The Cognitive Atlas: Toward a Knowledge Foundation for Cognitive Neuroscience

Cognitive neuroscience aims to map mental processes onto brain function, which begs the question of what “mental processes” exist and how they relate to the tasks that are used to manipulate and measure them. This topic has been addressed informally in prior work, but we propose that cumulative progress in cognitive neuroscience requires a more systematic approach to representing the mental entities that are being mapped to brain function and the tasks used to manipulate and measure mental processes. We describe a new open collaborative project that aims to provide a knowledge base for cognitive neuroscience, called the Cognitive Atlas (accessible online at http://www.cognitiveatlas.org), and outline how this project has the potential to drive novel discoveries about both mind and brain

Knowledge-Rich Self-Supervision for Biomedical Entity Linking

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision ($\tt KRISS$) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces $\tt KRISSBERT$, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy

The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

Integrating prior knowledge into factorization approaches for relational learning

An efficient way to represent the domain knowledge is relational data, where information is recorded in form of relationships between entities. Relational data is becoming ubiquitous over the years for knowledge representation due to the fact that many real-word data is inherently interlinked. Some well-known examples of relational data are: the World Wide Web (WWW), a system of interlinked hypertext documents; the Linked Open Data (LOD) cloud of the Semantic Web, a collection of published data and their interlinks; and finally the Internet of Things (IoT), a network of physical objects with internal states and communications ability. Relational data has been addressed by many different machine learning approaches, the most promising ones are in the area of relational learning, which is the focus of this thesis. While conventional machine learning algorithms consider entities as being independent instances randomly sampled from some statistical distribution and being represented as data points in a vector space, relational learning takes into account the overall network environment when predicting the label of an entity, an attribute value of an entity or the existence of a relationship between entities. An important feature is that relational learning can exploit contextual information that is more distant in the relational network. As the volume and structural complexity of the relational data increase constantly in the era of Big Data, scalability and the modeling power become crucial for relational learning algorithms. Previous relational learning algorithms either provide an intuitive representation of the model, such as Inductive Logic Programming (ILP) and Markov Logic Networks (MLNs), or assume a set of latent variables to explain the observed data, such as the Infinite Hidden Relational Model (IHRM), the Infinite Relational Model (IRM) and factorization approaches. Models with intuitive representations often involve some form of structure learning which leads to scalability problems due to a typically large search space. Factorizations are among the best-performing approaches for large-scale relational learning since the algebraic computations can easily be parallelized and since they can exploit data sparsity. Previous factorization approaches exploit only patterns in the relational data itself and the focus of the thesis is to investigate how additional prior information (comprehensive information), either in form of unstructured data (e.g., texts) or structured patterns (e.g., in form of rules) can be considered in the factorization approaches. The goal is to enhance the predictive power of factorization approaches by involving prior knowledge for the learning, and on the other hand to reduce the model complexity for efficient learning. This thesis contains two main contributions: The first contribution presents a general and novel framework for predicting relationships in multirelational data using a set of matrices describing the various instantiated relations in the network. The instantiated relations, derived or learnt from prior knowledge, are integrated as entities' attributes or entity-pairs' attributes into different adjacency matrices for the learning. All the information available is then combined in an additive way. Efficient learning is achieved using an alternating least squares approach exploiting sparse matrix algebra and low-rank approximation. As an illustration, several algorithms are proposed to include information extraction, deductive reasoning and contextual information in matrix factorizations for the Semantic Web scenario and for recommendation systems. Experiments on various data sets are conducted for each proposed algorithm to show the improvement in predictive power by combining matrix factorizations with prior knowledge in a modular way. In contrast to a matrix, a 3-way tensor si a more natural representation for the multirelational data where entities are connected by different types of relations. A 3-way tensor is a three dimensional array which represents the multirelational data by using the first two dimensions for entities and using the third dimension for different types of relations. In the thesis, an analysis on the computational complexity of tensor models shows that the decomposition rank is key for the success of an efficient tensor decomposition algorithm, and that the factorization rank can be reduced by including observable patterns. Based on these theoretical considerations, a second contribution of this thesis develops a novel tensor decomposition approach - an Additive Relational Effects (ARE) model - which combines the strengths of factorization approaches and prior knowledge in an additive way to discover different relational effects from the relational data. As a result, ARE consists of a decomposition part which derives the strong relational leaning effects from a highly scalable tensor decomposition approach RESCAL and a Tucker 1 tensor which integrates the prior knowledge as instantiated relations. An efficient least squares approach is proposed to compute the combined model ARE. The additive model contains weights that reflect the degree of reliability of the prior knowledge, as evaluated by the data. Experiments on several benchmark data sets show that the inclusion of prior knowledge can lead to better performing models at a low tensor rank, with significant benefits for run-time and storage requirements. In particular, the results show that ARE outperforms state-of-the-art relational learning algorithms including intuitive models such as MRC, which is an approach based on Markov Logic with structure learning, factorization approaches such as Tucker, CP, Bayesian Clustered Tensor Factorization (BCTF), the Latent Factor Model (LFM), RESCAL, and other latent models such as the IRM. A final experiment on a Cora data set for paper topic classification shows the improvement of ARE over RESCAL in both predictive power and runtime performance, since ARE requires a significantly lower rank

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology

Biomedical ontologies contain errors. Crowdsourcing, defined as taking a job traditionally performed by a designated agent and outsourcing it to an undefined large group of people, provides scalable access to humans. Therefore, the crowd has the potential overcome the limited accuracy and scalability found in current ontology quality assurance approaches. Crowd-based methods have identified errors in SNOMED CT, a large, clinical ontology, with an accuracy similar to that of experts, suggesting that crowdsourcing is indeed a feasible approach for identifying ontology errors. This work uses that same crowd-based methodology, as well as a panel of experts, to verify a subset of the Gene Ontology (200 relationships). Experts identified 16 errors, generally in relationships referencing acids and metals. The crowd performed poorly in identifying those errors, with an area under the receiver operating characteristic curve ranging from 0.44 to 0.73, depending on the methods configuration. However, when the crowd verified what experts considered to be easy relationships with useful definitions, they performed reasonably well. Notably, there are significantly fewer Google search results for Gene Ontology concepts than SNOMED CT concepts. This disparity may account for the difference in performance – fewer search results indicate a more difficult task for the worker. The number of Internet search results could serve as a method to assess which tasks are appropriate for the crowd. These results suggest that the crowd fits better as an expert assistant, helping experts with their verification by completing the easy tasks and allowing experts to focus on the difficult tasks, rather than an expert replacement

Entity-centric knowledge discovery for idiosyncratic domains

Technical and scientific knowledge is produced at an ever-accelerating pace, leading to increasing issues when trying to automatically organize or process it, e.g., when searching for relevant prior work. Knowledge can today be produced both in unstructured (plain text) and structured (metadata or linked data) forms. However, unstructured content is still themost dominant formused to represent scientific knowledge. In order to facilitate the extraction and discovery of relevant content, new automated and scalable methods for processing, structuring and organizing scientific knowledge are called for. In this context, a number of applications are emerging, ranging fromNamed Entity Recognition (NER) and Entity Linking tools for scientific papers to specific platforms leveraging information extraction techniques to organize scientific knowledge. In this thesis, we tackle the tasks of Entity Recognition, Disambiguation and Linking in idiosyncratic domains with an emphasis on scientific literature. Furthermore, we study the related task of co-reference resolution with a specific focus on named entities. We start by exploring Named Entity Recognition, a task that aims to identify the boundaries of named entities in textual contents. We propose a newmethod to generate candidate named entities based on n-gram collocation statistics and design several entity recognition features to further classify them. In addition, we show how the use of external knowledge bases (either domain-specific like DBLP or generic like DBPedia) can be leveraged to improve the effectiveness of NER for idiosyncratic domains. Subsequently, we move to Entity Disambiguation, which is typically performed after entity recognition in order to link an entity to a knowledge base. We propose novel semi-supervised methods for word disambiguation leveraging the structure of a community-based ontology of scientific concepts. Our approach exploits the graph structure that connects different terms and their definitions to automatically identify the correct sense that was originally picked by the authors of a scientific publication. We then turn to co-reference resolution, a task aiming at identifying entities that appear using various forms throughout the text. We propose an approach to type entities leveraging an inverted index built on top of a knowledge base, and to subsequently re-assign entities based on the semantic relatedness of the introduced types. Finally, we describe an application which goal is to help researchers discover and manage scientific publications. We focus on the problem of selecting relevant tags to organize collections of research papers in that context. We experimentally demonstrate that the use of a community-authored ontology together with information about the position of the concepts in the documents allows to significantly increase the precision of tag selection over standard methods

Robust Entity Linking in Heterogeneous Domains

Entity Linking is the task of mapping terms in arbitrary documents to entities in a knowledge base by identifying the correct semantic meaning. It is applied in the extraction of structured data in RDF (Resource Description Framework) from textual documents, but equally so in facilitating artificial intelligence applications, such as Semantic Search, Reasoning and Question and Answering. Most existing Entity Linking systems were optimized for specific domains (e.g., general domain, biomedical domain), knowledge base types (e.g., DBpedia, Wikipedia), or document structures (e.g., tables) and types (e.g., news articles, tweets). This led to very specialized systems that lack robustness and are only applicable for very specific tasks. In this regard, this work focuses on the research and development of a robust Entity Linking system in terms of domains, knowledge base types, and document structures and types. To create a robust Entity Linking system, we first analyze the following three crucial components of an Entity Linking algorithm in terms of robustness criteria: (i) the underlying knowledge base, (ii) the entity relatedness measure, and (iii) the textual context matching technique. Based on the analyzed components, our scientific contributions are three-fold. First, we show that a federated approach leveraging knowledge from various knowledge base types can significantly improve robustness in Entity Linking systems. Second, we propose a new state-of-the-art, robust entity relatedness measure for topical coherence computation based on semantic entity embeddings. Third, we present the neural-network-based approach Doc2Vec as a textual context matching technique for robust Entity Linking. Based on our previous findings and outcomes, our main contribution in this work is DoSeR (Disambiguation of Semantic Resources). DoSeR is a robust, knowledge-base-agnostic Entity Linking framework that extracts relevant entity information from multiple knowledge bases in a fully automatic way. The integrated algorithm represents a collective, graph-based approach that utilizes semantic entity and document embeddings for entity relatedness and textual context matching computation. Our evaluation shows, that DoSeR achieves state-of-the-art results over a wide range of different document structures (e.g., tables), document types (e.g., news documents) and domains (e.g., general domain, biomedical domain). In this context, DoSeR outperforms all other (publicly available) Entity Linking algorithms on most data sets

Conceptual Representations for Computational Concept Creation

Computational creativity seeks to understand computational mechanisms that can be characterized as creative. The creation of new concepts is a central challenge for any creative system. In this article, we outline different approaches to computational concept creation and then review conceptual representations relevant to concept creation, and therefore to computational creativity. The conceptual representations are organized in accordance with two important perspectives on the distinctions between them. One distinction is between symbolic, spatial and connectionist representations. The other is between descriptive and procedural representations. Additionally, conceptual representations used in particular creative domains, such as language, music, image and emotion, are reviewed separately. For every representation reviewed, we cover the inference it affords, the computational means of building it, and its application in concept creation.Peer reviewe

Injecting Inductive Biases into Distributed Representations of Text

Distributed real-valued vector representations of text (a.k.a. embeddings), learned by neural networks, encode various (linguistic) knowledge. To encode this knowledge into the embeddings the common approach is to train a large neural network on large corpora. There is, however, a growing concern regarding the sustainability and rationality of pursuing this approach further. We depart from the mainstream trend and instead, to incorporate the desired properties into embeddings, use inductive biases. First, we use Knowledge Graphs (KGs) as a data-based inductive bias to derive the semantic representation of words and sentences. The explicit semantics that is encoded in a structure of a KG allows us to acquire the semantic representations without the need of employing a large amount of text. We use graph embedding techniques to learn the semantic representation of words and the sequence-to-sequence model to learn the semantic representation of sentences. We demonstrate the efficacy of the inductive bias for learning embeddings for rare words and the ability of sentence embeddings to encode topological dependencies that exist between entities of a KG. Then, we explore the amount of information and sparsity as two key (data-agnostic) inductive biases to regulate the utilisation of the representation space. We impose these properties with Variational Autoencoders (VAEs). First, we regulate the amount of information encoded in a sentence embedding via constraint optimisation of a VAE objective function. We show that increasing amount of information allows to better discriminate sentences. Afterwards, to impose distributed sparsity we design a state-of-the-art Hierarchical Sparse VAE with a flexible posterior which captures the statistical characteristics of text effectively. While sparsity, in general, has desired computational and statistical representational properties, it is known to compensate task performance. We illustrate that with distributed sparsity, task performance could be maintained or even improved. The findings of the thesis advocate further development of inductive biases that could mitigate the dependence of representation learning quality on large data and model sizes

Ontology-based information extraction from learning management systems

In this work we present a system for information extraction from Learning Management Systems. This system is ontology-based. It retrieves information according to the structure of the ontology to populate the ontology. We graphically present statistics about the ontology data. These statistics present latent knowledge which is difficult to see in the traditional Learning Management System. To answer questions about the ontology, a question answering system was developed using Natural Language Processing in the conversion of the natural language question into an ontology query language; Sumário: Extração de Informação de Sistemas de Gestão para Educação Usando Ontologias Neste dissertação apresentamos um sistema de extracção de informação de sistemas de gestão para educação (Learning Management Systems). Este sistema é baseado em ontologias e extrai informação de acordo com a estrutura da ontologia para a popular. Também permite apresentar graficamente algumas estatísticas sobre os dados da ontologia. Estas estatísticas revelam o conhecimento latente que é difícil de ver num sistema tradicional de gestão para a educação. Para poder responder a perguntas sobre os dados da ontologia, um sistema de resposta automática a perguntas em língua natural foi desenvolvido usando Processamento de Língua Natural para converter as perguntas para linguagem de interrogação de ontologias