Similarity Types Research Articles

MFIB 2.0: a major update of the database of protein complexes formed by mutual folding of the constituting protein chains

Abstract While the majority of proteins with available structures are able to fold independently and mediate interactions only after acquiring their folded state, a subset of the known protein complexes contains protein chains that are intrinsically disordered in isolation. The Mutual Folding Induced by Binding (MFIB) database collects and classifies protein complexes, wherein all constituent protein chains would be unstable/disordered in isolation but fold into a well-defined 3D complex structure upon binding. This phenomenon is often termed as cooperative folding and binding or mutual synergistic folding (MSF). Here we present a major update to the database: we collected and annotated hundreds of new protein complexes fulfilling the criteria of MSF, leading to an almost six-fold increase in the size of the database. Many novel features have also been introduced, such as clustering of the complexes based on structural similarity and domain types, assigning different evidence levels to each entry and adding the evidence coverage label that allowed us to include complexes of multi(sub)domain monomers with partial MSF. The MFIB 2.0 database is available at https://mfib.pbrg.hu.

Research on Intelligent Design of Geometric Factor Encoding for Aircraft Engine Turbine Structures

In recent years, with the rapid development of computer technology and artificial intelligence design technology, multiple possible design solutions can be quickly generated by transforming the experience and knowledge of structural design into computer executable rules and algorithms. To achieve intelligent design of aircraft engines, this paper proposes an encoding model for the turbine rotor structure of aircraft engines using geometric encoding technology. The turbine rotor structure of aircraft engines is divided into several units according to geometric similarity types, these units continue to be divided into attribute sets according to their functional types, connection relationships, and material properties. These attribute sets can be encoded using geometric encoding technology. The experiment simulated that these codes, for the point cloud modeling of turbine rotor structure, can be quickly achieved and they combine various algorithms to display the point cloud model of the turbine rotor in the Microsoft Visual studio MFC class library. The results show that by creating geometric codes for the turbine rotor of aircraft engines, it is possible to quickly create and display point cloud models of the turbine rotor structure, laying the foundation for subsequent application of machine learning to solve and find the optimal design solution.

A Malicious Information Traceability Model Based on Neighborhood Similarity and Multiple Types of Interaction

A Malicious Information Traceability Model Based on Neighborhood Similarity and Multiple Types of Interaction

Parasocial interactions with media characters: the role of perceived and actual sociodemographic and psychological similarity.

Similarity between media character and viewer is an important predictor of parasocial interactions. Thereby, similarities are often limited to single characteristics or to the similarities viewers perceive between themselves and characters. This article expands the existing literature in two ways. First, the effects of actual and perceived similarity on parasocial interactions are compared. Second, similarity is understood in a broad way. With age, gender, job, relationship, and living situation are assessed for sociodemographic similarities. Psychological similarities are considered with the Big Five personality traits, loneliness, and self-esteem. The study employs a multimethod design with a field study using tracking data, experience sampling surveys, and content analysis. With the content analysis, characters' characteristics can be indicated independent from the viewers to assess actual similarity in a more objective way. In these everyday viewing settings, parasocial interactions increased with similarities in extraversion and perceived Big Five traits and decreased with similarities in age and consciousness. The other assessed similarity types did not influence parasocial interactions. Taken together, the study underlines the importance of differentiating between actual and perceived similarity when analyzing viewer PSI with media characters, and to specify the particular type of similarity.

Forest Land Quality Evaluation and the Protection Zoning of Subtropical Humid Evergreen Broadleaf Forest Region Based on the PSO-TOPSIS Model and the Local Indicator of Spatial Association: A Case Study of Hefeng County, Hubei Province, China

Forest land is the carrier for growing forests. It is of great significance to evaluate the forest land quality scientifically and delineate forestland protection zones reasonably for realizing better forest land management, promoting ecological civilization construction, and coping with global climate change. In this study, taking Hefeng County, Hubei Province, a subtropical humid evergreen broad-leaved forest region in China, as the study area, 14 indicators were selected from four dimensions—climatic conditions, terrain, soil conditions, and socioeconomics—to construct a forest land quality evaluation index system. Based on the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) model, we introduced the Particle Swarm Optimization (PSO) algorithm to design the evaluation model to evaluate the forest land quality and analyze the distribution of forest land quality in Hefeng. Further, we used the Local Indicator of Spatial Association (LISA) to explore the spatial distribution of forest land quality and delineate the forest land protection zones. The results showed the following: (1) the overall quality of forest land was high, with some variability between regions. The range of Forest Land Quality Index (FLQI) in Hefeng was 0.4091–0.8601, with a mean value of 0.6337. The forest land quality grades were mainly first and second grade, with the higher-grade forest land mainly distributed in the central and southeastern low mountain regions of Zouma, Wuli, and Yanzi. The lower-grade forest land was mainly distributed in the northwestern middle and high mountain regions of Zhongying, Taiping, and Rongmei. (2) The global spatial autocorrelation index of forest land quality in Hefeng County was 0.7562, indicating that the forest land quality in the county had a strong spatial similarity. The spatial distribution of similarity types high-high (HH) and low-low (LL) was more clustered, while the spatial distribution of dissimilarity types high-low (HL) and low-high (LH) was generally dispersed. (3) Based on the LISA of forest land quality, forest land protection zones were divided into three types: key protection zones (KPZs), active protection zones (APZs), and general protection zones (GPZs). The forest land protection zoning basically coincided with the forest land quality. Combining the characteristics of self-correlated types in different forestland protection zones, corresponding management and protection measures were proposed. This showed that the PSO-TOPSIS model can be effectively used for forest land quality evaluation. At the same time, the spatial attributes of forest land were incorporated into the development of forest land protection zoning scheme, which expands the method of forest land protection zoning, and can provide a scientific basis and methodological reference for the reasonable formulation of forest land use planning in Hefeng County, while also serving as a reference for similar regions and countries.

Students' difficulties in similar triangle questions

Similar triangles in questions are usually given as separate, adjacent or overlapped. Furthermore, similarity types such as Side-Angle-Side (S.A.S.), Side-Side-Side (S.S.S.) and Angle-Angle (A.A.) are requested in the questions. Students have more trouble in other types of questions. The purpose of this study is to investigate the difficulties of students about similar triangles and the reasons for these difficulties. This research was carried out with the case study method, which is one of the qualitative research approaches. The study was conducted with 55 Science High School 9th grade students and 9 open-ended questions were used to examine students' knowledge about “similarity in triangles”. Furthermore, 5 students were interviewed to find out the reasons for their solutions. Descriptive analysis method was used to analyze the data. As a result, it can be concluded that students have difficulties mostly in overlapped triangles and Angle-Angle type questions. On the other hand, it can be concluded that students are quite successful where similar triangles are given separately. In the light of the findings obtained in this study, it can be advised for lecturers to focus on the questions where similar triangles are overlapped while explaining the similarity in the triangle.
 Keywords: Similarity, Triangles, Difficulties, High School Students.

Phenotypically Similar Rare Disease Identification from an Integrative Knowledge Graph for Data Harmonization: Preliminary Study.

BackgroundAlthough many efforts have been made to develop comprehensive disease resources that capture rare disease information for the purpose of clinical decision making and education, there is no standardized protocol for defining and harmonizing rare diseases across multiple resources. This introduces data redundancy and inconsistency that may ultimately increase confusion and difficulty for the wide use of these resources. To overcome such encumbrances, we report our preliminary study to identify phenotypical similarity among genetic and rare diseases (GARD) that are presenting similar clinical manifestations, and support further data harmonization.ObjectiveTo support rare disease data harmonization, we aim to systematically identify phenotypically similar GARD diseases from a disease-oriented integrative knowledge graph and determine their similarity types.MethodsWe identified phenotypically similar GARD diseases programmatically with 2 methods: (1) We measured disease similarity by comparing disease mappings between GARD and other rare disease resources, incorporating manual assessment; 2) we derived clinical manifestations presenting among sibling diseases from disease classifications and prioritized the identified similar diseases based on their phenotypes and genotypes.ResultsFor disease similarity comparison, approximately 87% (341/392) identified, phenotypically similar disease pairs were validated; 80% (271/392) of these disease pairs were accurately identified as phenotypically similar based on similarity score. The evaluation result shows a high precision (94%) and a satisfactory quality (86% F measure). By deriving phenotypical similarity from Monarch Disease Ontology (MONDO) and Orphanet disease classification trees, we identified a total of 360 disease pairs with at least 1 shared clinical phenotype and gene, which were applied for prioritizing clinical relevance. A total of 662 phenotypically similar disease pairs were identified and will be applied for GARD data harmonization.ConclusionsWe successfully identified phenotypically similar rare diseases among the GARD diseases via 2 approaches, disease mapping comparison and phenotypical similarity derivation from disease classification systems. The results will not only direct GARD data harmonization in expanding translational science research but will also accelerate data transparency and consistency across different disease resources and terminologies, helping to build a robust and up-to-date knowledge resource on rare diseases.

C443: a Methodology to See a Forest for the Trees

Often tree-based accounts of statistical learning problems yield multiple decision trees which together constitute a forest. Reasons for this include examining tree instability, improving prediction accuracy, accounting for missingness in the data, and taking into account multiple outcome variables. A key disadvantage of forests, unlike individual decision trees, is their lack of transparency. Hence, an obvious challenge is whether it is possible to recover some of the insightfulness of individual trees from a forest. In this paper, we will propose a conceptual framework and methodology to do so by reducing forests into one or a small number of summary trees, which may be used to gain insight into the central tendency as well as the heterogeneity of the forest. This is done by clustering the trees in the forest based on similarities between them. By means of simulated data, we will demonstrate how and why different similarity types in the proposed methodology may lead to markedly different conclusions, and explain when and why certain approaches may be recommended over other ones. We will finally illustrate the methodology with an empirical data set on the prediction of cocaine use on the basis of personality characteristics.

Using Graduation to Modify the Estimation of Lee–Carter Model for Small Populations

Many mortality models, such as the Lee–Carter model, have unsatisfactory estimation in the case of small populations. Increasing population size is a natural choice to stabilize the estimation, if we can find a larger reference population that has a mortality profile similar to that of the small population. Aggregating historical data of the small populations is a fine candidate for the reference population. However, it is often not feasible in practice and we need to rely on other reference populations. In this study, we explore whether graduation methods can be used if the mortality profile of a small population differs from that of the reference population. To explore the appropriate occasion to use graduation methods, we create several mortality scenarios and similarity types between small and reference populations. We propose combining the graduation methods and mortality models, either graduating mortality rates first or applying the mortality model first, and determine whether they can improve the model fit. We use computer simulation to determine whether the proposed approach has better mortality estimation than the Lee–Carter model and the the Li–Lee model. We found that the Li–Lee model always has smaller estimation errors than the Lee–Carter model, and the proposed approach has smaller estimation errors than the Li–Lee model in most cases.

Learning in complex, multi-component cognitive systems: Different learning challenges within the same system.

Using word learning as an example of a complex system, we investigated how differences in the structure of the subcomponents in which learning occurs can have significant consequences for the challenge of integrating new information within such systems. Learning a new word involves integrating information into the two key stages/subcomponents of processing within the word production system. In the first stage, multiple semantic features are mapped onto a single word. Conversely, in the second stage, a single word is mapped onto multiple segmental features. We tested whether the unitary goal of word learning leads to different local outcomes in these two stages because of their reversed mapping patterns. Neurotypical individuals (N = 17) learned names and semantic features for pictures of unfamiliar objects presented in semantically related, segmentally related and unrelated blocks. Both similarity types interfered with word learning. However, feature learning was differentially affected within the two subcomponents of word production. Semantic similarity facilitated learning distinctive semantic features (i.e., features unique to each item), whereas segmental similarity facilitated learning shared segmental features (i.e., features common to several items in a block). These results are compatible with an incremental learning model in which learning not only strengthens certain associations but also weakens others according to the local goals of each subcomponent. More generally, they demonstrate that the same overall learning goal can lead to opposite learning outcomes in the subcomponents of a complex system. The general principles uncovered may extend beyond word learning to other complex systems with multiple subcomponents. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

On Fedorov's parallelohedra - a review and new results

After a short introduction to the topic of Fedorov's parallelohedra, the fundamentals of this topic are reviewed in sections 2 and 3. The cone of positive-definite quadratic forms is described in section 4 where also new results on its shape are given. In the following sections aggregates of parallelohedra having certain properties are investigated and their connected domains in the cone of quadratic forms are determined. Results on combinatorial types of parallelohedra and their refined classification into contraction and similarity types are summarized in section 5. New results on Σ- and Ω-domains are discussed in sections 6 and 7, respectively.

Why are these similar? Investigating item similarity types in a large digital library

We introduce a new problem, identifying the type of relation that holds between a pair of similar items in a digital library. Being able to provide a reason why items are similar has applications in recommendation, personalization, and search. We investigate the problem within the context of Europeana, a large digital library containing items related to cultural heritage. A range of types of similarity in this collection were identified. A set of 1,500 pairs of items from the collection were annotated using crowdsourcing. A high intertagger agreement (average 71.5 Pearson correlation) was obtained and demonstrates that the task is well defined. We also present several approaches to automatically identifying the type of similarity. The best system applies linear regression and achieves a mean Pearson correlation of 71.3, close to human performance. The problem formulation and data set described here were used in a public evaluation exercise, the *SEM shared task on Semantic Textual Similarity. The task attracted the participation of 6 teams, who submitted 14 system runs. All annotations, evaluation scripts, and system runs are freely available.

Partitions of [formula omitted] and completely ultrametrizable spaces

We prove that, for every n, the topological space ωnω (where ωn has the discrete topology) can be partitioned into ℵn copies of the Baire space. Using this fact, we then prove two new theorems about completely ultrametrizable spaces. We say that Y is a condensation of X if there is a continuous bijection f:X→Y. First, it is proved that ωω is a condensation of ωnω if and only if ωω can be partitioned into ℵn Borel sets, and some consistency results are given regarding such partitions. It is also proved that it is consistent with ZFC that, for any n<ω, c=ωn and there are exactly n+3 similarity types of perfect completely ultrametrizable spaces of size c. These results answer two questions of the first author from [1].

Elementary theory of similarity and its application in biology and geography: Multiple-site measures of similarity and dissimilarity

A system of axioms of multiple-site similarity measures is considered that is defined on a series of finite descriptive sets. The concept of equivalence of multiple-site similarity measures is proposed. Equivalence classes of multiple-site similarity measures are distinguished. For linear fractional multiple-site similarity measures, types and subtypes are distinguished. A new concept of the consistency of equivalence classes of multiple-site similarity measures is introduced on different-cardinality sequences of series of descriptive sets. Illustrative examples of multiple-site similarity measures are taken from biology and geography.

Categories of partial algebras for critical points between varieties of algebras

We denote by Conc A the $${(\vee, 0)}$$ -semilattice of all finitely generated congruences of an algebra A. A lifting of a $${(\vee, 0)}$$ -semilattice S is an algebra A such that $${S \cong {\rm Con}_{\rm c} A}$$ . The assignment Conc can be extended to a functor. The notion of lifting is generalized to diagrams of $${(\vee, 0)}$$ -semilattices. A gamp is a partial algebra endowed with a partial subalgebra together with a semilattice-valued distance; gamps form a category that lends itself to a universal algebraic-type study. The raison d’être of gamps is that any algebra can be approximated by its finite subgamps, even in case it is not locally finite. Let $${\mathcal{V}}$$ and $${\mathcal{W}}$$ be varieties of algebras (on finite, possibly distinct, similarity types). Let P be a finite lattice. We assume the existence of a combinatorial object, called an $${\aleph_0}$$ -lifter of P, of infinite cardinality $${\lambda}$$ . Let $${\vec{A}}$$ be a P-indexed diagram of finite algebras in $${\mathcal{V}}$$ . If $${{\rm Con}_{\rm c} \circ \vec{A}}$$ has no partial lifting in the category of gamps of $${\mathcal{W}}$$ , then there is an algebra $${A \in \mathcal{V}}$$ of cardinality $${\lambda}$$ such that Conc A is not isomorphic to Conc B for any $${B \in \mathcal{W}}$$ . This makes it possible to generalize several known results. In particular, we prove the following theorem, without assuming that $${\mathcal{W}}$$ is locally finite. Let $${\mathcal{V}}$$ be locally finite and let $${\mathcal{W}}$$ be congruence-proper (i.e., congruence lattices of infinite members of $${\mathcal{W}}$$ are infinite). The following equivalence holds. Every countable $${(\vee, 0)}$$ -semilattice with a lifting in $${\mathcal{V}}$$ has a lifting in $${\mathcal{W}}$$ if and only if every $${\omega}$$ -indexed diagram of finite $${(\vee, 0)}$$ -semilattices with a lifting in $${\mathcal{V}}$$ has a lifting in $${\mathcal{W}}$$ . Gamps are also applied to the study of congruence-preserving extensions. Let $${\mathcal{V}}$$ be a non-semidistributive variety of lattices and let n ≥ 2 be an integer. There is a bounded lattice $${A \in \mathcal{V}}$$ of cardinality $${\aleph_1}$$ with no congruence n-permutable, congruence-preserving extension. The lattice A is constructed as a condensate of a square-indexed diagram of lattices.

Entity Translation Mining from Comparable Corpora: Combining Graph Mapping with Corpus Latent Features

This paper addresses the problem of mining named entity translations from comparable corpora, specifically, mining English and Chinese named entity translation. We first observe that existing approaches use one or more of the following named entity similarity metrics: entity, entity context, and relationship. Motivated by this observation, we propose a new holistic approach by 1) combining all similarity types used and 2) additionally considering relationship context similarity between pairs of named entities, a missing quadrant in the taxonomy of similarity metrics. We abstract the named entity translation problem as the matching of two named entity graphs extracted from the comparable corpora. Specifically, named entity graphs are first constructed from comparable corpora to extract relationship between named entities. Entity similarity and entity context similarity are then calculated from every pair of bilingual named entities. A reinforcing method is utilized to reflect relationship similarity and relationship context similarity between named entities. We also discover features lost in the graph extraction process and integrate this into our framework. According to our experimental results, our holistic graph-based approach and its enhancement using corpus latent features are highly effective and our framework significantly outperforms previous approaches.

Analogical Transfer in EFL Reading Comprehension : The Roles of Similarity Types and Causality Between Texts

Analogical Transfer in EFL Reading Comprehension : The Roles of Similarity Types and Causality Between Texts

Trees, Ultrametrics, and Noncommutative Geometry

Noncommutative geometry is used to study the local geometry of ultrametric spaces and the geometry of trees at infinity. Connes’s example of the noncommutative space of Penrose tilings is interpreted as a non-Hausdorff orbit space of a compact, ultrametric space under the action of its local isometry group. This is generalized to compact, locally rigid, ultrametric spaces. The local isometry types and the local similarity types in those spaces can be analyzed using groupoid C∗-algebras. The concept of a locally rigid action of a countable group Γ on a compact, ultrametric space by local similarities is introduced. It is proved that there is a faithful unitary representation of Γ into the germ groupoid C∗-algebra of the action. The prototypical example is the standard action of Thompson’s group V on the ultrametric Cantor set. In this case, the C∗-algebra is the Cuntz algebra O2 and representations originally due to Birget and Nekrashevych are recovered. End spaces of trees are sources of ultrametric spaces. Some connections are made between locally rigid, ultrametric spaces and a concept in the theory of tree lattices of Bass and Lubotzky.

On the Fractional Collection Efficiencies of the Similarity Types of Cyclones for Steady and Pulsating Dust-Laden Gas Flow

On the Fractional Collection Efficiencies of the Similarity Types of Cyclones for Steady and Pulsating Dust-Laden Gas Flow

PubChem3D: Biologically relevant 3-D similarity

BackgroundThe use of 3-D similarity techniques in the analysis of biological data and virtual screening is pervasive, but what is a biologically meaningful 3-D similarity value? Can one find statistically significant separation between "active/active" and "active/inactive" spaces? These questions are explored using 734,486 biologically tested chemical structures, 1,389 biological assay data sets, and six different 3-D similarity types utilized by PubChem analysis tools.ResultsThe similarity value distributions of 269.7 billion unique conformer pairs from 734,486 biologically tested compounds (all-against-all) from PubChem were utilized to help work towards an answer to the question: what is a biologically meaningful 3-D similarity score? The average and standard deviation for the six similarity measures STST-opt, CTST-opt, ComboTST-opt, STCT-opt, CTCT-opt, and ComboTCT-opt were 0.54 ± 0.10, 0.07 ± 0.05, 0.62 ± 0.13, 0.41 ± 0.11, 0.18 ± 0.06, and 0.59 ± 0.14, respectively. Considering that this random distribution of biologically tested compounds was constructed using a single theoretical conformer per compound (the "default" conformer provided by PubChem), further study may be necessary using multiple diverse conformers per compound; however, given the breadth of the compound set, the single conformer per compound results may still apply to the case of multi-conformer per compound 3-D similarity value distributions. As such, this work is a critical step, covering a very wide corpus of chemical structures and biological assays, creating a statistical framework to build upon.The second part of this study explored the question of whether it was possible to realize a statistically meaningful 3-D similarity value separation between reputed biological assay "inactives" and "actives". Using the terminology of noninactive-noninactive (NN) pairs and the noninactive-inactive (NI) pairs to represent comparison of the "active/active" and "active/inactive" spaces, respectively, each of the 1,389 biological assays was examined by their 3-D similarity score differences between the NN and NI pairs and analyzed across all assays and by assay category types. While a consistent trend of separation was observed, this result was not statistically unambiguous after considering the respective standard deviations. While not all "actives" in a biological assay are amenable to this type of analysis, e.g., due to different mechanisms of action or binding configurations, the ambiguous separation may also be due to employing a single conformer per compound in this study. With that said, there were a subset of biological assays where a clear separation between the NN and NI pairs found. In addition, use of combo Tanimoto (ComboT) alone, independent of superposition optimization type, appears to be the most efficient 3-D score type in identifying these cases.ConclusionThis study provides a statistical guideline for analyzing biological assay data in terms of 3-D similarity and PubChem structure-activity analysis tools. When using a single conformer per compound, a relatively small number of assays appear to be able to separate "active/active" space from "active/inactive" space.