Background: Nanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real-time. Through detecting the change of ion currency signals during a DNA/RNA fragment's pass through a nanopore, genotypes are determined. Currently, the accuracy of nanopore basecalling has a higher error rate than the basecalling of short-read sequencing. Through utilizing deep neural networks, the-state-of-the art nanopore basecallers achieve basecalling accuracy in a range from 85% to 95%. Result: In this work, we proposed a novel basecalling approach from a perspective of instance segmentation. Different from previous approaches of doing typical sequence labeling, we formulated the basecalling problem as a multi-label segmentation task. Meanwhile, we proposed a refined U-net model which we call UR-net that can model sequential dependencies for a one-dimensional segmentation task. The experiment results show that the proposed basecaller URnano achieves competitive results on the in-species data, compared to the recently proposed CTC-featured basecallers. Conclusion: Our results show that formulating the basecalling problem as a one-dimensional segmentation task is a promising approach, which does basecalling and segmentation jointly.

We present an overview of the CLEF-2019 Lab ProtestNews on Extracting Protests from News in the context of generalizable natural language processing. The lab consists of document, sentence, and token level information classification and extraction tasks that were referred as task 1, task 2, and task 3 respectively in the scope of this lab. The tasks required the participants to identify protest relevant information from English local news at one or more aforementioned levels in a cross-context setting, which is cross-country in the scope of this lab. The training and development data were collected from India and test data was collected from India and China. The lab attracted 58 teams to participate in the lab. 12 and 9 of these teams submitted results and working notes respectively. We have observed neural networks yield the best results and the performance drops significantly for majority of the submissions in the cross-country setting, which is China.

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Deep neural network based machine learning models are shown to perform poorly on unseen or out-of-domain examples by numerous recent studies. Transfer learning aims to avoid overfitting and to improve generalizability by leveraging the information obtained from multiple tasks. Yet, the benefits of transfer learning depend largely on task selection and finding the right method of sharing. In this thesis, we hypothesize that current deep neural network based transfer learning models do not achieve their fullest potential for various tasks and there are still many task combinations that will benefit from transfer learning that are not considered by the current models. To this end, we started our research by implementing a novel multi-task learner with relaxed annotated data requirements and obtained a performance improvement on two NLP tasks. We will further devise models to tackle tasks from multiple areas of machine learning, such as Bioinformatics and Computer Vision, in addition to NLP.

Background Nanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real time. Through detecting the change of ion currency signals during a DNA/RNA fragment's pass through a nanopore, genotypes are determined. Currently, the accuracy of nanopore base-calling has a higher error rate than short-read base-calling. Through utilizing deep neural networks, the-state-of-the art nanopore base-callers achieve base-calling accuracy in a range from 85% to 95%. Result In this work, we proposed a novel base-calling approach from a perspective of instance segmentation. Different from the previous sequence labeling approaches, we formulated the base-calling problem as a multi-label segmentation task. Meanwhile, we proposed a refined U-net model which we call UR-net that can model sequential dependencies for a one-dimensional segmentation task. The experiment results show that the proposed base-caller URnano achieves competitive results compared to recently proposed CTC-featured base-caller Chiron, on the same amount of training and test data for in-domain evaluation. Our results show that formulating the base-calling problem as a one-dimensional segmentation task is a promising approach.

Place name recognition is one of the key tasks in Information Extraction. In this paper, we tackle this task in English News from India. We first analyze the results obtained by using available tools and corpora and then train our own models to obtain better results. Most of the previous work done on entity recognition for English makes use of similar corpora for both training and testing. Yet we observe that the performance drops significantly when we test the models on different datasets. For this reason, we have trained various models using combinations of several corpora. Our results show that training models using combinations of several corpora improves the relative performance of these models but still more research on this area is necessary to obtain place name recognizers that generalize to any given dataset.