Exploiting Latent Features of Text and Graphs

As the size and scope of online data continues to grow, new machine learning techniques become necessary to best capitalize on the wealth of available information. However, the models that help convert data into knowledge require nontrivial processes to make sense of large collections of text and massive online graphs. In both scenarios, modern machine learning pipelines produce embeddings --- semantically rich vectors of latent features --- to convert human constructs for machine understanding. In this dissertation we focus on information available within biomedical science, including human-written abstracts of scientific papers, as well as machine-generated graphs of biomedical entity relationships. We present the Moliere system, and our method for identifying new discoveries through the use of natural language processing and graph mining algorithms. We propose heuristically-based ranking criteria to augment Moliere, and leverage this ranking to identify a new gene-treatment target for HIV-associated Neurodegenerative Disorders. We additionally focus on the latent features of graphs, and propose a new bipartite graph embedding technique. Using our graph embedding, we advance the state-of-the-art in hypergraph partitioning quality. Having newfound intuition of graph embeddings, we present Agatha, a deep-learning approach to hypothesis generation. This system learns a data-driven ranking criteria derived from the embeddings of our large proposed biomedical semantic graph. To produce human-readable results, we additionally propose CBAG, a technique for conditional biomedical abstract generation

A study on developing novel methods for relation extraction

Relation Extraction (RE) is a task of Natural Language Processing (NLP) to detect and classify the relations between two entities. Relation extraction in the biomedical and scientific literature domain is challenging as text can contain multiple pairs of entities in the same instance. During the course of this research, we developed an RE framework (RelEx), which consists of five main RE paradigms: rule-based, machine learning-based, Convolutional Neural Network (CNN)-based, Bidirectional Encoder Representations from Transformers (BERT)-based, and Graph Convolutional Networks (GCNs)-based approaches. RelEx\u27s rule-based approach uses co-location information of the entities to determine whether a relation exists between a selected entity and the other entities. RelEx\u27s machine learning-based approach consists of traditional feature representations into traditional machine learning algorithms. RelEx\u27s CNN-based approach consists of three CNN architectures: Segment-CNN, single-label Sentence-CNN, and multi-label Sentence-CNN. RelEx\u27s BERT-based approach utilizes BERT\u27s contextualized word embeddings into a feed-forward neural network. Finally, RelEx\u27s GCN-based approach consists of two GCN-based architectures: GCN-Vanilla, GCN-BERT. We evaluated variations of these approaches in two different domains across four distinct relation types. Overall our findings showed that the rule-based approach is applicable for data with fewer instances in the training data. In contrast, the CNN-based, BERT-based, and GCN-based approaches perform better with labeled data with many training instances. These approaches automatically identify patterns in the data efficiently, whereas rule-based approaches require expert knowledge to generate rules. The CNN-based, BERT-based approaches capture the local contextual information within a sentence or document by embedding both semantic and syntactic information in a learned representation. However, their ability to capture the long-range dependency global information in a text is limited. GCN-based approaches capture the global association information by performing convolution operations on neighbor nodes in a graph and incorporating information from neighbors. Combining GCN with BERT integrates the local contextual and global association information of the words and generates better representations for the words

A Robust Hybrid Neural Network Architecture for Blind Source Separation of Speech Signals Exploiting Deep Learning

In the contemporary era, blind source separation has emerged as a highly appealing and significant research topic within the field of signal processing. The imperative for the integration of blind source separation techniques within the context of beyond fifth-generation and sixth-generation networks arises from the increasing demand for reliable and efficient communication systems that can effectively handle the challenges posed by high-density networks, dynamic interference environments, and the coexistence of diverse signal sources, thereby enabling enhanced signal extraction and separation for improved system performance. Particularly, audio processing presents a critical domain where the challenge lies in effectively handling files containing a mixture of human speech, silence, and music. Addressing this challenge, speech separation systems can be regarded as a specialized form of human speech recognition or audio signal classification systems that are leveraged to separate, identify, or delineate segments of audio signals encompassing human speech. In various applications such as volume reduction, quality enhancement, detection, and identification, the need arises to separate human speech by eliminating silence, music, or environmental noise from the audio signals. Consequently, the development of robust methods for accurate and efficient speech separation holds paramount importance in optimizing audio signal processing tasks. This study proposes a novel three-way neural network architecture that incorporates transfer learning, a pre-trained dual-path recurrent neural network, and a transformer. In addition to learning the time series associated with audio signals, this network possesses the unique capability of direct context-awareness for modeling the speech sequence within the transformer framework. A comprehensive array of simulations is meticulously conducted to evaluate the performance of the proposed model, which is benchmarked with seven prominent state-of-the-art deep learning-based architectures. The results obtained from these evaluations demonstrate notable advancements in multiple objective metrics. Specifically, our proposed solution showcases an average improvement of 4.60% in terms of short-time objective intelligibility, 14.84% in source-to-distortion ratio, and 9.87% in scale-invariant signal-to-noise ratio. These extraordinary advancements surpass those achieved by the nearest rival, namely the dual-path recurrent neural network time-domain audio separation network, firmly establishing the superiority of our proposed model's performance

Mapping (Dis-)Information Flow about the MH17 Plane Crash

Digital media enables not only fast sharing of information, but also disinformation. One prominent case of an event leading to circulation of disinformation on social media is the MH17 plane crash. Studies analysing the spread of information about this event on Twitter have focused on small, manually annotated datasets, or used proxys for data annotation. In this work, we examine to what extent text classifiers can be used to label data for subsequent content analysis, in particular we focus on predicting pro-Russian and pro-Ukrainian Twitter content related to the MH17 plane crash. Even though we find that a neural classifier improves over a hashtag based baseline, labeling pro-Russian and pro-Ukrainian content with high precision remains a challenging problem. We provide an error analysis underlining the difficulty of the task and identify factors that might help improve classification in future work. Finally, we show how the classifier can facilitate the annotation task for human annotators

Fundamentals

Volume 1 establishes the foundations of this new field. It goes through all the steps from data collection, their summary and clustering, to different aspects of resource-aware learning, i.e., hardware, memory, energy, and communication awareness. Machine learning methods are inspected with respect to resource requirements and how to enhance scalability on diverse computing architectures ranging from embedded systems to large computing clusters

Fundamentals

Volume 1 establishes the foundations of this new field. It goes through all the steps from data collection, their summary and clustering, to different aspects of resource-aware learning, i.e., hardware, memory, energy, and communication awareness. Machine learning methods are inspected with respect to resource requirements and how to enhance scalability on diverse computing architectures ranging from embedded systems to large computing clusters