The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a result, new methods such as Pangolin, which can scale to the millions of samples of SARS-CoV-2 currently available, have appeared. Such a tool is tailored to take as input assembled, aligned and curated full-length sequences, such as those found in the GISAID database. As high-throughput sequencing technologies continue to advance, such assembly, alignment and curation may become a bottleneck, creating a need for methods which can process raw sequencing reads directly. In this paper, we propose Reads2Vec, an alignment-free embedding approach that can generate a fixed-length feature vector representation directly from the raw sequencing reads without requiring assembly. Furthermore, since such an embedding is a numerical representation, it may be applied to highly optimized classification and clustering algorithms. Experiments on simulated data show that our proposed embedding obtains better classification results and better clustering properties contrary to existing alignment-free baselines. In a study on real data, we show that alignment-free embeddings have better clustering properties than the Pangolin tool and that the spike region of the SARS-CoV-2 genome heavily informs the alignment-free clusterings, which is consistent with current biological knowledge of SARS-CoV-2.

We consider the computation of statistical moments to operator equations with stochastic data. We remark that application of PINNs -- referred to as TPINNs -- allows to solve the induced tensor operator equations under minimal changes of existing PINNs code. This scheme can overcome the curse of dimensionality and covers non-linear and time-dependent operators. We propose two types of architectures, referred to as vanilla and multi-output TPINNs, and investigate their benefits and limitations. Exhaustive numerical experiments are performed; demonstrating applicability and performance; raising a variety of new promising research avenues.

MargNet consists of a combination of Convolutional Neural Network (CNN) and Artificial Neural Network (ANN) architectures. Using a carefully curated dataset consisting of 240,000 compact objects and an additional 150,000 faint objects, the machine learns classification directly from the data, minimising the need for human intervention. MargNet is the first classifier focusing exclusively on compact galaxies and performs better than other methods to classify compact galaxies from stars and quasars, even at fainter magnitudes. This model and feature engineering in such deep learning architectures will provide greater success in identifying objects in the ongoing and upcoming surveys, such as Dark Energy Survey (DES) and images from the Vera C. Rubin Observatory.

In this thesis, we investigated the relevance, faithfulness, and succinctness aspects of Long Form Question Answering (LFQA). LFQA aims to generate an in-depth, paragraph-length answer for a given question, to help bridge the gap between real scenarios and the existing open-domain QA models which can only extract short-span answers. LFQA is quite challenging and under-explored. Few works have been done to build an effective LFQA system. It is even more challenging to generate a good-quality long-form answer relevant to the query and faithful to facts, since a considerable amount of redundant, complementary, or contradictory information will be contained in the retrieved documents. Moreover, no prior work has been investigated to generate succinct answers. We are among the first to research the LFQA task. We pioneered the research direction to improve the answer quality in terms of 1) query-relevance, 2) answer faithfulness, and 3) answer succinctness.

Leveraging network information for prediction tasks has become a common practice in many domains. Being an important part of targeted marketing, influencer detection can potentially benefit from incorporating dynamic network representation. In this work, we investigate different dynamic Graph Neural Networks (GNNs) configurations for influencer detection and evaluate their prediction performance using a unique corporate data set. We show that using deep multi-head attention in GNN and encoding temporal attributes significantly improves performance. Furthermore, our empirical evaluation illustrates that capturing neighborhood representation is more beneficial that using network centrality measures.

We propose a new approach for paragraph recognition in document images by spatial graph convolutional networks (GCN) applied on OCR text boxes. Two steps, namely line splitting and line clustering, are performed to extract paragraphs from the lines in OCR results. Each step uses a beta-skeleton graph constructed from bounding boxes, where the graph edges provide efficient support for graph convolution operations. With only pure layout input features, the GCN model size is 3~4 orders of magnitude smaller compared to R-CNN based models, while achieving comparable or better accuracies on PubLayNet and other datasets. Furthermore, the GCN models show good generalization from synthetic training data to real-world images, and good adaptivity for variable document styles.

Question-answering (QA) that comes naturally to humans is a critical component in seamless human-computer interaction. It has emerged as one of the most convenient and natural methods to interact with the web and is especially desirable in voice-controlled environments. Despite being one of the oldest research areas, the current QA system faces the critical challenge of handling multilingual queries. To build an Artificial Intelligent (AI) agent that can serve multilingual end users, a QA system is required to be language versatile and tailored to suit the multilingual environment. Recent advances in QA models have enabled surpassing human performance primarily due to the availability of a sizable amount of high-quality datasets. However, the majority of such annotated datasets are expensive to create and are only confined to the English language, making it challenging to acknowledge progress in foreign languages. Therefore, to measure a similar improvement in the multilingual QA system, it is necessary to invest in high-quality multilingual evaluation benchmarks. In this dissertation, we focus on advancing QA techniques for handling end-user queries in multilingual environments. This dissertation consists of two parts. In the first part, we explore multilingualism and a new dimension of multilingualism referred to as code-mixing. Second, we propose a technique to solve the task of multi-hop question generation by exploiting multiple documents. Experiments show our models achieve state-of-the-art performance on answer extraction, ranking, and generation tasks on multiple domains of MQA, VQA, and language generation. The proposed techniques are generic and can be widely used in various domains and languages to advance QA systems.

Sign language translation (SLT) is an active field of study that encompasses human-computer interaction, computer vision, natural language processing and machine learning. Progress on this field could lead to higher levels of integration of deaf people. This paper presents, to the best of our knowledge, the first continuous Argentinian Sign Language (LSA) dataset. It contains 14,880 sentence level videos of LSA extracted from the CN Sordos YouTube channel with labels and keypoints annotations for each signer. We also present a method for inferring the active signer, a detailed analysis of the characteristics of the dataset, a visualization tool to explore the dataset and a neural SLT model to serve as baseline for future experiments.

In open-ended natural-language generation, existing text decoding methods typically struggle to produce text which is both diverse and high-quality. Greedy and beam search are known to suffer from text degeneration and linguistic diversity issues, while temperature, top-k, and nucleus sampling often yield diverse but low-quality outputs. In this work, we present crowd sampling, a family of decoding methods based on Bayesian risk minimization, to address this diversity-quality trade-off. Inspired by the principle of "the wisdom of the crowd," crowd sampling seeks to select a candidate from a pool of candidates that has the least expected risk (i.e., highest expected reward) under a generative model according to a given utility function. Crowd sampling can be seen as a generalization of numerous existing methods, including majority voting, and in practice, it can be used as a drop-in replacement for existing sampling methods. Extensive experiments show that crowd sampling delivers improvements of 3-7 ROUGE and BLEU points across a wide range of tasks, including summarization, data-to-text, translation, and textual style transfer, while achieving new state-of-the-art results on WebNLG and WMT'16.

Pseudo-label (PL) filtering forms a crucial part of Self-Training (ST) methods for unsupervised domain adaptation. Dropout-based Uncertainty-driven Self-Training (DUST) proceeds by first training a teacher model on source domain labeled data. Then, the teacher model is used to provide PLs for the unlabeled target domain data. Finally, we train a student on augmented labeled and pseudo-labeled data. The process is iterative, where the student becomes the teacher for the next DUST iteration. A crucial step that precedes the student model training in each DUST iteration is filtering out noisy PLs that could lead the student model astray. In DUST, we proposed a simple, effective, and theoretically sound PL filtering strategy based on the teacher model's uncertainty about its predictions on unlabeled speech utterances. We estimate the model's uncertainty by computing disagreement amongst multiple samples drawn from the teacher model during inference by injecting noise via dropout. In this work, we show that DUST's PL filtering, as initially used, may fail under severe source and target domain mismatch. We suggest several approaches to eliminate or alleviate this issue. Further, we bring insights from the research in neural network model calibration to DUST and show that a well-calibrated model correlates strongly with a positive outcome of the DUST PL filtering step.