機械学習モデルからの知識抽出と生命情報学への応用

京都大学新制・課程博士博士(情報学)甲第23397号情博第766号新制||情||131(附属図書館)京都大学大学院情報学研究科知能情報学専攻(主査)教授 阿久津 達也, 教授 山本 章博, 教授 鹿島 久嗣学位規則第4条第1項該当Doctor of InformaticsKyoto UniversityDFA

On the Nature and Types of Anomalies: A Review

Anomalies are occurrences in a dataset that are in some way unusual and do not fit the general patterns. The concept of the anomaly is generally ill-defined and perceived as vague and domain-dependent. Moreover, despite some 250 years of publications on the topic, no comprehensive and concrete overviews of the different types of anomalies have hitherto been published. By means of an extensive literature review this study therefore offers the first theoretically principled and domain-independent typology of data anomalies, and presents a full overview of anomaly types and subtypes. To concretely define the concept of the anomaly and its different manifestations, the typology employs five dimensions: data type, cardinality of relationship, anomaly level, data structure and data distribution. These fundamental and data-centric dimensions naturally yield 3 broad groups, 9 basic types and 61 subtypes of anomalies. The typology facilitates the evaluation of the functional capabilities of anomaly detection algorithms, contributes to explainable data science, and provides insights into relevant topics such as local versus global anomalies.Comment: 38 pages (30 pages content), 10 figures, 3 tables. Preprint; review comments will be appreciated. Improvements in version 2: Explicit mention of fifth anomaly dimension; Added section on explainable anomaly detection; Added section on variations on the anomaly concept; Various minor additions and improvement

Improving Automatic Transcription Using Natural Language Processing

Digital Democracy is a CalMatters and California Polytechnic State University initia-tive to promote transparency in state government by increasing access to the Califor-nia legislature. While Digital Democracy is made up of many resources, one founda-tional step of the project is obtaining accurate, timely transcripts of California Senateand Assembly hearings. The information extracted from these transcripts providescrucial data for subsequent steps in the pipeline. In the context of Digital Democracy,upleveling is when humans verify, correct, and annotate the transcript results afterthe legislative hearings have been automatically transcribed. The upleveling processis done with the assistance of a software application called the Transcription Tool.The human upleveling process is the most costly and time-consuming step of the Dig-ital Democracy pipeline. In this thesis, we hypothesize that we can make significantreductions to the time needed for upleveling by using Natural Language Processing(NLP) systems and techniques. The main contribution of this thesis is engineeringa new automatic transcription pipeline. Specifically, this thesis integrates a new au-tomatic speech recognition service, a new speaker diarization model, additional textpost-processing changes, and a new process for speaker identification. To evaluate the system’s improvements, we measure the accuracy and speed of the newly integrated features and record editor upleveling time both before and after the additions

Neural Graph Transfer Learning in Natural Language Processing Tasks

Natural language is essential in our daily lives as we rely on languages to communicate and exchange information. A fundamental goal for natural language processing (NLP) is to let the machine understand natural language to help or replace human experts to mine knowledge and complete tasks. Many NLP tasks deal with sequential data. For example, a sentence is considered as a sequence of works. Very recently, deep learning-based language models (i.e.,BERT \citep{devlin2018bert}) achieved significant improvement in many existing tasks, including text classification and natural language inference. However, not all tasks can be formulated using sequence models. Specifically, graph-structured data is also fundamental in NLP, including entity linking, entity classification, relation extraction, abstractive meaning representation, and knowledge graphs \citep{santoro2017simple,hamilton2017representation,kipf2016semi}. In this scenario, BERT-based pretrained models may not be suitable. Graph Convolutional Neural Network (GCN) \citep{kipf2016semi} is a deep neural network model designed for graphs. It has shown great potential in text classification, link prediction, question answering and so on. This dissertation presents novel graph models for NLP tasks, including text classification, prerequisite chain learning, and coreference resolution. We focus on different perspectives of graph convolutional network modeling: for text classification, a novel graph construction method is proposed which allows interpretability for the prediction; for prerequisite chain learning, we propose multiple aggregation functions that utilize neighbors for better information exchange; for coreference resolution, we study how graph pretraining can help when labeled data is limited. Moreover, an important branch is to apply pretrained language models for the mentioned tasks. So, this dissertation also focuses on the transfer learning method that generalizes pretrained models to other domains, including medical, cross-lingual, and web data. Finally, we propose a new task called unsupervised cross-domain prerequisite chain learning, and study novel graph-based methods to transfer knowledge over graphs

Quality of Information in Mobile Crowdsensing: Survey and Research Challenges

Smartphones have become the most pervasive devices in people's lives, and are clearly transforming the way we live and perceive technology. Today's smartphones benefit from almost ubiquitous Internet connectivity and come equipped with a plethora of inexpensive yet powerful embedded sensors, such as accelerometer, gyroscope, microphone, and camera. This unique combination has enabled revolutionary applications based on the mobile crowdsensing paradigm, such as real-time road traffic monitoring, air and noise pollution, crime control, and wildlife monitoring, just to name a few. Differently from prior sensing paradigms, humans are now the primary actors of the sensing process, since they become fundamental in retrieving reliable and up-to-date information about the event being monitored. As humans may behave unreliably or maliciously, assessing and guaranteeing Quality of Information (QoI) becomes more important than ever. In this paper, we provide a new framework for defining and enforcing the QoI in mobile crowdsensing, and analyze in depth the current state-of-the-art on the topic. We also outline novel research challenges, along with possible directions of future work.Comment: To appear in ACM Transactions on Sensor Networks (TOSN

Big data analytics in high-throughput phenotyping

Doctor of PhilosophyDepartment of Computer ScienceMitchell L. NeilsenAs the global population rises, advancements in plant diversity and crop yield is necessary for resource stability and nutritional security. In the next thirty years, the global population will pass 9 billion. Genetic advancements have become inexpensive and widely available to address this issue; however, phenotypic acquisition development has stagnated. Plant breeding programs have begun to support efforts in data mining, computer vision, and graphics to alleviate the gap from genetic advancements. This dissertation creates a bridge between computer vision research and phenotyping by designing and analyzing various deep neural networks for concrete applications while presenting new and novel approaches. The significant contributions are research advancements to the current state-of-the-art in mobile high-throughput phenotyping (HTP), which promotes more efficient plant science workflow tasks. Novel tools and utilities created for automatic code generation, maintenance, and source translation are featured. Promoted tools replace boiler-plate segments and redundant tasks. Finally, this research investigates various state-of-the-art deep neural network architectures to derive methods for object identification and enumeration. Seed kernel counting is a crucial task in the plant research workflow. This dissertation explains techniques and tools for generating data to scale training. New dataset creation methodologies are debuted and aim to replace the classical approach to labeling data. Although HTP is a general topic, this research focuses on various grains and plant-seed phenotypes. Applying deep neural networks to seed kernels for classification and object detection is a relatively new topic. This research uses a novel open-source dataset that supports future architectures for detecting kernels. State-of-the-art pre-trained regional convolutional neural networks (RCNN) perform poorly on seeds. The proposed counting architectures outperform the models above by focusing on learning a labeled integer count rather than anchor points for localization. Concurrently, pre-trained models on the seed dataset, a composition of geometrically primitive-like objects, boasts improvements to evaluation metrics in comparison to the Common Object in Context (COCO) dataset. A widely accepted problem in image processing is the segmentation of foreground objects from the background. This dissertation shows that state-of-the-art regional convolutional neural networks (RCNN) perform poorly in cases where foreground objects are similar to the background. Instead, transfer learning leverages salient features and boosts performance on noisy background datasets. The accumulation of new ideas and evidence of growth for mobile computer vision surmise a bright future for data-acquisition in various fields of HTP. The results obtained provide horizons and a solid foundation for future research to stabilize and continue the growth of phenotypic acquisition and crop yield

Multi-view Representation Learning for Unifying Languages, Knowledge and Vision

The growth of content on the web has raised various challenges, yet also provided numerous opportunities. Content exists in varied forms such as text appearing in different languages, entity-relationship graph represented as structured knowledge and as a visual embodiment like images/videos. They are often referred to as modalities. In many instances, the different amalgamation of modalities co-exists to complement each other or to provide consensus. Thus making the content either heterogeneous or homogeneous. Having an additional point of view for each instance in the content is beneficial for data-driven learning and intelligent content processing. However, despite having availability of such content. Most advancements made in data-driven learning (i.e., machine learning) is by solving tasks separately for the single modality. The similar endeavor was not shown for the challenges which required input either from all or subset of them. In this dissertation, we develop models and techniques that can leverage multiple views of heterogeneous or homogeneous content and build a shared representation for aiding several applications which require a combination of modalities mentioned above. In particular, we aim to address applications such as content-based search, categorization, and generation by providing several novel contributions. First, we develop models for heterogeneous content by jointly modeling diverse representations emerging from two views depicting text and image by learning their correlation. To be specific, modeling such correlation is helpful to retrieve cross-modal content. Second, we replace the heterogeneous content with homogeneous to learn a common space representation for content categorization across languages. Furthermore, we develop models that take input from both homogeneous and heterogeneous content to facilitate the construction of common space representation from more than two views. Specifically, representation is used to generate one view from another. Lastly, we describe a model that can handle missing views, and demonstrate that the model can generate missing views by utilizing external knowledge. We argue that techniques the models leverage internally provide many practical benefits and lot of immediate value applications. From the modeling perspective, our contributed model design in this thesis can be summarized under the phrase Multi-view Representation Learning( MVRL ). These models are variations and extensions of shallow statistical and deep neural networks approaches that can jointly optimize and exploit all views of the input content arising from different independent representations. We show that our models advance state of the art, but not limited to tasks such as cross-modal retrieval, cross-language text classification, image-caption generation in multiple languages and caption generation for images containing unseen visual object categories