Types Of Background Knowledge Research Articles

Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation.

Biological background knowledge plays an important role in the manual quality assurance (QA) of biological database records. One such QA task is the detection of inconsistencies in literature-based Gene Ontology Annotation (GOA). This manual verification ensures the accuracy of the GO annotations based on a comprehensive review of the literature used as evidence, Gene Ontology (GO) terms, and annotated genes in GOA records. While automatic approaches for the detection of semantic inconsistencies in GOA have been developed, they operate within predetermined contexts, lacking the ability to leverage broader evidence, especially relevant domain-specific background knowledge. This paper investigates various types of background knowledge that could improve the detection of prevalent inconsistencies in GOA. In addition, the paper proposes several approaches to integrate background knowledge into the automatic GOA inconsistency detection process. We have extended a previously developed GOA inconsistency dataset with several kinds of GOA-related background knowledge, including GeneRIF statements, biological concepts mentioned within evidence texts, GO hierarchy and existing GO annotations of the specific gene. We have proposed several effective approaches to integrate background knowledge as part of the automatic GOA inconsistency detection process. The proposed approaches can improve automatic detection of self-consistency and several of the most prevalent types of inconsistencies. https://github.com/jiyuc/de-inconsistency.

Semi-supervised clustering with two types of background knowledge: Fusing pairwise constraints and monotonicity constraints

This study addresses the problem of performing clustering in the presence of two types of background knowledge: pairwise constraints and monotonicity constraints. Pairwise constraint relate pair of instances, indicating if they must or must not belong to the same cluster, while monotonicity constraints impose and order relationship between the cluster labels, and are applied to the dataset globally. To fuse these to types of background knowledge, the formal framework to perform clustering under monotonicity constraints is, firstly, defined, resulting in a specific distance measure. Pairwise constraints are integrated afterwards by designing an objective function which combines the proposed distance measure and a pairwise constraint-based penalty term, in order to fuse both types of information. This objective function can be optimized with an EM optimization scheme. The proposed method serves as the first approach to the problem it addresses, as it is the first method designed to work with the two types of background knowledge mentioned above. Our proposal is tested with previous approaches from different clustering paradigms in monotonic datasets, including a real-world case of study. Bayesian statistical tests are used to provide empirical evidence in favor of our proposal, and fund subsequent conclusions: the proposed method can be used obtain better results than previous approaches within the monotonic constrained clustering paradigm.

Score-Based Learning of Graphical Event Models with Background Knowledge Augmentation

Graphical event models (GEMs) are representations of temporal point process dynamics between different event types. Many real-world applications however involve limited event stream data, making it challenging to learn GEMs from data alone. In this paper, we introduce approaches that can work together in a score-based learning paradigm, to augment data with potentially different types of background knowledge. We propose novel scores for learning an important parametric class of GEMs; in particular, we propose a Bayesian score for leveraging prior information as well as a more practical simplification that involves fewer parameters, analogous to Bayesian networks. We also introduce a framework for incorporating easily assessed qualitative background knowledge from domain experts, in the form of statements such as `event X depends on event Y' or `event Y makes event X more likely'. The proposed framework has Bayesian interpretations and can be deployed by any score-based learner. Through an extensive empirical investigation, we demonstrate the practical benefits of background knowledge augmentation while learning GEMs for applications in the low-data regime.

Optical Medieval Music Recognition Using Background Knowledge

This paper deals with the effect of exploiting background knowledge for improving an OMR (Optical Music Recognition) deep learning pipeline for transcribing medieval, monophonic, handwritten music from the 12th–14th century, whose usage has been neglected in the literature. Various types of background knowledge about overlapping notes and text, clefs, graphical connections (neumes) and their implications on the position in staff of the notes were used and evaluated. Moreover, the effect of different encoder/decoder architectures and of different datasets for training a mixed model and for document-specific fine-tuning based on an extended OMR pipeline with an additional post-processing step were evaluated. The use of background models improves all metrics and in particular the melody accuracy rate (mAR), which is based on the insert, delete and replace operations necessary to convert the generated melody into the correct melody. When using a mixed model and evaluating on a different dataset, our best model achieves without fine-tuning and without post-processing a mAR of 90.4%, which is raised by nearly 30% to 93.2% mAR using background knowledge. With additional fine-tuning, the contribution of post-processing is even greater: the basic mAR of 90.5% is raised by more than 50% to 95.8% mAR.

Being a Patient Representative Is More Work Than Being a Patient Advocate-Done Right, It Is Also Likely to Be More Effective.

For a patient to be effective as a “patient representative” within a health-related organization, work and more than just accepting an honorific title is required. I argue that for a patient to be most effective as a patient representative requires different types of background knowledge and commitment than being a “patient advocate”. Patients need to be cautious about how, when, and where they take on an official role of either an “advocate” or “representative”, if they truly want to be a positive influence on health outcomes.

High-Precision Soil Moisture Mapping Based on Multi-Model Coupling and Background Knowledge, Over Vegetated Areas Using Chinese GF-3 and GF-1 Satellite Data

This paper proposes a combined approach comprising a set of methods for the high-precision mapping of soil moisture in a study area located in Jiangsu Province of China, based on the Chinese C-band synthetic aperture radar data of GF-3 and high spatial-resolution optical data of GF-1, in situ experimental datasets and background knowledge. The study was conducted in three stages: First, in the process of eliminating the effect of vegetation canopy, an empirical vegetation water content model and a water cloud model with localized parameters were developed to obtain the bare soil backscattering coefficient. Second, four commonly used models (advanced integral equation model (AIEM), look-up table (LUT) method, Oh model, and the Dubois model) were coupled to acquire nine soil moisture retrieval maps and algorithms. Finally, a simple and effective optimal solution method was proposed to select and combine the nine algorithms based on classification strategies devised using three types of background knowledge. A comprehensive evaluation was carried out on each soil moisture map in terms of the root-mean-square-error (RMSE), Pearson correlation coefficient (PCC), mean absolute error (MAE), and mean bias (bias). The results show that for the nine individual algorithms, the estimated model constructed using the AIEM (mv1) was significantly more accurate than those constructed using the other models (RMSE = 0.0321 cm³/cm³, MAE = 0.0260 cm³/cm³, and PCC = 0.9115), followed by the Oh model (m_v5) and LUT inversion method under HH polarization (mv2). Compared with the independent algorithms, the optimal solution methods have significant advantages; the soil moisture map obtained using the classification strategy based on the percentage content of clay was the most satisfactory (RMSE = 0.0271 cm³/cm³, MAE = 0.0225 cm³/cm³, and PCC = 0.9364). This combined method could not only effectively integrate the optical and radar satellite data but also couple a variety of commonly used inversion models, and at the same time, background knowledge was introduced into the optimal solution method. Thus, we provide a new method for the high-precision mapping of soil moisture in areas with a complex underlying surface.

Students and evaluation of web-based misinformation about vaccination: critical reading or passive acceptance of claims?

ABSTRACTWith the advent of Web 2.0 media, there is a greater prevalence of science misinformation available to the public. This issue is particularly problematic for novices who often believe that science in the media is factual and objective, even though an expected outcome of secondary education is to develop students’ abilities to critically evaluate information. By conducting cognitive Think Alouds and retrospective interviews with high school students, this study examined (1) their stances towards flawed claims in a Web media article about vaccination, (2) types of background knowledge used to make their assessments, and (3) responses when asked directly to critique the claims. Results of qualitative coding indicated that students who were most critical of the claims based their evaluation on knowledge of appropriate scientific reasoning and literacy skills. In contrast, students who accepted the claims relied on novice-level content knowledge, or a flawed understanding of scientific reasoning. Lastly, some students initially accepted the claims became critical in retrospect when explicitly asked to critique the article during the interview phase. Findings from this investigation suggest a need for more opportunities for students to critique science information, and a greater curricular emphasis on teaching evaluation skills and knowledge of valid scientific reasoning.

Formal Concept Analysis with Constraints by EM Operators

Formal concept analysis is a method of exploratory data analysisthat aims at the extraction of natural cluster from object-attributedata tables. We present a way to add user's background knowledge toformal concept analysis. The type of background knowledge we dealwith relates to relative importance of attributes in the input data.We introduce EM operators which constrain in attributes of formalconcept analysis. The main aim is to make extraction of conceptsfrom the input data more focused by taking into account thebackground knowledge. Particularly, only concepts which arecompatible with the constraint are extracted from data. Therefore,the number of extracted concepts becomes smaller since we leave outnon-interesting concepts. We concentrate on foundational aspectssuch as mathematical feasibility and computational tractability.

Partial k-Anonymity for Privacy-Preserving Social Network Data Publishing

With the popularity of social networks, privacy issues with regard to publishing social network data have gained intensive focus from academia. We analyzed the current privacy-preserving techniques for publishing social network data and defined a privacy-preserving model with privacy guarantee [Formula: see text]. With our definitions, the existing privacy-preserving methods, [Formula: see text]-anonymity and randomization can be combined together to protect data privacy. We also considered the privacy threat with label information and modify the [Formula: see text]-anonymity technique of tabular data to protect the published data from being attacked by the combination of two types of background knowledge, the structural and label knowledge. We devised a partial [Formula: see text]-anonymity algorithm and implemented it in Python and open source packages. We compared the algorithm with related [Formula: see text]-anonymity and random techniques on three real-world datasets. The experimental results show that the partial [Formula: see text]-anonymity algorithm preserves more data utilities than the [Formula: see text]-anonymity and randomization algorithms.

Using ontologies to model human navigation behavior in information networks: A study based on Wikipedia.

The need to examine the behavior of different user groups is a fundamental requirement when building information systems. In this paper, we present Ontology-based Decentralized Search (OBDS), a novel method to model the navigation behavior of users equipped with different types of background knowledge. Ontology-based Decentralized Search combines decentralized search, an established method for navigation in social networks, and ontologies to model navigation behavior in information networks. The method uses ontologies as an explicit representation of background knowledge to inform the navigation process and guide it towards navigation targets. By using different ontologies, users equipped with different types of background knowledge can be represented. We demonstrate our method using four biomedical ontologies and their associated Wikipedia articles. We compare our simulation results with base line approaches and with results obtained from a user study. We find that our method produces click paths that have properties similar to those originating from human navigators. The results suggest that our method can be used to model human navigation behavior in systems that are based on information networks, such as Wikipedia. This paper makes the following contributions: (i) To the best of our knowledge, this is the first work to demonstrate the utility of ontologies in modeling human navigation and (ii) it yields new insights and understanding about the mechanisms of human navigation in information networks.

Grammatically biased learning: Learning logic programs using an explicit antecedent description language

Every concept learning system produces hypotheses that are written in some sort of constrained language called the concept description language, and for most learning systems, the concept description language is fixed. This paper describes a learning system that makes a large part of the concept description language an explicit input, and discusses some of the possible applications of providing this additional input. In particular, we discuss a technique for learning a logic program such that the antecedent of each clause in the program can be generated by a special antecedent description language; it is shown that this technique can be used to make use of many different types of background knowledge, including constraints on how predicates can be used, programming clichés, overgeneral theories, incomplete theories, and theories syntactically close to the target theory. The approach thus unifies many of the problems previously studied in the field of knowledge-based learning.