Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle, or perhaps not noted at all. Much work is being done on the database and storage side of things, ensuring that there exists a space to store experiment-specific details, but current mechanisms for recording details are cumbersome for scientists to use. We propose a new metadata description language, named MEDFORD, in which scientists can record all details relevant to their research. Human-readable, easily-editable, and templatable, MEDFORD serves as a collection point for all notes that a researcher could find relevant to their research, be it for internal use or for future replication. MEDFORD has been applied to coral research, documenting research from RNA-seq analyses to photo collections.
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Human Activity Recognition (HAR) is a crucial technology for many applications such as smart homes, surveillance, human assistance and health care. This technology utilises pattern recognition and can contribute to the development of human-in-the-loop control of different systems such as orthoses and exoskeletons. The majority of reported studies use a small dataset collected from an experiment for a specific purpose. The downsides of this approach include: 1) it is hard to generalise the outcome to different people with different biomechanical characteristics and health conditions, and 2) it cannot be implemented in applications other than the original experiment. To address these deficiencies, the current study investigates using a publicly available dataset collected for pathology diagnosis purposes to train Machine Learning (ML) algorithms. A dataset containing knee motion of participants performing different exercises has been used to classify human activity. The algorithms used in this study are Gaussian Naive Bayes, Decision Tree, Random Forest, K-Nearest Neighbors Vote, Support Vector Machine and Gradient Boosting. Furthermore, two training approaches are compared to raw data (de-noised) and manually extracted features. The results show up to 0.94 performance of the Area Under the ROC Curve (AUC) metric for 11-fold cross-validation for Gradient Boosting algorithm using raw data. This outcome reflects the validity and potential use of the proposed approach for this type of dataset.
Topic-controllable summarization is an emerging research area with a wide range of potential applications. However, existing approaches suffer from significant limitations. First, there is currently no established evaluation metric for this task. Furthermore, existing methods built upon recurrent architectures, which can significantly limit their performance compared to more recent Transformer-based architectures, while they also require modifications to the model's architecture for controlling the topic. In this work, we propose a new topic-oriented evaluation measure to automatically evaluate the generated summaries based on the topic affinity between the generated summary and the desired topic. We also conducted a user study that validates the reliability of this measure. Finally, we propose simple, yet powerful methods for topic-controllable summarization either incorporating topic embeddings into the model's architecture or employing control tokens to guide the summary generation. Experimental results show that control tokens can achieve better performance compared to more complicated embedding-based approaches while being at the same time significantly faster.
Context: A tertiary study can be performed to identify related reviews on a topic of interest. However, the elaboration of an appropriate and effective search string to detect secondary studies is challenging for Software Engineering (SE) researchers. Objective: The main goal of this study is to propose a suitable search string to detect secondary studies in SE, addressing issues such as the quantity of applied terms, relevance, recall and precision. Method: We analyzed seven tertiary studies under two perspectives: (1) structure -- strings' terms to detect secondary studies; and (2) field: where searching -- titles alone or abstracts alone or titles and abstracts together, among others. We validate our string by performing a two-step validation process. Firstly, we evaluated the capability to retrieve secondary studies over a set of 1537 secondary studies included in 24 tertiary studies in SE. Secondly, we evaluated the general capacity of retrieving secondary studies over an automated search using the Scopus digital library. Results: Our string was capable to retrieve an optimum value of over 90\% of the included secondary studies (recall) with a high general precision of almost 60\%. Conclusion: The suitable search string for finding secondary studies in SE contains the terms "systematic review", "literature review", "systematic mapping", "mapping study" and "systematic map".
This paper presents first successful steps in designing search agents that learn meta-strategies for iterative query refinement in information-seeking tasks. Our approach uses machine reading to guide the selection of refinement terms from aggregated search results. Agents are then empowered with simple but effective search operators to exert fine-grained and transparent control over queries and search results. We develop a novel way of generating synthetic search sessions, which leverages the power of transformer-based language models through (self-)supervised learning. We also present a reinforcement learning agent with dynamically constrained actions that learns interactive search strategies from scratch. Our search agents obtain retrieval and answer quality performance comparable to recent neural methods, using only a traditional term-based BM25 ranking function and interpretable discrete reranking and filtering actions.
Artificial intelligence (AI) has become a part of everyday conversation and our lives. It is considered as the new electricity that is revolutionizing the world. AI is heavily invested in both industry and academy. However, there is also a lot of hype in the current AI debate. AI based on so-called deep learning has achieved impressive results in many problems, but its limits are already visible. AI has been under research since the 1940s, and the industry has seen many ups and downs due to over-expectations and related disappointments that have followed. The purpose of this book is to give a realistic picture of AI, its history, its potential and limitations. We believe that AI is a helper, not a ruler of humans. We begin by describing what AI is and how it has evolved over the decades. After fundamentals, we explain the importance of massive data for the current mainstream of artificial intelligence. The most common representations for AI, methods, and machine learning are covered. In addition, the main application areas are introduced. Computer vision has been central to the development of AI. The book provides a general introduction to computer vision, and includes an exposure to the results and applications of our own research. Emotions are central to human intelligence, but little use has been made in AI. We present the basics of emotional intelligence and our own research on the topic. We discuss super-intelligence that transcends human understanding, explaining why such achievement seems impossible on the basis of present knowledge,and how AI could be improved. Finally, a summary is made of the current state of AI and what to do in the future. In the appendix, we look at the development of AI education, especially from the perspective of contents at our own university.
Graph machine learning has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To tackle the challenge, automated graph machine learning, which aims at discovering the best hyper-parameter and neural architecture configuration for different graph tasks/data without manual design, is gaining an increasing number of attentions from the research community. In this paper, we extensively discuss automated graph machine approaches, covering hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We briefly overview existing libraries designed for either graph machine learning or automated machine learning respectively, and further in depth introduce AutoGL, our dedicated and the world's first open-source library for automated graph machine learning. Last but not least, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive discussion of approaches, libraries as well as directions for automated graph machine learning.
Machine learning plays a role in many deployed decision systems, often in ways that are difficult or impossible to understand by human stakeholders. Explaining, in a human-understandable way, the relationship between the input and output of machine learning models is essential to the development of trustworthy machine-learning-based systems. A burgeoning body of research seeks to define the goals and methods of explainability in machine learning. In this paper, we seek to review and categorize research on counterfactual explanations, a specific class of explanation that provides a link between what could have happened had input to a model been changed in a particular way. Modern approaches to counterfactual explainability in machine learning draw connections to the established legal doctrine in many countries, making them appealing to fielded systems in high-impact areas such as finance and healthcare. Thus, we design a rubric with desirable properties of counterfactual explanation algorithms and comprehensively evaluate all currently-proposed algorithms against that rubric. Our rubric provides easy comparison and comprehension of the advantages and disadvantages of different approaches and serves as an introduction to major research themes in this field. We also identify gaps and discuss promising research directions in the space of counterfactual explainability.
Reinforcement learning (RL) is a popular paradigm for addressing sequential decision tasks in which the agent has only limited environmental feedback. Despite many advances over the past three decades, learning in many domains still requires a large amount of interaction with the environment, which can be prohibitively expensive in realistic scenarios. To address this problem, transfer learning has been applied to reinforcement learning such that experience gained in one task can be leveraged when starting to learn the next, harder task. More recently, several lines of research have explored how tasks, or data samples themselves, can be sequenced into a curriculum for the purpose of learning a problem that may otherwise be too difficult to learn from scratch. In this article, we present a framework for curriculum learning (CL) in reinforcement learning, and use it to survey and classify existing CL methods in terms of their assumptions, capabilities, and goals. Finally, we use our framework to find open problems and suggest directions for future RL curriculum learning research.
A Survey of Reinforcement Learning Techniques: Strategies, Recent Development, and Future Directions
Reinforcement learning is one of the core components in designing an artificial intelligent system emphasizing real-time response. Reinforcement learning influences the system to take actions within an arbitrary environment either having previous knowledge about the environment model or not. In this paper, we present a comprehensive study on Reinforcement Learning focusing on various dimensions including challenges, the recent development of different state-of-the-art techniques, and future directions. The fundamental objective of this paper is to provide a framework for the presentation of available methods of reinforcement learning that is informative enough and simple to follow for the new researchers and academics in this domain considering the latest concerns. First, we illustrated the core techniques of reinforcement learning in an easily understandable and comparable way. Finally, we analyzed and depicted the recent developments in reinforcement learning approaches. My analysis pointed out that most of the models focused on tuning policy values rather than tuning other things in a particular state of reasoning.
Machine learning techniques have deeply rooted in our everyday life. However, since it is knowledge- and labor-intensive to pursue good learning performance, human experts are heavily involved in every aspect of machine learning. In order to make machine learning techniques easier to apply and reduce the demand for experienced human experts, automated machine learning (AutoML) has emerged as a hot topic with both industrial and academic interest. In this paper, we provide an up to date survey on AutoML. First, we introduce and define the AutoML problem, with inspiration from both realms of automation and machine learning. Then, we propose a general AutoML framework that not only covers most existing approaches to date but also can guide the design for new methods. Subsequently, we categorize and review the existing works from two aspects, i.e., the problem setup and the employed techniques. Finally, we provide a detailed analysis of AutoML approaches and explain the reasons underneath their successful applications. We hope this survey can serve as not only an insightful guideline for AutoML beginners but also an inspiration for future research.
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