Text Mining Methods for Analyzing Online Health Information and Communication

The Internet provides an alternative way to share health information. Specifically, social network systems such as Twitter, Facebook, Reddit, and disease specific online support forums are increasingly being used to share information on health related topics. This could be in the form of personal health information disclosure to seek suggestions or answering other patients\u27 questions based on their history. This social media uptake gives a new angle to improve the current health communication landscape with consumer generated content from social platforms. With these online modes of communication, health providers can offer more immediate support to the people seeking advice. Non-profit organizations and federal agencies can also diffuse preventative information in such networks for better outcomes. Researchers in health communication can mine user generated content on social networks to understand themes and derive insights into patient experiences that may be impractical to glean through traditional surveys. The main difficulty in mining social health data is in separating the signal from the noise. Social data is characterized by informal nature of content, typos, emoticons, tonal variations (e.g. sarcasm), and ambiguities arising from polysemous words, all of which make it difficult in building automated systems for deriving insights from such sources. In this dissertation, we present four efforts to mine health related insights from user generated social data. In the first effort, we build a model to identify marketing tweets on electronic cigarettes (e-cigs) and assess different topics in marketing and non-marketing messages on e-cigs on Twitter. In our next effort, we build ensemble models to classify messages on a mental health forum for triaging posts whose authors need immediate attention from trained moderators to prevent self-harm. The third effort deals with models from our participation in a shared task on identifying tweets that discuss adverse drug reactions and those that mention medication intake. In the final task, we build a classifier that identifies whether a particular tweet about the popular Juul e-cig indicates the tweeter actually using the product. Our methods range from linear classifiers (e.g., logistic regression), classical nonlinear models (e.g., nearest neighbors), recent deep neural networks (e.g., convolutional neural networks), and ensembles of all these models in using different supervised training regimens (e.g., co-training). The focus is more on task specific system building than on building specific individual models. Overall, we demonstrate that it is possible to glean insights from social data on health related topics through natural language processing and machine learning with use-cases from substance use and mental health

Optimizing text mining methods for improving biomedical natural language processing

The overwhelming amount and the increasing rate of publication in the biomedical domain make it difficult for life sciences researchers to acquire and maintain all information that is necessary for their research. Pubmed (the primary citation database for the biomedical literature) currently contains over 21 million article abstracts and more than one million of them were published in 2020 alone. Even though existing article databases provide capable keyword search services, typical everyday-life queries usually return thousands of relevant articles. For instance, a cancer research scientist may need to acquire a complete list of genes that interact with BRCA1 (breast cancer 1) gene. The PubMed keyword search for BRCA1 returns over 16,500 article abstracts, making manual inspection of the retrieved documents impractical. Missing even one of the interacting gene partners in this scenario may jeopardize successful development of a potential new drug or vaccine. Although manually curated databases of biomolecular interactions exist, they are usually not up-to-date and they require notable human effort to maintain. To summarize, new discoveries are constantly being shared within the community via scientific publishing, but unfortunately the probability of missing vital information for research in life sciences is increasing. In response to this problem, the biomedical natural language processing (BioNLP) community of researchers has emerged and strives to assist life sciences researchers by building modern language processing and text mining tools that can be applied at large-scale and scan the whole publicly available literature and extract, classify, and aggregate the information found within, thus keeping life sciences researchers always up-to-date with the recent relevant discoveries and facilitating their research in numerous fields such as molecular biology, biomedical engineering, bioinformatics, genetics engineering and biochemistry. My research has almost exclusively focused on biomedical relation and event extraction tasks. These foundational information extraction tasks deal with automatic detection of biological processes, interactions and relations described in the biomedical literature. Precisely speaking, biomedical relation and event extraction systems can scan through a vast amount of biomedical texts and automatically detect and extract the semantic relations of biomedical named entities (e.g. genes, proteins, chemical compounds, and diseases). The structured outputs of such systems (i.e., the extracted relations or events) can be stored as relational databases or molecular interaction networks which can easily be queried, filtered, analyzed, visualized and integrated with other structured data sources. Extracting biomolecular interactions has always been the primary interest of BioNLP researcher because having knowledge about such interactions is crucially important in various research areas including precision medicine, drug discovery, drug repurposing, hypothesis generation, construction and curation of signaling pathways, and protein function and structure prediction. State-of-the-art relation and event extraction methods are based on supervised machine learning, requiring manually annotated data for training. Manual annotation for the biomedical domain requires domain expertise and it is time-consuming. Hence, having minimal training data for building information extraction systems is a common case in the biomedical domain. This demands development of methods that can make the most out of available training data and this thesis gathers all my research efforts and contributions in that direction. It is worth mentioning that biomedical natural language processing has undergone a revolution since I started my research in this field almost ten years ago. As a member of the BioNLP community, I have witnessed the emergence, improvement– and in some cases, the disappearance–of many methods, each pushing the performance of the best previous method one step further. I can broadly divide the last ten years into three periods. Once I started my research, feature-based methods that relied on heavy feature engineering were dominant and popular. Then, significant advancements in the hardware technology, as well as several breakthroughs in the algorithms and methods enabled machine learning practitioners to seriously utilize artificial neural networks for real-world applications. In this period, convolutional, recurrent, and attention-based neural network models became dominant and superior. Finally, the introduction of transformer-based language representation models such as BERT and GPT impacted the field and resulted in unprecedented performance improvements on many data sets. When reading this thesis, I demand the reader to take into account the course of history and judge the methods and results based on what could have been done in that particular period of the history

Analysis of Tweets for Social Media Health Applications

abstract: Social networking sites like Twitter have provided people a platform to connect with each other, to discuss and share information and news or to entertain themselves. As the number of users continues to grow there has been explosive growth in the data generated by these users. Such a vast data source has provided researchers a way to study and monitor public health. Accurately analyzing tweets is a difficult task mainly because of their short length, the inventive spellings and creative language expressions. Instead of focusing at the topic level, identifying tweets that have personal health experience mentions would be more helpful to researchers, governments and other organizations. Another important limitation in the current systems for social media health applications is the use of a disease-specific model and dataset to study a particular disease. Identifying adverse drug reactions is an important part of the drug development process. Detecting and extracting adverse drug mentions in tweets can supplement the list of adverse drug reactions that result from the drug trials and can help in the improvement of the drugs. This thesis aims to address these two challenges and proposes three systems. A generalizable system to identify personal health experience mentions across different disease domains, a system for automatic classifications of adverse effects mentions in tweets and a system to extract adverse drug mentions from tweets. The proposed systems use the transfer learning from language models to achieve notable scores on Social Media Mining for Health Applications(SMM4H) 2019 (Weissenbacher et al. 2019) shared tasks.Dissertation/ThesisMasters Thesis Computer Science 201

Data and systems for medication-related text classification and concept normalization from Twitter: insights from the Social Media Mining for Health (SMM4H)-2017 shared task

Objective: We executed the Social Media Mining for Health (SMM4H) 2017 shared tasks to enable the community-driven development and large-scale evaluation of automatic text processing methods for the classification and normalization of health-related text from social media. An additional objective was to publicly release manually annotated data.Materials and Methods: We organized 3 independent subtasks: automatic classification of self-reports of 1) adverse drug reactions (ADRs) and 2) medication consumption, from medication-mentioning tweets, and 3) normalization of ADR expressions. Training data consisted of 15 717 annotated tweets for (1), 10 260 for (2), and 6650 ADR phrases and identifiers for (3); and exhibited typical properties of social-media-based health-related texts. Systems were evaluated using 9961, 7513, and 2500 instances for the 3 subtasks, respectively. We evaluated performances of classes of methods and ensembles of system combinations following the shared tasks.Results: Among 55 system runs, the best system scores for the 3 subtasks were 0.435 (ADR class F1-score) for subtask-1, 0.693 (micro-averaged F1-score over two classes) for subtask-2, and 88.5% (accuracy) for subtask-3. Ensembles of system combinations obtained best scores of 0.476, 0.702, and 88.7%, outperforming individual systems.Discussion: Among individual systems, support vector machines and convolutional neural networks showed high performance. Performance gains achieved by ensembles of system combinations suggest that such strategies may be suitable for operational systems relying on difficult text classification tasks (eg, subtask-1).Conclusions: Data imbalance and lack of context remain challenges for natural language processing of social media text. Annotated data from the shared task have been made available as reference standards for future studies (http://dx.doi.org/10.17632/rxwfb3tysd.1).</div

Deep Neural Models for Medical Concept Normalization in User-Generated Texts

In this work, we consider the medical concept normalization problem, i.e., the problem of mapping a health-related entity mention in a free-form text to a concept in a controlled vocabulary, usually to the standard thesaurus in the Unified Medical Language System (UMLS). This is a challenging task since medical terminology is very different when coming from health care professionals or from the general public in the form of social media texts. We approach it as a sequence learning problem with powerful neural networks such as recurrent neural networks and contextualized word representation models trained to obtain semantic representations of social media expressions. Our experimental evaluation over three different benchmarks shows that neural architectures leverage the semantic meaning of the entity mention and significantly outperform an existing state of the art models.Comment: This is preprint of the paper "Deep Neural Models for Medical Concept Normalization in User-Generated Texts" to be published at ACL 2019 - 57th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Student Research Worksho

Ordinal Convolutional Neural Networks for Predicting RDoC Positive Valence Psychiatric Symptom Severity Scores

Background—The CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing (NLP) provided a set of 1000 neuropsychiatric notes to participants as part of a competition to predict psychiatric symptom severity scores. This paper summarizes our methods, results, and experiences based on our participation in the second track of the shared task. Objective—Classical methods of text classification usually fall into one of three problem types: binary, multi-class, and multi-label classification. In this effort, we study ordinal regression problems with text data where misclassifications are penalized differently based on how far apart the ground truth and model predictions are on the ordinal scale. Specifically, we present our entries (methods and results) in the N-GRID shared task in predicting research domain criteria (RDoC) positive valence ordinal symptom severity scores (absent, mild, moderate, and severe) from psychiatric notes. Methods—We propose a novel convolutional neural network (CNN) model designed to handle ordinal regression tasks on psychiatric notes. Broadly speaking, our model combines an ordinal loss function, a CNN, and conventional feature engineering (wide features) into a single model which is learned end-to-end. Given interpretability is an important concern with nonlinear models, we apply a recent approach called locally interpretable model-agnostic explanation (LIME) to identify important words that lead to instance specific predictions. Results—Our best model entered into the shared task placed third among 24 teams and scored a macro mean absolute error (MMAE) based normalized score (100 · (1 − M M AE)) of 83.86. Since the competition, we improved our score (using basic ensembling) to 85.55, comparable with the winning shared task entry. Applying LIME to model predictions, we demonstrate the feasibility of instance specific prediction interpretation by identifying words that led to a particular decision