large unannotated corpus of relevant documents and further fine-tuned to the task perform rather well. However, the augmentation of word embeddings with semantic features can help improve the performance (primarily by boosting precision) of drug-related named entity recognition from electronic health records.

Extracting adverse drug reactions and their context using sequence labelling ensembles in TAC2017

Adverse drug reactions (ADRs) are unwanted or harmful effects experienced after the administration of a certain drug or a combination of drugs, presenting a challenge for drug development and drug administration. In this paper, we present a set of taggers for extracting adverse drug reactions and related entities, including factors, severity, negations, drug class and animal. The systems used a mix of rule-based, machine learning (CRF) and deep learning (BLSTM with word2vec embeddings) methodologies in order to annotate the data. The systems were submitted to adverse drug reaction shared task, organised during Text Analytics Conference in 2017 by National Institute for Standards and Technology, archiving F1-scores of 76.00 and 75.61 respectively.

From web crawled text to project descriptions: automatic summarizing of social innovation projects

In the past decade, social innovation projects have gained the attention of policy makers, as they address important social issues in an innovative manner. A database of social innovation is an important source of information that can expand collaboration between social innovators, drive policy and serve as an important resource for research. Such a database needs to have projects described and summarized. In this paper, we propose and compare several methods (e.g. SVM-based, recurrent neural network based, ensambled) for describing projects based on the text that is available on project websites. We also address and propose a new metric for automated evaluation of summaries based on topic modelling.

A framework for information extraction from tables in biomedical literature

The scientific literature is growing exponentially, and professionals are no more able to cope with the current amount of publications. Text mining provided in the past methods to retrieve and extract information from text; however, most of these approaches ignored tables and figures. The research done in mining table data still does not have an integrated approach for mining that would consider all complexities and challenges of a table. Our research is examining the methods for extracting numerical (number of patients, age, gender distribution) and textual (adverse reactions) information from tables in the clinical literature. We present a requirement analysis template and an integral methodology for information extraction from tables in clinical domain that contains 7 steps: (1) table detection, (2) functional processing, (3) structural processing, (4) semantic tagging, (5) pragmatic processing, (6) cell selection and (7) syntactic processing and extraction. Our approach performed with the F-measure ranged between 82 and 92%, depending on the variable, task and its complexity.

Creating a contemporary corpus of similes in Serbian by using natural language processing

Simile is a figure of speech that compares two things through the use of connection words, but where comparison is not intended to be taken literally. They are often used in everyday communication, but they are also a part of linguistic cultural heritage. In this paper we present a methodology for semi-automated collection of similes from the World Wide Web using text mining and machine learning techniques. We expanded an existing corpus by collecting 442 similes from the internet and adding them to the existing corpus collected by Vuk Stefanovic Karadzic that contained 333 similes. We, also, introduce crowdsourcing to the collection of figures of speech, which helped us to build corpus containing 787 unique similes.

As Cool as a Cucumber: Towards a Corpus of Contemporary Similes in Serbian

Similes are natural language expressions used to compare unlikely things, where the comparison is not taken literally. They are often used in everyday communication and are an important part of cultural heritage. Having an up-to-date corpus of similes is challenging, as they are constantly coined and/or adapted to the contemporary times. In this paper we present a methodology for semi-automated collection of similes from the world wide web using text mining techniques. We expanded an existing corpus of traditional similes (containing 333 similes) by collecting 446 additional expressions. We, also, explore how crowdsourcing can be used to extract and curate new similes.

Equity forecast: Predicting long term stock price movement using machine learning

Long term investment is one of the major investment strategies. However, calculating intrinsic value of some company and evaluating shares for long term investment is not easy, since analyst have to care about a large number of financial indicators and evaluate them in a right manner. So far, little help in predicting the direction of the company value over the longer period of time has been provided from the machines. In this paper we present a machine learning aided approach to evaluate the equity's future price over the long time. Our method is able to correctly predict whether some company's value will be 10% higher or not over the period of one year in 76.5% of cases.