Javed Aslam


2020

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An Ensemble Approach for Automatic Structuring of Radiology Reports
Morteza Pourreza Shahri | Amir Tahmasebi | Bingyang Ye | Henghui Zhu | Javed Aslam | Timothy Ferris
Proceedings of the 3rd Clinical Natural Language Processing Workshop

Automatic structuring of electronic medical records is of high demand for clinical workflow solutions to facilitate extraction, storage, and querying of patient care information. However, developing a scalable solution is extremely challenging, specifically for radiology reports, as most healthcare institutes use either no template or department/institute specific templates. Moreover, radiologists’ reporting style varies from one to another as sentences are written in a telegraphic format and do not follow general English grammar rules. In this work, we present an ensemble method that consolidates the predictions of three models, capturing various attributes of textual information for automatic labeling of sentences with section labels. These three models are: 1) Focus Sentence model, capturing context of the target sentence; 2) Surrounding Context model, capturing the neighboring context of the target sentence; and finally, 3) Formatting/Layout model, aimed at learning report formatting cues. We utilize Bi-directional LSTMs, followed by sentence encoders, to acquire the context. Furthermore, we define several features that incorporate the structure of reports. We compare our proposed approach against multiple baselines and state-of-the-art approaches on a proprietary dataset as well as 100 manually annotated radiology notes from the MIMIC-III dataset, which we are making publicly available. Our proposed approach significantly outperforms other approaches by achieving 97.1% accuracy.

2019

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Adapting RNN Sequence Prediction Model to Multi-label Set Prediction
Kechen Qin | Cheng Li | Virgil Pavlu | Javed Aslam
Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers)

We present an adaptation of RNN sequence models to the problem of multi-label classification for text, where the target is a set of labels, not a sequence. Previous such RNN models define probabilities for sequences but not for sets; attempts to obtain a set probability are after-thoughts of the network design, including pre-specifying the label order, or relating the sequence probability to the set probability in ad hoc ways. Our formulation is derived from a principled notion of set probability, as the sum of probabilities of corresponding permutation sequences for the set. We provide a new training objective that maximizes this set probability, and a new prediction objective that finds the most probable set on a test document. These new objectives are theoretically appealing because they give the RNN model freedom to discover the best label order, which often is the natural one (but different among documents). We develop efficient procedures to tackle the computation difficulties involved in training and prediction. Experiments on benchmark datasets demonstrate that we outperform state-of-the-art methods for this task.