The recent advancement of pre-trained Transformer models has propelled the development of effective text mining models across various biomedical tasks. However, these models are primarily learned on the textual data and often lack the domain knowledg
e of the entities to capture the context beyond the sentence. In this study, we introduced a novel framework that enables the model to learn multi-omnics biological information about entities (proteins) with the help of additional multi-modal cues like molecular structure. Towards this, rather developing modality-specific architectures, we devise a generalized and optimized graph based multi-modal learning mechanism that utilizes the GraphBERT model to encode the textual and molecular structure information and exploit the underlying features of various modalities to enable end-to-end learning. We evaluated our proposed method on ProteinProtein Interaction task from the biomedical corpus, where our proposed generalized approach is observed to be benefited by the additional domain-specific modality.
Existing studies on using social media for deriving mental health status of users focus on the depression detection task. However, for case management and referral to psychiatrists, healthcare workers require practical and scalable depressive disorde
r screening and triage system. This study aims to design and evaluate a decision support system (DSS) to reliably determine the depressive triage level by capturing fine-grained depressive symptoms expressed in user tweets through the emulation of Patient Health Questionnaire-9 (PHQ-9) that is routinely used in clinical practice. The reliable detection of depressive symptoms from tweets is challenging because the 280-character limit on tweets incentivizes the use of creative artifacts in the utterances and figurative usage contributes to effective expression. We propose a novel BERT based robust multi-task learning framework to accurately identify the depressive symptoms using the auxiliary task of figurative usage detection. Specifically, our proposed novel task sharing mechanism, co-task aware attention, enables automatic selection of optimal information across the BERT layers and tasks by soft-sharing of parameters. Our results show that modeling figurative usage can demonstrably improve the models robustness and reliability for distinguishing the depression symptoms.
The unprecedented growth of Internet users has resulted in an abundance of unstructured information on social media including health forums, where patients request health-related information or opinions from other users. Previous studies have shown t
hat online peer support has limited effectiveness without expert intervention. Therefore, a system capable of assessing the severity of health state from the patients social media posts can help health professionals (HP) in prioritizing the users post. In this study, we inspect the efficacy of different aspects of Natural Language Understanding (NLU) to identify the severity of the users health state in relation to two perspectives(tasks) (a) Medical Condition (i.e., Recover, Exist, Deteriorate, Other) and (b) Medication (i.e., Effective, Ineffective, Serious Adverse Effect, Other) in online health communities. We propose a multiview learning framework that models both the textual content as well as contextual-information to assess the severity of the users health state. Specifically, our model utilizes the NLU views such as sentiment, emotions, personality, and use of figurative language to extract the contextual information. The diverse NLU views demonstrate its effectiveness on both the tasks and as well as on the individual disease to assess a users health.
To minimize the accelerating amount of time invested in the biomedical literature search, numerous approaches for automated knowledge extraction have been proposed. Relation extraction is one such task where semantic relations between the entities ar
e identified from the free text. In the biomedical domain, extraction of regulatory pathways, metabolic processes, adverse drug reaction or disease models necessitates knowledge from the individual relations, for example, physical or regulatory interactions between genes, proteins, drugs, chemical, disease or phenotype. In this paper, we study the relation extraction task from three major biomedical and clinical tasks, namely drug-drug interaction, protein-protein interaction, and medical concept relation extraction. Towards this, we model the relation extraction problem in multi-task learning (MTL) framework and introduce for the first time the concept of structured self-attentive network complemented with the adversarial learning approach for the prediction of relationships from the biomedical and clinical text. The fundamental notion of MTL is to simultaneously learn multiple problems together by utilizing the concepts of the shared representation. Additionally, we also generate the highly efficient single task model which exploits the shortest dependency path embedding learned over the attentive gated recurrent unit to compare our proposed MTL models. The framework we propose significantly improves overall the baselines (deep learning techniques) and single-task models for predicting the relationships, without compromising on the performance of all the tasks.
