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.

Search for Medical Records: NICTA at TREC 2011 Medical Track

Abstract: NICTA (National ICT Australia) participated in the Medical Records track of TREC 2011 with seven automatic runs. The main techniques used in our submissions involved using Boolean retrieval for filtering, query transformation, and query expansion. Evaluation of our best run ranks our submissions higher than the median of all systems for this track, and stands at rank seven among 109 automatic runs which were submitted by the 29 participating groups.

Survey of Text-based Epidemic Intelligence: A Computational Linguistic Perspective

Abstract: Epidemic intelligence deals with the detection of disease outbreaks using formal (such as hospital records) and informal sources (such as user-generated text on the web) of information. In this survey, we discuss approaches for epidemic intelligence that use textual datasets, referring to it as `text-based epidemic intelligence'. We view past work in terms of two broad categories: health mention classification (selecting relevant text from a large volume) and health event detection (predicting epidemic events from a collection of relevant text). The focus of our discussion is the underlying computational linguistic techniques in the two categories. The survey also provides details of the state-of-the-art in annotation techniques, resources and evaluation strategies for epidemic intelligence.

Using Social Media to Enhance Emergency Situation Awareness: Extended Abstract

Abstract: Social media platforms, such as Twitter, offer a rich source of real-time information about real-world events, particularly during mass emergencies. Sifting valuable information from social media provides useful insight into time-critical situations for emergency officers to understand the impact of hazards and act on emergency responses in a timely manner. This work focuses on analyzing Twitter messages generated during natural disasters, and shows how natural language processing and data mining techniques can be utilized to extract situation awareness information from Twitter. We present key relevant approaches that we have investigated including burst detection, tweet filtering and classification, online clustering, and geotagging.

Figurative Usage Detection of Symptom Words to Improve Personal Health Mention Detection

Abstract: Personal health mention detection deals with predicting whether or not a given sentence is a report of a health condition. Past work mentions errors in this prediction when symptom words, i.e. names of symptoms of interest, are used in a figurative sense. Therefore, we combine a state-of-the-art figurative usage detection with CNN-based personal health mention detection. To do so, we present two methods: a pipeline-based approach and a feature augmentation-based approach. The introduction of figurative usage detection results in an average improvement of 2.21% F-score of personal health mention detection, in the case of the feature augmentation-based approach. This paper demonstrates the promise of using figurative usage detection to improve personal health mention detection.

Figurative Usage Detection of Symptom Words to Improve Personal Health Mention Detection

Abstract: Personal health mention detection deals with predicting whether or not a given sentence is a report of a health condition. Past work mentions errors in this prediction when symptom words, i.e., names of symptoms of interest, are used in a figurative sense. Therefore, we combine a state-of-the-art figurative usage detection with CNN-based personal health mention detection. To do so, we present two methods: a pipeline-based approach and a feature augmentation-based approach. The introduction of figurative usage detection results in an average improvement of 2.21% F-score of personal health mention detection, in the case of the feature augmentation-based approach. This paper demonstrates the promise of using figurative usage detection to improve personal health mention detection.

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.