Current Challenges in the Application of Algorithms in Multi-institutional Clinical Settings

The Coronavirus disease pandemic has highlighted the importance of artificial intelligence in multi-institutional clinical settings. Particularly in situations where the healthcare system is overloaded, and a lot of data is generated, artificial intelligence has great potential to provide automated solutions and to unlock the untapped potential of acquired data. This includes the areas of care, logistics, and diagnosis. For example, automated decision support applications could tremendously help physicians in their daily clinical routine. Especially in radiology and oncology, the exponential growth of imaging data, triggered by a rising number of patients, leads to a permanent overload of the healthcare system, making the use of artificial intelligence inevitable. However, the efficient and advantageous application of artificial intelligence in multi-institutional clinical settings faces several challenges, such as accountability and regulation hurdles, implementation challenges, and fairness considerations. This work focuses on the implementation challenges, which include the following questions: How to ensure well-curated and standardized data, how do algorithms from other domains perform on multi-institutional medical datasets, and how to train more robust and generalizable models? Also, questions of how to interpret results and whether there exist correlations between the performance of the models and the characteristics of the underlying data are part of the work. Therefore, besides presenting a technical solution for manual data annotation and tagging for medical images, a real-world federated learning implementation for image segmentation is introduced. Experiments on a multi-institutional prostate magnetic resonance imaging dataset showcase that models trained by federated learning can achieve similar performance to training on pooled data. Furthermore, Natural Language Processing algorithms with the tasks of semantic textual similarity, text classification, and text summarization are applied to multi-institutional, structured and free-text, oncology reports. The results show that performance gains are achieved by customizing state-of-the-art algorithms to the peculiarities of the medical datasets, such as the occurrence of medications, numbers, or dates. In addition, performance influences are observed depending on the characteristics of the data, such as lexical complexity. The generated results, human baselines, and retrospective human evaluations demonstrate that artificial intelligence algorithms have great potential for use in clinical settings. However, due to the difficulty of processing domain-specific data, there still exists a performance gap between the algorithms and the medical experts. In the future, it is therefore essential to improve the interoperability and standardization of data, as well as to continue working on algorithms to perform well on medical, possibly, domain-shifted data from multiple clinical centers

Enhance Representation Learning of Clinical Narrative with Neural Networks for Clinical Predictive Modeling

Medicine is undergoing a technological revolution. Understanding human health from clinical data has major challenges from technical and practical perspectives, thus prompting methods that understand large, complex, and noisy data. These methods are particularly necessary for natural language data from clinical narratives/notes, which contain some of the richest information on a patient. Meanwhile, deep neural networks have achieved superior performance in a wide variety of natural language processing (NLP) tasks because of their capacity to encode meaningful but abstract representations and learn the entire task end-to-end. In this thesis, I investigate representation learning of clinical narratives with deep neural networks through a number of tasks ranging from clinical concept extraction, clinical note modeling, and patient-level language representation. I present methods utilizing representation learning with neural networks to support understanding of clinical text documents. I first introduce the notion of representation learning from natural language processing and patient data modeling. Then, I investigate word-level representation learning to improve clinical concept extraction from clinical notes. I present two works on learning word representations and evaluate them to extract important concepts from clinical notes. The first study focuses on cancer-related information, and the second study evaluates shared-task data. The aims of these two studies are to automatically extract important entities from clinical notes. Next, I present a series of deep neural networks to encode hierarchical, longitudinal, and contextual information for modeling a series of clinical notes. I also evaluate the models by predicting clinical outcomes of interest, including mortality, length of stay, and phenotype predictions. Finally, I propose a novel representation learning architecture to develop a generalized and transferable language representation at the patient level. I also identify pre-training tasks appropriate for constructing a generalizable language representation. The main focus is to improve predictive performance of phenotypes with limited data, a challenging task due to a lack of data. Overall, this dissertation addresses issues in natural language processing for medicine, including clinical text classification and modeling. These studies show major barriers to understanding large-scale clinical notes. It is believed that developing deep representation learning methods for distilling enormous amounts of heterogeneous data into patient-level language representations will improve evidence-based clinical understanding. The approach to solving these issues by learning representations could be used across clinical applications despite noisy data. I conclude that considering different linguistic components in natural language and sequential information between clinical events is important. Such results have implications beyond the immediate context of predictions and further suggest future directions for clinical machine learning research to improve clinical outcomes. This could be a starting point for future phenotyping methods based on natural language processing that construct patient-level language representations to improve clinical predictions. While significant progress has been made, many open questions remain, so I will highlight a few works to demonstrate promising directions

Analyzing and Interpreting Neural Networks for NLP: A Report on the First BlackboxNLP Workshop

The EMNLP 2018 workshop BlackboxNLP was dedicated to resources and techniques specifically developed for analyzing and understanding the inner-workings and representations acquired by neural models of language. Approaches included: systematic manipulation of input to neural networks and investigating the impact on their performance, testing whether interpretable knowledge can be decoded from intermediate representations acquired by neural networks, proposing modifications to neural network architectures to make their knowledge state or generated output more explainable, and examining the performance of networks on simplified or formal languages. Here we review a number of representative studies in each category

NLP and ML Methods for Pre-processing, Clustering and Classification of Technical Logbook Datasets

Technical logbooks are a challenging and under-explored text type in automated event identification. These texts are typically short and written in non-standard yet technical language, posing challenges to off-the-shelf NLP pipelines. These datasets typically represent a domain (a technical field such as automotive) and an application (e.g., maintenance). The granularity of issue types described in these datasets additionally leads to class imbalance, making it challenging for models to accurately predict which issue each logbook entry describes. In this research, we focus on the problem of technical issue pre-processing, clustering, and classification by considering logbook datasets from the automotive, aviation, and facility maintenance domains. We developed MaintNet, a collaborative open source library including logbook datasets from various domains and a pre-processing pipeline to clean unstructured datasets. Additionally, we adapted a feedback loop strategy from computer vision for handling extreme class imbalance, which resamples the training data based on its error in the prediction process. We further investigated the benefits of using transfer learning from sources within the same domain (but different applications), from within the same application (but different domains), and from all available data to improve the performance of the classification models. Finally, we evaluated several data augmentation approaches including synonym replacement, random swap, and random deletion to address the issue of data scarcity in technical logbooks

Will Sentiment Analysis Need Subculture? A New Data Augmentation Approach

The renowned proverb that "The pen is mightier than the sword" underscores the formidable influence wielded by text expressions in shaping sentiments. Indeed, well-crafted written can deeply resonate within cultures, conveying profound sentiments. Nowadays, the omnipresence of the Internet has fostered a subculture that congregates around the contemporary milieu. The subculture artfully articulates the intricacies of human feelings by ardently pursuing the allure of novelty, a fact that cannot be disregarded in the sentiment analysis. This paper strives to enrich data through the lens of subculture, to address the insufficient training data faced by sentiment analysis. To this end, a new approach of subculture-based data augmentation (SCDA) is proposed, which engenders six enhanced texts for each training text by leveraging the creation of six diverse subculture expression generators. The extensive experiments attest to the effectiveness and potential of SCDA. The results also shed light on the phenomenon that disparate subculture expressions elicit varying degrees of sentiment stimulation. Moreover, an intriguing conjecture arises, suggesting the linear reversibility of certain subculture expressions. It is our fervent aspiration that this study serves as a catalyst in fostering heightened perceptiveness towards the tapestry of information, sentiment and culture, thereby enriching our collective understanding.Comment: JASIS

Linguistically-Informed Neural Architectures for Lexical, Syntactic and Semantic Tasks in Sanskrit

The primary focus of this thesis is to make Sanskrit manuscripts more accessible to the end-users through natural language technologies. The morphological richness, compounding, free word orderliness, and low-resource nature of Sanskrit pose significant challenges for developing deep learning solutions. We identify four fundamental tasks, which are crucial for developing a robust NLP technology for Sanskrit: word segmentation, dependency parsing, compound type identification, and poetry analysis. The first task, Sanskrit Word Segmentation (SWS), is a fundamental text processing task for any other downstream applications. However, it is challenging due to the sandhi phenomenon that modifies characters at word boundaries. Similarly, the existing dependency parsing approaches struggle with morphologically rich and low-resource languages like Sanskrit. Compound type identification is also challenging for Sanskrit due to the context-sensitive semantic relation between components. All these challenges result in sub-optimal performance in NLP applications like question answering and machine translation. Finally, Sanskrit poetry has not been extensively studied in computational linguistics. While addressing these challenges, this thesis makes various contributions: (1) The thesis proposes linguistically-informed neural architectures for these tasks. (2) We showcase the interpretability and multilingual extension of the proposed systems. (3) Our proposed systems report state-of-the-art performance. (4) Finally, we present a neural toolkit named SanskritShala, a web-based application that provides real-time analysis of input for various NLP tasks. Overall, this thesis contributes to making Sanskrit manuscripts more accessible by developing robust NLP technology and releasing various resources, datasets, and web-based toolkit.Comment: Ph.D. dissertatio

Proceedings of the Seventh Italian Conference on Computational Linguistics CLiC-it 2020

On behalf of the Program Committee, a very warm welcome to the Seventh Italian Conference on Computational Linguistics (CLiC-it 2020). This edition of the conference is held in Bologna and organised by the University of Bologna. The CLiC-it conference series is an initiative of the Italian Association for Computational Linguistics (AILC) which, after six years of activity, has clearly established itself as the premier national forum for research and development in the fields of Computational Linguistics and Natural Language Processing, where leading researchers and practitioners from academia and industry meet to share their research results, experiences, and challenges

Multimodal Assessment of Cognitive Decline: Applications in Alzheimer’s Disease and Depression

The initial diagnosis and assessment of cognitive decline are generally based around the judgement of clinicians, and commonly used semi-structured interviews, guided by pre-determined sets of topics, in a clinical set-up. Publicly available multimodal datasets have provided an opportunity to explore a range of experiments in the automatic detecting of cognitive decline. Drawing on the latest developments in representation learning, machine learning, and natural language processing, we seek to develop models capable of identifying cognitive decline with an eye to discovering the differences and commonalities that should be considered in computational treatment of mental health disorders. We present models that learn the indicators of cognitive decline from audio and visual modalities as well as lexical, syntactic, disfluency and pause information. Our study is carried out in two parts: moderation analysis and predictive modelling. We do some experiments with different fusion techniques. Our approaches are motivated by some of the recent efforts in multimodal fusion for classifying cognitive states to capture the interaction between modalities and maximise the use and combination of each modality. We create tools for detecting cognitive decline and use them to analyze three major datasets containing speech produced by people with and without cognitive decline. These findings are being used to develop multimodal models for the detection of depression and Alzheimer’s dementia