A network approach for managing and processing big cancer data in clouds

Translational cancer research requires integrative analysis of multiple levels of big cancer data to identify and treat cancer. In order to address the issues that data is decentralised, growing and continually being updated, and the content living or archiving on different information sources partially overlaps creating redundancies as well as contradictions and inconsistencies, we develop a data network model and technology for constructing and managing big cancer data. To support our data network approach for data process and analysis, we employ a semantic content network approach and adopt the CELAR cloud platform. The prototype implementation shows that the CELAR cloud can satisfy the on-demanding needs of various data resources for management and process of big cancer data

Transfer learning: bridging the gap between deep learning and domain-specific text mining

Inspired by the success of deep learning techniques in Natural Language Processing (NLP), this dissertation tackles the domain-specific text mining problems for which the generic deep learning approaches would fail. More specifically, the domain-specific problems are: (1) success prediction in crowdfunding, (2) variants identification in biomedical literature, and (3) text data augmentation for domains with low-resources. In the first part, transfer learning in a multimodal perspective is utilized to facilitate solving the project success prediction on the crowdfunding application. Even though the information in a project profile can be of different modalities such as text, images, and metadata, most existing prediction approaches leverage only the text modality. It is promising to utilize the visual images in project profiles to find out how images could contribute to the success prediction. An advanced neural network scheme is designed and evaluated combining information learned from different modalities for project success prediction. In the second part, transfer learning is combined with deep learning techniques to solve genomic variants Named Entity Recognition (NER) problems in biomedical literature. Most of the advanced generic NER algorithms can fail due to the restricted training corpus. However, those generic deep learning algorithms are capable of learning from a canonical corpus, without any effort on feature engineering. This work aims to build an end-to-end deep learning approach to transfer the domain-specific knowledge to those advanced generic NER algorithms, addressing the challenges in low-resource training and requiring neither hand-crafted features nor post-processing rules. For the last part, transfer learning with knowledge distillation and active learning are utilized to solve text augmentation for domains with low-resources. Most of the recent text augmentation methods heavily rely on large external resources. This work is dedicates to solving the text augmentation problem adaptively and consistently with minimal resources for token-level tasks like NER. The solution can also assure the reliability of machine labels for noisy data and can enhance training consistency with noisy labels. All the works are evaluated on different domain-specific benchmarks, respectively. Experimental results demonstrate the effectiveness of those proposed methods. The advantages also indicate promising potential for transfer learning in domain-specific applications

Adverse drug reaction extraction on electronic health records written in Spanish

148 p.This work focuses on the automatic extraction of Adverse Drug Reactions (ADRs) in Electronic HealthRecords (EHRs). That is, extracting a response to a medicine which is noxious and unintended and whichoccurs at doses normally used. From Natural Language Processing (NLP) perspective, this wasapproached as a relation extraction task in which the drug is the causative agent of a disease, sign orsymptom, that is, the adverse reaction.ADR extraction from EHRs involves major challenges. First, ADRs are rare events. That is, relationsbetween drugs and diseases found in an EHR are seldom ADRs (are often unrelated or, instead, related astreatment). This implies the inference from samples with skewed class distribution. Second, EHRs arewritten by experts often under time pressure, employing both rich medical jargon together with colloquialexpressions (not always grammatical) and it is not infrequent to find misspells and both standard andnon-standard abbreviations. All this leads to a high lexical variability.We explored several ADR detection algorithms and representations to characterize the ADR candidates.In addition, we have assessed the tolerance of the ADR detection model to external noise such as theincorrect detection of implied medical entities implied in the ADR extraction, i.e. drugs and diseases. Westtled the first steps on ADR extraction in Spanish using a corpus of real EHRs