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17 pages, 351 KB  
Article
Christ Jesus as Object of Cultic Worship in Philippians 3:3b: A Linguistic Study
by Jose Luis Dizon
Religions 2025, 16(9), 1100; https://doi.org/10.3390/rel16091100 - 26 Aug 2025
Viewed by 880
Abstract
The grammar and syntax of Philippians 3.3 presents a number of ambiguities, particularly in terms of the grammatical object of the verb “worship” (Gk. λατρεύοντες). Most modern translations render the middle phrase of the verse as “worship by the Spirit of God and [...] Read more.
The grammar and syntax of Philippians 3.3 presents a number of ambiguities, particularly in terms of the grammatical object of the verb “worship” (Gk. λατρεύοντες). Most modern translations render the middle phrase of the verse as “worship by the Spirit of God and boast in Christ Jesus” (e.g., CSB, ESV, NLT, NRSV, RSV, etc.). This rendering implies an intransitive use of λατρεύοντες. However, the word order of the verse, as well as the parsing of λατρεύοντες, strongly suggest it is better to understand “Christ Jesus” as the grammatical object of the verb. This essay challenges the prevailing translation of the verse, and argues that the middle phrase should better be translated as “by the Spirit worship and boast in Christ Jesus,” to reflect the grammatical relation between “worship” and “Christ Jesus.” This re-rendering is highly significant for our understanding of Paul’s Christology, as well as contemporary debates over early vs. late high Christology, as it shows points towards Jesus being worshipped as a divine figure by the early Christians, even as early the lifetime of the Apostle. Full article
(This article belongs to the Special Issue Constructive Interdisciplinary Approaches to Pauline Theology)
18 pages, 712 KB  
Article
The Discussions of Monkeypox Misinformation on Social Media
by Or Elroy and Abraham Yosipof
Data 2025, 10(9), 137; https://doi.org/10.3390/data10090137 - 25 Aug 2025
Viewed by 915
Abstract
The global outbreak of the monkeypox virus was declared a health emergency by the World Health Organization (WHO). During such emergencies, misinformation about health suggestions can spread rapidly, leading to serious consequences. This study investigates the relationships between tweet readability, user engagement, and [...] Read more.
The global outbreak of the monkeypox virus was declared a health emergency by the World Health Organization (WHO). During such emergencies, misinformation about health suggestions can spread rapidly, leading to serious consequences. This study investigates the relationships between tweet readability, user engagement, and susceptibility to misinformation. Our conceptual model posits that tweet readability influences user engagement, which in turn affects the spread of misinformation. Specifically, we hypothesize that tweets with higher readability and grammatical correctness garner more user engagement and that misinformation tweets tend to be less readable than accurate information tweets. To test these hypotheses, we collected over 1.4 million tweets related to monkeypox discussions on X (formerly Twitter) and trained a semi-supervised learning classifier to categorize them as misinformation or not-misinformation. We analyzed the readability and grammar levels of these tweets using established metrics. Our findings indicate that readability and grammatical correctness significantly boost user engagement with accurate information, thereby enhancing its dissemination. Conversely, misinformation tweets are generally less readable, which reduces their spread. This study contributes to the advancement of knowledge by elucidating the role of readability in combating misinformation. Practically, it suggests that improving the readability and grammatical correctness of accurate information can enhance user engagement and consequently mitigate the spread of misinformation during health emergencies. These insights offer valuable strategies for public health communication and social media platforms to more effectively address misinformation. Full article
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7 pages, 771 KB  
Proceeding Paper
Dynamic Oral English Assessment System Based on Large Language Models for Learners
by Jiaqi Yu and Hafriza Binti Burhanudeen
Eng. Proc. 2025, 98(1), 32; https://doi.org/10.3390/engproc2025098032 - 7 Jul 2025
Viewed by 574
Abstract
The rapid development of science and technology enables technological innovations to change the way of English oral learning. Based on the use of a large language model (LLM), we developed a novel dynamic evaluation system for oral English, LLM-DAELSL, which combines daily oral [...] Read more.
The rapid development of science and technology enables technological innovations to change the way of English oral learning. Based on the use of a large language model (LLM), we developed a novel dynamic evaluation system for oral English, LLM-DAELSL, which combines daily oral habits and a textbook outline. The model integrates commonly used vocabulary from everyday social speech and authoritative prior knowledge, such as oral language textbooks. It also combines traditional large-scale semantic models with probabilistic algorithms to serve as an oral assessment tool for undergraduate students majoring in English-related fields in universities. The model provides corrective feedback to effectively enhance the proficiency of English learners through guided training at any time and place. The technological principle of the model involves inputting prior template knowledge into the language model for reverse guidance and utilizing the textbooks provided by China’s Ministry of Education. The model facilitates the practice and evaluation of pronunciation, grammar, vocabulary, and fluency. The six-month tracking results showed that the oral proficiency of the system learners was significantly improved in the four aspects, which provides a reference for other language learning method developments. Full article
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19 pages, 298 KB  
Perspective
Mitigating Enteric Methane Emissions: An Analysis of Emerging Media Frames and Consumer Narrative Tensions on Natural Solutions and Techno-Fixes
by Louise Manning, Adele Wylie and Michael K. Goodman
Sustainability 2025, 17(10), 4406; https://doi.org/10.3390/su17104406 - 13 May 2025
Viewed by 990
Abstract
Reducing enteric methane production from ruminant livestock has been positioned as a key intervention to reduce global greenhouse gas emissions. Bovaer©, a feed additive purported to reduce enteric methane emissions in dairy cows by nearly a third, has received regulatory authorization in many [...] Read more.
Reducing enteric methane production from ruminant livestock has been positioned as a key intervention to reduce global greenhouse gas emissions. Bovaer©, a feed additive purported to reduce enteric methane emissions in dairy cows by nearly a third, has received regulatory authorization in many countries. However, there is a dearth of evidence on the consumer’s response to the use of such products. In the three weeks after 27 November 2024, there was a significant increase in media communications associated with the use of Bovaer© in Europe, and especially the United Kingdom (UK). This structured review of academic and gray literature and an iterative non-systematic survey of media discourse online explored and characterized the narratives that emerged in this three-week period of intense activity in both social media and mainstream media communications in order to critique the narratives and grammars within the public response and the implications for policymakers, industry and academia. The main narrative that emerged reflected the science-consumer tensions associated with the use of Bovaer© and the four sub-narratives shaping it (mainstream media influence and narrative framing, distrust in science and lack of relatability, conspiracy theories and fear-based narratives, consumer buycotts and market responses). Organizations adopting technological solutions to address ‘wicked’ societal problems need to understand the factors that trigger, amplify and attenuate social concern as expressed in mainstream and social media and need to adopt appropriate communication and dissemination activities to reduce the circulation of mis-dis-mal-information and promote information that is appropriate for multiple audiences and levels of understanding. Full article
(This article belongs to the Special Issue Sustainable Development of Agricultural Systems)
50 pages, 2918 KB  
Article
Classical Data in Quantum Machine Learning Algorithms: Amplitude Encoding and the Relation Between Entropy and Linguistic Ambiguity
by Jurek Eisinger, Ward Gauderis, Lin de Huybrecht and Geraint A. Wiggins
Entropy 2025, 27(4), 433; https://doi.org/10.3390/e27040433 - 16 Apr 2025
Cited by 1 | Viewed by 2132
Abstract
The Categorical Compositional Distributional (DisCoCat) model has been proven to be very successful in modelling sentence meaning as the interaction of word meanings. Words are modelled as quantum states, interacting guided by grammar. This model of language has been extended to density matrices [...] Read more.
The Categorical Compositional Distributional (DisCoCat) model has been proven to be very successful in modelling sentence meaning as the interaction of word meanings. Words are modelled as quantum states, interacting guided by grammar. This model of language has been extended to density matrices to account for ambiguity in language. Density matrices describe probability distributions over quantum states, and in this work we relate the mixedness of density matrices to ambiguity in the sentences they represent. The von Neumann entropy and the fidelity are used as measures of this mixedness. Via the process of amplitude encoding, we introduce classical data into quantum machine learning algorithms. First, the findings suggest that in quantum natural language processing, amplitude-encoding data onto a quantum computer can be a useful tool to improve the performance of the quantum machine learning models used. Second, the effect that these encoded data have on the above-introduced relation between entropy and ambiguity is investigated. We conclude that amplitude-encoding classical data in quantum machine learning algorithms makes the relation between the entropy of a density matrix and ambiguity in the sentence modelled by this density matrix much more intuitively interpretable. Full article
(This article belongs to the Collection Feature Papers in Information Theory)
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20 pages, 401 KB  
Article
Entering Foreign Lands: How Acceptable Is Extraction from Adjunct Clauses to L1 Users of English in L2 Danish?
by Anne Mette Nyvad and Ken Ramshøj Christensen
Languages 2025, 10(4), 63; https://doi.org/10.3390/languages10040063 - 27 Mar 2025
Viewed by 1299
Abstract
Adjunct clauses have traditionally been assumed to be syntactic configurations from which extraction is universally impossible. However, numerous studies have challenged this assumption and extraction from finite adjunct clauses has been shown to be acceptable to varying degrees in the Mainland Scandinavian languages, [...] Read more.
Adjunct clauses have traditionally been assumed to be syntactic configurations from which extraction is universally impossible. However, numerous studies have challenged this assumption and extraction from finite adjunct clauses has been shown to be acceptable to varying degrees in the Mainland Scandinavian languages, as well as in English. The relative acceptability of extraction appears to depend on a number of factors, including the type of adjunct clause and the type of extraction dependency. Research on L2 learning has shown that learners often transfer properties of their L1 grammar into their L2 during the process of learning a second language. Our previous studies on L1 English and L1 Danish found a surprising contrast in which L1 English users found relativization out of adverbial clauses to be better than L1 Danish users did. Based on these findings, we conducted an L2 acceptability judgment experiment on extraction from three types of finite adjunct clauses in Danish (corresponding to English if-, when- and because-clauses) in order to test whether language-specific parameters related to extractability are transferred from L1 to L2. Our results show that the judgments from L2 Danish speakers are intermediate between and significantly different from L1 English and L1 Danish, which does not suggest a parameter resetting. Full article
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24 pages, 7634 KB  
Article
GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish
by Yunfeng Zhao, Jin Gao, Hong Feng and Li Jiang
Biology 2025, 14(1), 63; https://doi.org/10.3390/biology14010063 - 13 Jan 2025
Cited by 1 | Viewed by 1283
Abstract
The shape of the skull plays a crucial role in the evolution and adaptation of species to their environments. In the case of aquaculture fish, the size of the head is also an important economic trait, as it is linked to fillet yield [...] Read more.
The shape of the skull plays a crucial role in the evolution and adaptation of species to their environments. In the case of aquaculture fish, the size of the head is also an important economic trait, as it is linked to fillet yield and ornamental value. This study applies our GRAMMAR-Lambda method to perform a genome-wide association study analysis on loci related to head size in catfish. Compared with traditional GWAS methods, the GRAMMAR-Lambda method offers higher computational efficiency, statistical power, and stability, especially in complex population structures. This research identifies many candidate genes closely related to cranial morphology in terms of head length, width, and depth in catfish, including bmpr1bb, fgfrl1b, nipbl, foxp2, and pax5, etc. Based on the results of gene–gene interaction analysis, we speculate that there may be frequent genetic interactions between chromosome 19 and chromosome 29 in bone development. Additionally, many candidate genes, gene families, and mechanisms (such as SOCE mechanisms) affecting skeletal development and morphology have been identified. These findings contribute to our understanding of the genetic architecture of head size and will support marker-assisted breeding in aquaculture, also reflecting the potential application of the GRAMMAR-Lambda method in genetic studies of complex traits. Full article
(This article belongs to the Special Issue Internal Defense System and Evolution of Aquatic Animals)
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16 pages, 4036 KB  
Article
Decoding the Molecular Grammar of TIA1-Dependent Stress Granules in Proteostasis and Welander Distal Myopathy Under Oxidative Stress
by Isabel Alcalde-Rey, Beatriz Ramos Velasco, José Alcalde and José M. Izquierdo
Cells 2024, 13(23), 1961; https://doi.org/10.3390/cells13231961 - 27 Nov 2024
Cited by 2 | Viewed by 1569
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein (RBP) that plays a multifunctional role in RNA metabolism. TIA1 has three RNA-Recognition Motifs (RRMs) and a prion-like carboxyl C-terminal domain (LCD) with intrinsically disordered regions (IDR) implicated in the dynamics (i.e., formation, assembly, [...] Read more.
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein (RBP) that plays a multifunctional role in RNA metabolism. TIA1 has three RNA-Recognition Motifs (RRMs) and a prion-like carboxyl C-terminal domain (LCD) with intrinsically disordered regions (IDR) implicated in the dynamics (i.e., formation, assembly, and disassembly) of transient RNA-protein aggregates known as stress granules (SGs). A protein related to TIA1 is its paralog TIA1-related/like protein (TIAR/TIAL1), whose amino acid sequence, structural organisation, and molecular and cellular functions are highly conserved with TIA1. Both proteins are the main components of SGs, which are non-membranous RNA-protein condensates formed under stress to promote cell survival. Welander distal myopathy (WDM) is a late-onset muscular dystrophy that has been linked to a single-nucleotide substitution (c.1362G>A; p.E384K) in the gene encoding the TIA1 protein, which impacts TIA1-dependent SGs dynamics. Herein, we have analysed cellular and molecular aspects by targeting mutagenesis to position 384 to understand its molecular grammar in an amino acid/proteinogenic-dependent or -independent manner under oxidative stress. The observations suggest differential, even opposing, behaviours between TIA1 and TIAR in the presence of specific amino acids with negative and positive charges, and also uncharged acids, at equivalent positions of TIA1 and TIAR, respectively. Collectively, these findings illustrate a characteristic molecular grammar of TIAR- and TIA1-dependent SGs under oxidative conditions, suggesting a gain of versatility between two structurally and functionally highly conserved/related proteins. Full article
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16 pages, 1265 KB  
Article
The Changing Muslim World: Energy, Extraction, and the Racialization of Islam in Protestant Missions
by Matthew J. Smith
Religions 2024, 15(10), 1262; https://doi.org/10.3390/rel15101262 - 16 Oct 2024
Viewed by 2126
Abstract
This essay examines the role of Anglo Protestant missions in the Persian Gulf in racializing “the Moslem world” for the emergent white world order at the beginning of the 20th century. More specifically, I consider the way Protestant missionaries extracted knowledge about Islam, [...] Read more.
This essay examines the role of Anglo Protestant missions in the Persian Gulf in racializing “the Moslem world” for the emergent white world order at the beginning of the 20th century. More specifically, I consider the way Protestant missionaries extracted knowledge about Islam, racializing “the Moslem world” as a civilizational “unit” devoid of energetic life—and therefore incompatible with the modern world—even as they simultaneously mediated the rise of oil extraction along the Persian Gulf in that same period. Extraction was not only evident in the material relations of empire, but also in the way Protestant missionary discourse shaped “the Muslim world” into a racial unit in need of management and optimization. I consider two energetic grammars used by Protestant missionaries to signify the changes occurring in “the Moslem World”, namely, Samuel Zwemer’s use of “disintegration” and Basil Mathews use of “ferment”. I argue that it was in these material and discursive entanglements of oil extraction where knowledge about Islam became an important tool of European colonial governance, and where energetic grammars of religion became critical to the biopolitical production and management of racialized Muslim populations. Full article
(This article belongs to the Special Issue Religion in Extractive Zones)
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14 pages, 278 KB  
Article
Secondary School Teachers’ Educational Philosophies: Differences Regarding Work Experience, Type of School, and Education Programs
by Sani Ćavar and Tonća Jukić
Educ. Sci. 2024, 14(9), 936; https://doi.org/10.3390/educsci14090936 - 26 Aug 2024
Cited by 1 | Viewed by 1982
Abstract
Teachers’ educational philosophies have a great influence on teachers’ actions in the classroom. They are partly influenced by the dominant pedagogical paradigm expressed in the strategic educational documents, but there are also some other factors that influence teachers’ educational philosophies. This research aimed [...] Read more.
Teachers’ educational philosophies have a great influence on teachers’ actions in the classroom. They are partly influenced by the dominant pedagogical paradigm expressed in the strategic educational documents, but there are also some other factors that influence teachers’ educational philosophies. This research aimed to determine secondary school teachers’ educational philosophies and whether they differ in relation to a teacher’s work experience, type of school, and educational program. A total of 355 secondary school teachers in Split–Dalmatia County in the Republic of Croatia participated in the research. The philosophy preference assessment scale consisting of two subscales (traditional and contemporary educational philosophies), was applied. The results showed that: secondary school teachers generally agreed more with contemporary than traditional educational philosophies; grammar school teachers agreed more with contemporary and vocational school teachers with traditional educational philosophies; the education program was a significant factor only for the subscale of traditional educational philosophies; and years of work experience was not a significant factor for either subscale. The results are discussed in the context of the relationship between teachers’ educational philosophies, values, beliefs, and teaching experiences and the need for teachers to raise awareness of their educational philosophies and continuously compare and harmonise them with their educational practice. Full article
34 pages, 433 KB  
Article
Precedence Table Construction Algorithm for CFGs Regardless of Being OPGs
by Leonardo Lizcano, Eduardo Angulo and José Márquez
Algorithms 2024, 17(8), 345; https://doi.org/10.3390/a17080345 - 7 Aug 2024
Viewed by 1446
Abstract
Operator precedence grammars (OPG) are context-free grammars (CFG) that are characterized by the absence of two adjacent non-terminal symbols in the body of each production (right-hand side). Operator precedence languages (OPL) are deterministic and context-free. Three possible precedence relations between pairs of terminal [...] Read more.
Operator precedence grammars (OPG) are context-free grammars (CFG) that are characterized by the absence of two adjacent non-terminal symbols in the body of each production (right-hand side). Operator precedence languages (OPL) are deterministic and context-free. Three possible precedence relations between pairs of terminal symbols are established for these languages. Many CFGs are not OPGs because the operator precedence cannot be applied to them as they do not comply with the basic rule. To solve this problem, we have conducted a thorough redefinition of the Left and Right sets of terminals that are the basis for calculating the precedence relations, and we have defined a new Leftmost set. The algorithms for calculating them are also described in detail. Our work’s most significant contribution is that we establish precedence relationships between terminals by overcoming the basic rule of not having two consecutive non-terminals using an algorithm that allows building the operator precedence table for a CFG regardless of whether it is an OPG. The paper shows the complexities of the proposed algorithms and possible exceptions to the proposed rules. We present examples by using an OPG and two non-OPGs to illustrate the operation of the proposed algorithms. With these, the operator precedence table is built, and bottom-up parsing is carried out correctly. Full article
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18 pages, 258 KB  
Article
Carnap and Wittgenstein: Tolerance, Arbitrariness, and Truth
by Oskari Kuusela
Philosophies 2024, 9(4), 114; https://doi.org/10.3390/philosophies9040114 - 30 Jul 2024
Cited by 1 | Viewed by 1825
Abstract
This article discusses the relationship between Ludwig Wittgenstein’s and Rudolf Carnap’s philosophies of logic during the time of Wittgenstein’s interactions with the Vienna Circle and up to 1934 when the German edition of Carnap’s The Logical Syntax of Language was published. Whilst Section [...] Read more.
This article discusses the relationship between Ludwig Wittgenstein’s and Rudolf Carnap’s philosophies of logic during the time of Wittgenstein’s interactions with the Vienna Circle and up to 1934 when the German edition of Carnap’s The Logical Syntax of Language was published. Whilst Section 1 focuses on the relationship between Carnap and Wittgenstein’s Tractatus, including Wittgenstein’s accusation of plagiarism against Carnap in 1932, Section 2 discusses the relationship between Carnap’s principle of tolerance and Wittgenstein’s similar principle of the arbitrariness of grammar. I argue that, although Carnap’s claim in Logical Syntax to ‘go beyond’ Wittgenstein has certain justification in relation to the Tractatus, so does Wittgenstein’s priority claim. The relationship between Carnap’s philosophy of logic and the Tractatus is thus more complicated than is often recognized. If the reference point is Wittgenstein in the early 1930s, however, Carnap cannot be described as going beyond him, and by 1934, Wittgenstein had advanced further than Carnap would ever venture. Despite evidence that Carnap knew about Wittgenstein’s principle of the arbitrariness of syntax well before his first articulations of his principle of tolerance, the extent of the influence of Wittgenstein’s principle on Carnap remains unclear. What can be established with certainty is that Wittgenstein’s principle predates Carnap’s and that Carnap resisted acknowledging him despite being urged to do so. Arguably, Wittgenstein’s account of syntax as both arbitrary and non-arbitrary is also superior in clarity to Carnap’s misleading claim about a ‘complete freedom’ implied by the principle of tolerance, because such a freedom only exists for idle syntactical systems that are not put to work. In Section 3, I discuss the relationship between Carnap’s notion of expediency and Wittgenstein’s account of the correctness or truth of logical accounts. As my discussion of Wittgenstein’s account brings out, Carnap’s rejection of truth in logic for expediency as the goal of logical clarifications does not follow from the principle of tolerance and is not justified by it. It remains unclear what justifies Carnap’s rejection of truth as the goal of logical clarification. Again, Wittgenstein’s account seems preferable, given the vacuity of the claim that expediency constitutes the basis of choice between different logical languages and clarifications. Full article
23 pages, 1305 KB  
Article
Code-Switching at the Interfaces
by Antje Muntendam and M. Carmen Parafita Couto
Languages 2024, 9(8), 258; https://doi.org/10.3390/languages9080258 - 25 Jul 2024
Cited by 1 | Viewed by 5388
Abstract
One characteristic of multilingual speakers is that in everyday life, they may integrate elements from their languages in the same sentence or discourse, a practice known as code-switching. This paper examines code-switching at the interfaces, in particular as related to information structure. Despite [...] Read more.
One characteristic of multilingual speakers is that in everyday life, they may integrate elements from their languages in the same sentence or discourse, a practice known as code-switching. This paper examines code-switching at the interfaces, in particular as related to information structure. Despite the fact that a core question of modern linguistic theory is how syntactic and information-structural theories interact in accounting for licensing of different grammatical phenomena, there has been relatively little literature on code-switching and information structure. In this paper, we provide an overview of the available literature on code-switching across different language combinations, focusing in particular on subject pronoun–verb switches, ellipsis, light verbs, topic/focus particles, and code-switching between sign languages. We argue that the study of the interplay between information structure and code-switching sheds light on our understanding of multilingual grammars and language competence more generally. In this regard, we discuss theoretical and methodological considerations to guide future studies. Full article
(This article belongs to the Special Issue Syntax and Discourse at the Crossroads)
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13 pages, 622 KB  
Article
A Graph Convolutional Network Based on Sentiment Support for Aspect-Level Sentiment Analysis
by Ruiding Gao, Lei Jiang, Ziwei Zou, Yuan Li and Yurong Hu
Appl. Sci. 2024, 14(7), 2738; https://doi.org/10.3390/app14072738 - 25 Mar 2024
Cited by 8 | Viewed by 1816
Abstract
Aspect-level sentiment analysis is a research focal point for natural language comprehension. An attention mechanism is a very important approach for aspect-level sentiment analysis, but it only fuses sentences from a semantic perspective and ignores grammatical information in the sentences. Graph convolutional networks [...] Read more.
Aspect-level sentiment analysis is a research focal point for natural language comprehension. An attention mechanism is a very important approach for aspect-level sentiment analysis, but it only fuses sentences from a semantic perspective and ignores grammatical information in the sentences. Graph convolutional networks (GCNs) are a better method for processing syntactic information; however, they still face problems in effectively combining semantic and syntactic information. This paper presents a sentiment-supported graph convolutional network (SSGCN). This SSGCN first obtains the semantic information of the text through aspect-aware attention and self-attention; then, a grammar mask matrix and a GCN are applied to preliminarily combine semantic information with grammatical information. Afterward, the processing of these information features is divided into three steps. To begin with, features related to the semantics and grammatical features of aspect words are extracted. The second step obtains the enhanced features of the semantic and grammatical information through sentiment support words. Finally, it concatenates the two features, thus enhancing the effectiveness of the attention mechanism formed from the combination of semantic and grammatical information. The experimental results show that compared with benchmark models, the SSGCN had an improved accuracy of 6.33–0.5%. In macro F1 evaluation, its improvement range was 11.68–0.5%. Full article
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19 pages, 3441 KB  
Article
Interpretable Multi-Scale Deep Learning for RNA Methylation Analysis across Multiple Species
by Rulan Wang, Chia-Ru Chung and Tzong-Yi Lee
Int. J. Mol. Sci. 2024, 25(5), 2869; https://doi.org/10.3390/ijms25052869 - 1 Mar 2024
Cited by 4 | Viewed by 2694
Abstract
RNA modification plays a crucial role in cellular regulation. However, traditional high-throughput sequencing methods for elucidating their functional mechanisms are time-consuming and labor-intensive, despite extensive research. Moreover, existing methods often limit their focus to specific species, neglecting the simultaneous exploration of RNA modifications [...] Read more.
RNA modification plays a crucial role in cellular regulation. However, traditional high-throughput sequencing methods for elucidating their functional mechanisms are time-consuming and labor-intensive, despite extensive research. Moreover, existing methods often limit their focus to specific species, neglecting the simultaneous exploration of RNA modifications across diverse species. Therefore, a versatile computational approach is necessary for interpretable analysis of RNA modifications across species. A multi-scale biological language-based deep learning model is proposed for interpretable, sequential-level prediction of diverse RNA modifications. Benchmark comparisons across species demonstrate the model’s superiority in predicting various RNA methylation types over current state-of-the-art methods. The cross-species validation and attention weight visualization also highlight the model’s capability to capture sequential and functional semantics from genomic backgrounds. Our analysis of RNA modifications helps us find the potential existence of “biological grammars” in each modification type, which could be effective for mapping methylation-related sequential patterns and understanding the underlying biological mechanisms of RNA modifications. Full article
(This article belongs to the Special Issue Recent Research on Bioinformatics for Precision Medicine)
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