Browsing by Author "Jang, Hyeju"

Now showing 1 - 4 of 4
  • Thumbnail Image
    Item
    Classification of Alzheimer’s Disease Leveraging Multi-task Machine Learning Analysis of Speech and Eye-Movement Data
    (Frontiers Media, 2021-09-20) Jang, Hyeju; Soroski, Thomas; Rizzo, Matteo; Barral, Oswald; Harisinghani, Anuj; Newton-Mason, Sally; Granby, Saffrin; da Cunha Vasco, Thiago Monnerat Stutz; Lewis, Caitlin; Tutt, Pavan; Carenini, Giuseppe; Conati, Cristina; Field, Thalia S.; Computer Science, Luddy School of Informatics, Computing, and Engineering
    Alzheimer’s disease (AD) is a progressive neurodegenerative condition that results in impaired performance in multiple cognitive domains. Preclinical changes in eye movements and language can occur with the disease, and progress alongside worsening cognition. In this article, we present the results from a machine learning analysis of a novel multimodal dataset for AD classification. The cohort includes data from two novel tasks not previously assessed in classification models for AD (pupil fixation and description of a pleasant past experience), as well as two established tasks (picture description and paragraph reading). Our dataset includes language and eye movement data from 79 memory clinic patients with diagnoses of mild-moderate AD, mild cognitive impairment (MCI), or subjective memory complaints (SMC), and 83 older adult controls. The analysis of the individual novel tasks showed similar classification accuracy when compared to established tasks, demonstrating their discriminative ability for memory clinic patients. Fusing the multimodal data across tasks yielded the highest overall AUC of 0.83 ± 0.01, indicating that the data from novel tasks are complementary to established tasks.
  • Thumbnail Image
    Item
    Evaluating Web-Based Automatic Transcription for Alzheimer Speech Data: Transcript Comparison and Machine Learning Analysis
    (JMIR, 2022) Soroski, Thomas; Vasco, Thiago da Cunha; Newton-Mason, Sally; Granby, Saffrin; Lewis, Caitlin; Harisinghani, Anuj; Rizzo, Matteo; Conati, Cristina; Murray, Gabriel; Carenini, Giuseppe; Field, Thalia S.; Jang, Hyeju; Computer Science, Luddy School of Informatics, Computing, and Engineering
    Background: Speech data for medical research can be collected noninvasively and in large volumes. Speech analysis has shown promise in diagnosing neurodegenerative disease. To effectively leverage speech data, transcription is important, as there is valuable information contained in lexical content. Manual transcription, while highly accurate, limits the potential scalability and cost savings associated with language-based screening. Objective: To better understand the use of automatic transcription for classification of neurodegenerative disease, namely, Alzheimer disease (AD), mild cognitive impairment (MCI), or subjective memory complaints (SMC) versus healthy controls, we compared automatically generated transcripts against transcripts that went through manual correction. Methods: We recruited individuals from a memory clinic (“patients”) with a diagnosis of mild-to-moderate AD, (n=44, 30%), MCI (n=20, 13%), SMC (n=8, 5%), as well as healthy controls (n=77, 52%) living in the community. Participants were asked to describe a standardized picture, read a paragraph, and recall a pleasant life experience. We compared transcripts generated using Google speech-to-text software to manually verified transcripts by examining transcription confidence scores, transcription error rates, and machine learning classification accuracy. For the classification tasks, logistic regression, Gaussian naive Bayes, and random forests were used. Results: The transcription software showed higher confidence scores (P<.001) and lower error rates (P>.05) for speech from healthy controls compared with patients. Classification models using human-verified transcripts significantly (P<.001) outperformed automatically generated transcript models for both spontaneous speech tasks. This comparison showed no difference in the reading task. Manually adding pauses to transcripts had no impact on classification performance. However, manually correcting both spontaneous speech tasks led to significantly higher performances in the machine learning models. Conclusions: We found that automatically transcribed speech data could be used to distinguish patients with a diagnosis of AD, MCI, or SMC from controls. We recommend a human verification step to improve the performance of automatic transcripts, especially for spontaneous tasks. Moreover, human verification can focus on correcting errors and adding punctuation to transcripts. However, manual addition of pauses is not needed, which can simplify the human verification step to more efficiently process large volumes of speech data.
  • Thumbnail Image
    Item
    Network Alignment Using Topological and Node Embedding Features
    (2024-08) Almulhim, Aljohara; Al Hasan, Mohammad; Tuceryan, Mihran; Durresi, Arjan; Mukhopadhyay, Snehasis; Jang, Hyeju
    In today's big data environment, development of robust knowledge discovery solutions depends on integration of data from various sources. For example, intelligence agencies fuse data from multiple sources to identify criminal activities; e-commerce platforms consolidate user activities on various platforms and devices to build better user profile; scientists connect data from various modality to develop new drugs, and treatments. In all such activities, entities from different data sources need to be aligned---first, to ensure accurate analysis and more importantly, to discover novel knowledge regarding these entities. If the data sources are networks, aligning entities from different sources leads to the task of network alignment, which is the focus of this thesis. The main objective of this task is to find an optimal one-to-one correspondence among nodes in two or more networks utilizing graph topology and nodes/edges attributes. In existing works, diverse computational schemes have been adopted for solving the network alignment task; these schemes include finding eigen-decomposition of similarity matrices, solving quadratic assignment problems via sub-gradient optimization, and designing iterative greedy matching techniques. Contemporary works approach this problem using a deep learning framework by learning node representations to identify matches. Node matching's key challenges include computational complexity and scalability. However, privacy concerns or unavailability often prevent the utilization of node attributes in real-world scenarios. In light of this, we aim to solve this problem by relying solely on the graph structure, without the need for prior knowledge, external attributes, or guidance from landmark nodes. Clearly, topology-based matching emerges as a hard problem when compared to other network matching tasks. In this thesis, I propose two original works to solve network topology-based alignment task. The first work, Graphlet-based Alignment (Graphlet-Align), employs a topological approach to network alignment. Graphlet-Align represents each node with a local graphlet count based signature and use that as feature for deriving node to node similarity across a pair of networks. By using these similarity values in a bipartite matching algorithm Graphlet-Align obtains a preliminary alignment. It then uses high-order information extending to k-hop neighborhood of a node to further refine the alignment, achieving better accuracy. We validated Graphlet-Align's efficacy by applying it to various large real-world networks, achieving accuracy improvements ranging from $20\%$ to $72\%$ over state-of-the-art methods on both duplicated and noisy graphs. Expanding on this paradigm that focuses solely on topology for solving graph alignment, in my second work, I develop a self-supervised learning framework known as Self-Supervised Topological Alignment (SST-Align). SST-Align uses graphlet-based signature for creating self-supervised node alignment labels, and then use those labels to generate node embedding vectors of both the networks in a joint space from which node alignment task can be effectively and accurately solved. It starts with an optimization process that applies average pooling on top of the extracted graphlet signature to construct an initial node assignment. Next, a self-supervised Siamese network architecture utilizes both the initial node assignment and graph convolutional networks to generate node embeddings through a contrastive loss. By applying kd-tree similarity to the two networks' embeddings, we achieve the final node mapping. Extensive testing on real-world graph alignment datasets shows that our developed methodology has competitive results compared to seven existing competing models in terms of node mapping accuracy. Additionally, we establish the Ablation Study to evaluate the two-stage accuracy, excluding the learning representation part and comparing the mapping accuracy accordingly. This thesis enhances the theoretical understanding of topological features in the analysis of graph data for network alignment task, hence facilitating future advancements toward the field.
  • Thumbnail Image
    Item
    T3-Vis: a visual analytic framework for Training and fine-Tuning Transformers in NLP
    (ACL Anthology, 2021) Li, Raymond; Xiao, Wen; Wang, Lanjun; Jang, Hyeju; Carenini, Giuseppe; Computer Science, Luddy School of Informatics, Computing, and Engineering
    Transformers are the dominant architecture in NLP, but their training and fine-tuning is still very challenging. In this paper, we present the design and implementation of a visual analytic framework for assisting researchers in such process, by providing them with valuable insights about the model’s intrinsic properties and behaviours. Our framework offers an intuitive overview that allows the user to explore different facets of the model (e.g., hidden states, attention) through interactive visualization, and allows a suite of built-in algorithms that compute the importance of model components and different parts of the input sequence. Case studies and feedback from a user focus group indicate that the framework is useful, and suggest several improvements. Our framework is available at: https://github.com/raymondzmc/T3-Vis.