Sarvnaz Karimi

Bio: Sarvnaz Karimi is an academic researcher from Commonwealth Scientific and Industrial Research Organisation. The author has contributed to research in topics: Computer science & Transliteration. The author has an hindex of 22, co-authored 94 publications receiving 1842 citations. Previous affiliations of Sarvnaz Karimi include University of Melbourne & RMIT University.

Does Multi-Task Learning Always Help?: An Evaluation on Health Informatics

Abstract: Multi-Task Learning (MTL) has been an attractive approach to deal with limited labeled datasets or leverage related tasks, for a variety of NLP problems. We examine the benefit of MTL for three specific pairs of health informatics tasks that deal with: (a) overlapping symptoms for the same classification problem (personal health mention classification for influenza and for a set of symptoms); (b) overlapping medical concepts for related classification problems (vaccine usage and drug usage detection); and, (c) related classification problems (vaccination intent and vaccination relevance detection). We experiment with a simple neural architecture: a shared layer followed by task-specific dense layers. The novelty of this work is that it compares alternatives for shared layers for these pairs of tasks. While our observations agree with the promise of MTL as compared to single-task learning, for health informatics, we show that the benefit also comes with caveats in terms of the choice of shared layers and the relatedness between the participating tasks.

Topic Models to Interpret MeSH – MEDLINE’s Medical Subject Headings

Abstract: We show how topic models are useful for interpreting and understanding MeSH, the Medical Subject Headings applied to articles in MEDLINE. We show how our resampled author model captures some of the advantages of both the topic model and the author-topic model. We demonstrate how the topic modeling approach can provide an alternative and complementary view of the relationship between MeSH headings that could be informative and helpful for people searching MEDLINE.

Investigating the Effect of Lexical Segmentation in Transformer-based Models on Medical Datasets

Abstract: Transformer-based models have been popular recently and have improved performance for many Natural Language Processing (NLP) Tasks, including those in the biomedical field. Previous research suggests that, when using these models, an in-domain vocabulary is more suitable than using an open-domain vocabulary. We investigate the effects of a specialised in-domain vocabulary trained from scratch on a biomedical corpus. Our research suggests that, although the in-domain vocabulary is useful, it is usually constrained by the corpora size because these models needs to be trained from scratch. Instead, it is more useful to have more data, perform additional pretraining steps with a corpus-specific vocabulary.1

An Effective Transition-based Model for Discontinuous NER

Abstract: Unlike widely used Named Entity Recognition (NER) data sets in generic domains, biomedical NER data sets often contain mentions consisting of discontinuous spans. Conventional sequence tagging techniques encode Markov assumptions that are efficient but preclude recovery of these mentions. We propose a simple, effective transition-based model with generic neural encoding for discontinuous NER. Through extensive experiments on three biomedical data sets, we show that our model can effectively recognize discontinuous mentions without sacrificing the accuracy on continuous mentions.

Machine learning

Abstract: Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Don't Stop Pretraining: Adapt Language Models to Domains and Tasks

Abstract: Language models pretrained on text from a wide variety of sources form the foundation of today’s NLP. In light of the success of these broad-coverage models, we investigate whether it is still helpful to tailor a pretrained model to the domain of a target task. We present a study across four domains (biomedical and computer science publications, news, and reviews) and eight classification tasks, showing that a second phase of pretraining in-domain (domain-adaptive pretraining) leads to performance gains, under both high- and low-resource settings. Moreover, adapting to the task’s unlabeled data (task-adaptive pretraining) improves performance even after domain-adaptive pretraining. Finally, we show that adapting to a task corpus augmented using simple data selection strategies is an effective alternative, especially when resources for domain-adaptive pretraining might be unavailable. Overall, we consistently find that multi-phase adaptive pretraining offers large gains in task performance.

Opportunities and obstacles for deep learning in biology and medicine.

Abstract: Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.