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Register a new userLifelong Learning based Disease Diagnosis on Clinical Notes
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Zifeng Wang
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Current deep learning based disease diagnosis systems usually fall short in catastrophic forgetting, i.e., directly fine-tuning the disease diagnosis model on new tasks usually leads to abrupt decay of performance on previous tasks. What is worse, the trained diagnosis system would be fixed once deployed but collecting training data that covers enough diseases is infeasible, which inspires us to develop a lifelong learning diagnosis system. In this work, we propose to adopt attention to combine medical entities and context, embedding episodic memory and consolidation to retain knowledge, such that the learned model is capable of adapting to sequential disease-diagnosis tasks. Moreover, we establish a new benchmark, named Jarvis-40, which contains clinical notes collected from various hospitals. Our experiments show that the proposed method can achieve state-of-the-art performance on the proposed benchmark.
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The identification of Alzheimers disease (AD) and its early stages using structural magnetic resonance imaging (MRI) has been attracting the attention of researchers. Various data-driven approaches have been introduced to capture subtle and local morphological changes of the brain accompanied by the disease progression. One of the typical approaches for capturing subtle changes is patch-level feature representation. However, the predetermined regions to extract patches can limit classification performance by interrupting the exploration of potential biomarkers. In addition, the existing patch-level analyses have difficulty explaining their decision-making. To address these problems, we propose the BrainBagNet with a position-based gate (PG-BrainBagNet), a framework for jointly learning pathological region localization and AD diagnosis in an end-to-end manner. In advance, as all scans are aligned to a template in image processing, the position of brain images can be represented through the 3D Cartesian space shared by the overall MRI scans. The proposed method represents the patch-level response from whole-brain MRI scans and discriminative brain-region from position information. Based on the outcomes, the patch-level class evidence is calculated, and then the image-level prediction is inferred by a transparent aggregation. The proposed models were evaluated on the ADNI datasets. In five-fold cross-validation, the classification performance of the proposed method outperformed that of the state-of-the-art methods in both AD diagnosis (AD vs. normal control) and mild cognitive impairment (MCI) conversion prediction (progressive MCI vs. stable MCI) tasks. In addition, changes in the identified discriminant regions and patch-level class evidence according to the patch size used for model training are presented and analyzed.
Early detection is crucial to prevent the progression of Alzheimers disease (AD). Thus, specialists can begin preventive treatment as soon as possible. They demand fast and precise assessment in the diagnosis of AD in the earliest and hardest to detect stages. The main objective of this work is to develop a system that automatically detects the presence of the disease in sagittal magnetic resonance images (MRI), which are not generally used. Sagittal MRIs from ADNI and OASIS data sets were employed. Experiments were conducted using Transfer Learning (TL) techniques in order to achieve more accurate results. There are two main conclusions to be drawn from this work: first, the damages related to AD and its stages can be distinguished in sagittal MRI and, second, the results obtained using DL models with sagittal MRIs are similar to the state-of-the-art, which uses the horizontal-plane MRI. Although sagittal-plane MRIs are not commonly used, this work proved that they were, at least, as effective as MRI from other planes at identifying AD in early stages. This could pave the way for further research. Finally, one should bear in mind that in certain fields, obtaining the examples for a data set can be very expensive. This study proved that DL models could be built in these fields, whereas TL is an essential tool for completing the task with fewer examples.
The identification of rare diseases from clinical notes with Natural Language Processing (NLP) is challenging due to the few cases available for machine learning and the need of data annotation from clinical experts. We propose a method using ontologies and weak supervision. The approach includes two steps: (i) Text-to-UMLS, linking text mentions to concepts in Unified Medical Language System (UMLS), with a named entity linking tool (e.g. SemEHR) and weak supervision based on customised rules and Bidirectional Encoder Representations from Transformers (BERT) based contextual representations, and (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). Using MIMIC-III US intensive care discharge summaries as a case study, we show that the Text-to-UMLS process can be greatly improved with weak supervision, without any annotated data from domain experts. Our analysis shows that the overall pipeline processing discharge summaries can surface rare disease cases, which are mostly uncaptured in manual ICD codes of the hospital admissions.
In biological learning, data are used to improve performance not only on the current task, but also on previously encountered and as yet unencountered tasks. In contrast, classical machine learning starts from a blank slate, or tabula rasa, using data only for the single task at hand. While typical transfer learning algorithms can improve performance on future tasks, their performance on prior tasks degrades upon learning new tasks (called catastrophic forgetting). Many recent approaches for continual or lifelong learning have attempted to maintain performance given new tasks. But striving to avoid forgetting sets the goal unnecessarily low: the goal of lifelong learning, whether biological or artificial, should be to improve performance on all tasks (including past and future) with any new data. We propose omnidirectional transfer learning algorithms, which includes two special cases of interest: decision forests and deep networks. Our key insight is the development of the omni-voter layer, which ensembles representations learned independently on all tasks to jointly decide how to proceed on any given new data point, thereby improving performance on both past and future tasks. Our algorithms demonstrate omnidirectional transfer in a variety of simulated and real data scenarios, including tabular data, image data, spoken data, and adversarial tasks. Moreover, they do so with quasilinear space and time complexity.
Much of NLP research has focused on crowdsourced static datasets and the supervised learning paradigm of training once and then evaluating test performance. As argued in de Vries et al. (2020), crowdsourced data has the issues of lack of naturalness and relevance to real-world use cases, while the static dataset paradigm does not allow for a model to learn from its experiences of using language (Silver et al., 2013). In contrast, one might hope for machine learning systems that become more useful as they interact with people. In this work, we build and deploy a role-playing game, whereby human players converse with learning agents situated in an open-domain fantasy world. We show that by training models on the conversations they have with humans in the game the models progressively improve, as measured by automatic metrics and online engagement scores. This learning is shown to be more efficient than crowdsourced data when applied to conversations with real users, as well as being far cheaper to collect.
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