scholarly journals Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder

Author(s):  
Jacqueline Peng ◽  
Mengge Zhao ◽  
James Havrilla ◽  
Cong Liu ◽  
Chunhua Weng ◽  
...  

Abstract Background Natural language processing (NLP) tools can facilitate the extraction of biomedical concepts from unstructured free texts, such as research articles or clinical notes. The NLP software tools CLAMP, cTAKES, and MetaMap are among the most widely used tools to extract biomedical concept entities. However, their performance in extracting disease-specific terminology from literature has not been compared extensively, especially for complex neuropsychiatric disorders with a diverse set of phenotypic and clinical manifestations. Methods We comparatively evaluated these NLP tools using autism spectrum disorder (ASD) as a case study. We collected 827 ASD-related terms based on previous literature as the benchmark list for performance evaluation. Then, we applied CLAMP, cTAKES, and MetaMap on 544 full-text articles and 20,408 abstracts from PubMed to extract ASD-related terms. We evaluated the predictive performance using precision, recall, and F1 score. Results We found that CLAMP has the best performance in terms of F1 score followed by cTAKES and then MetaMap. Our results show that CLAMP has much higher precision than cTAKES and MetaMap, while cTAKES and MetaMap have higher recall than CLAMP. Conclusion The analysis protocols used in this study can be applied to other neuropsychiatric or neurodevelopmental disorders that lack well-defined terminology sets to describe their phenotypic presentations.

2021 ◽  
Vol 12 ◽  
Author(s):  
Joel R. Adams ◽  
Alexandra C. Salem ◽  
Heather MacFarlane ◽  
Rosemary Ingham ◽  
Steven D. Bedrick ◽  
...  

Conversational impairments are well known among people with autism spectrum disorder (ASD), but their measurement requires time-consuming manual annotation of language samples. Natural language processing (NLP) has shown promise in identifying semantic difficulties when compared to clinician-annotated reference transcripts. Our goal was to develop a novel measure of lexico-semantic similarity – based on recent work in natural language processing (NLP) and recent applications of pseudo-value analysis – which could be applied to transcripts of children’s conversational language, without recourse to some ground-truth reference document. We hypothesized that: (a) semantic coherence, as measured by this method, would discriminate between children with and without ASD and (b) more variability would be found in the group with ASD. We used data from 70 4- to 8-year-old males with ASD (N = 38) or typically developing (TD; N = 32) enrolled in a language study. Participants were administered a battery of standardized diagnostic tests, including the Autism Diagnostic Observation Schedule (ADOS). ADOS was recorded and transcribed, and we analyzed children’s language output during the conversation/interview ADOS tasks. Transcripts were converted to vectors via a word2vec model trained on the Google News Corpus. Pairwise similarity across all subjects and a sample grand mean were calculated. Using a leave-one-out algorithm, a pseudo-value, detailed below, representing each subject’s contribution to the grand mean was generated. Means of pseudo-values were compared between the two groups. Analyses were co-varied for nonverbal IQ, mean length of utterance, and number of distinct word roots (NDR). Statistically significant differences were observed in means of pseudo-values between TD and ASD groups (p = 0.007). TD subjects had higher pseudo-value scores suggesting that similarity scores of TD subjects were more similar to the overall group mean. Variance of pseudo-values was greater in the ASD group. Nonverbal IQ, mean length of utterance, or NDR did not account for between group differences. The findings suggest that our pseudo-value-based method can be effectively used to identify specific semantic difficulties that characterize children with ASD without requiring a reference transcript.


Author(s):  
Emme O’Rourke ◽  
Emily L. Coderre

AbstractWhile many individuals with autism spectrum disorder (ASD) experience difficulties with language processing, non-linguistic semantic processing may be intact. We examined neural responses to an implicit semantic priming task by comparing N400 responses—an event-related potential related to semantic processing—in response to semantically related or unrelated pairs of words or pictures. Adults with ASD showed larger N400 responses than typically developing adults for pictures, but no group differences occurred for words. However, we also observed complex modulations of N400 amplitude by age and by level of autistic traits. These results offer important implications for how groups are delineated and compared in autism research.


2020 ◽  
pp. 153465012098345
Author(s):  
Mirela Cengher ◽  
Joy C. Clayborne ◽  
Adrianna E. Crouch ◽  
Julia T. O’Connor

Over 60% of children diagnosed with selective mutism are also diagnosed with Autism Spectrum Disorder. Previous research established that behavioral interventions are effective at increasing speech in children with both diagnoses. However, few studies conducted assessments to determine environmental variables that inhibit speech, and such assessments are necessary for the development of effective and efficient treatments. This case study describes an assessment that evaluated the function(s) of selective mutism. The results confirmed that the participant did not talk to avoid social interaction and that mutism occurred primarily in the presence of multiple, unfamiliar people. Our first treatment focused on increasing tolerance for social interaction, demonstrated by an increase in speech production in the presence of unfamiliar people. Our second treatment focused on increasing qualitative aspects of the participant’s speech (i.e., both responses and initiations). Finally, we taught the participant’s parents to implement the treatment in naturalistic settings, and the participant demonstrated generalization of treatment effects across people and settings. Implications for clinical practice and future research are discussed.


Author(s):  
Sourajit Roy ◽  
Pankaj Pathak ◽  
S. Nithya

During the advent of the 21st century, technical breakthroughs and developments took place. Natural Language Processing or NLP is one of their promising disciplines that has been increasingly dynamic via groundbreaking findings on most computer networks. Because of the digital revolution the amounts of data generated by M2M communication across devices and platforms such as Amazon Alexa, Apple Siri, Microsoft Cortana, etc. were significantly increased. This causes a great deal of unstructured data to be processed that does not fit in with standard computational models. In addition, the increasing problems of language complexity, data variability and voice ambiguity make implementing models increasingly harder. The current study provides an overview of the potential and breadth of the NLP market and its acceptance in industry-wide, in particular after Covid-19. It also gives a macroscopic picture of progress in natural language processing research, development and implementation.


2019 ◽  
Author(s):  
◽  
Kwame De Jongge-Moore

Problem Statistics indicate that Autism Spectrum Disorder (ASD) is on the increase in America and worldwide (Xu, Strathearn, Liu, & Bao, 2018; Baio et al., 2018). Autism spectrum disorder can impair an individual’s ability to engage in neurotypical behavior, which has the potential to increase their vulnerability to being shunned and bullied. This makes autism a major societal concern with significant costs to the individual, their family, private/public health insurance, state financial aid programs, and to the nation. This present study was undertaken to determine, in the opinions of those connected to the case, whether the interventions engaged in this case were effective and to what extent the educational and social interventions practiced in this specific case were responsible for enabling Carter to reach the place where the diagnosticians felt that he no longer met the criteria for receiving services for autism spectrum disorder. Purpose The purpose of this study was to identify social and educational interventions used in Carter's journey with Autism Spectrum Disorder and to document the social and educational interventions employed by several individuals who worked with him. Further, the study sought to describe the impact of these interventions on Carter, from the perspectives of the key individuals involved in the early education of the child. Additionally, the study set out to determine whether these interventions actually enabled Carter to no longer meet the criteria for receiving services for autism spectrum disorder. -- Method The study employed a qualitative case study approach which gathered data mainly through semi-structured interviews and focus groups. Other data sources included Carter’s mother's (Meghan's) account of her experience, key documents, and examples of learning activities found to be of benefit to the child. The nine individuals who were interviewed were invited to participate because they had been directly involved with the case. The data was analyzed using NVivo data analysis. Results The results from the analysis of the data study indicate that there was a positive relationship between the interventions reported and Carter's no longer meeting the criteria for services for ASD. The activities reported proved to be too numerous to be mentioned individually and were therefore grouped thematically. The two large groups were the social interventions and the educational interventions. The social interventions group was comprised of activities, such as Gymfants (gymnastics for young children), Children’s Choir, Adventurers Club, and attending regular school which promoted social interactions. These groups facilitated Carter’s working with others, taking directions from others, imitating others, leading, following, and taking turns. Language was key to these interactions. Educational interventions included; reading, attending homeschool, regular school, strategic games such as Connect Four, Uno, and geographical puzzles, floor puzzles; foreign language videos and science videos among other activities. These interventions incorporated language and encouraged Carter in individual work, seated work, pattern identification, and viewing for a purpose among other things. These interventions were planned by Meghan outside of the Individualized Educational Plan (IEP) and in addition to Speech Therapy. Conclusions As a result of this study, the reader can see that the curriculum developed for Carter by Meghan was directly related to his progress. The study concluded that Carter's family working together to provide the program of interventions contributed greatly to his no longer meeting the criteria to remain in the autism therapy program designed for him by the Individualized Educational Plan (IEP) team. It appeared that the intentionality of Carter’s support team had a significant relationship with his progress. It was also concluded that there was a strong relationship between Music as a theme and Carter's progress. The study concluded that the combination of educational and social interventions employed with Carter helped to eliminate the need for him to receive services for autism spectrum disorder. The study showed that intervention in autism requires parental involvement as the delivery of a variety of social and educational interventions through the medium of the home allowed for a natural, meaningful and permanent transfer of knowledge and growth in a number of areas. It is therefore obligatory that the parent/therapist/school partnership be supported and empowered.


Psibernetika ◽  
2019 ◽  
Vol 11 (2) ◽  
Author(s):  
Elita Kirana ◽  
Ediasri T Atmodiwirjo ◽  
Debora Basaria

<p><strong><em>ABSTRACT</em></strong><strong><em>: </em></strong><em>Children with autism have deficit characteristics in social communication and social interaction, as well as restricted and repetitive patterns of behavior, and limited interests or activities. As children grow and engage in a wider environment, this is become a problem because of the lack of social skills on children with autism. The purpose of this research is to improve the social skills of children with autism. There are several methods that can be applied to children with autism to improve their social skills. One of them is the DIR </em>(<em>Developmental, Individual Differences, &amp; Relationship Based</em>) <em>Floortime method. DIR Floortime aims to help children reach the stage of their emotional development through play activities. This type of research is a clinical case study, involving two middle childhood boys that are diagnosed with a mild level of autism. The instruments used in this study are Autism Social Skills Profile and Functional Emotional Assessment Scale. This research involves 20 sessions, conducted in May until June 2018, consisting of 10 sensory sessions and 10  symbolic sessions for each subject. The results of this research show an improvement in social skills in both participants, marked by an increase in the post test scores, but not significantly. Qualitatively, both subject demonstrates an improvement on social skills in their daily behavior after they had participated in the intervention.</em><strong><em></em></strong></p><p><strong><em>Keywords</em></strong><strong>: </strong><em>autism spectrum disorder, middle childhood, </em>DIR <em>Floortime,social skills</em></p><p><strong> </strong></p><p><strong>ABSTRAK</strong><strong>: </strong>Anak autistik memiliki karakteristik kesulitan dalam komunikasi dan interaksi sosial serta adanya yang minat terbatas, perilaku berulang, atau keterikatan dalam minat dan aktivitas. Hal ini menjadi masalah saat anak tumbuh seiring usia dan terlibat dalam lingkungan yang lebih luas karena kurangnya kemampuan sosial pada anak autistik. Penelitian ini bertujuan untuk meningkatkan kemampuan sosial anak autistik. Ada beberapa metode yang dapat diterapkan pada anak autistik untuk meningkatkan kemampuan sosial. Salah satunya adalah metode DIR (<em>Developmental, Individual Differences, &amp; Relationship Based</em>) <em>Floortime</em>. DIR<em> Floortime</em>  bertujuan membantu anak mencapai tahap perkembangan emosionalnya melalui kegiatan bermain. Jenis penelitian ini adalah case study yang melibatkan dua orang partisipan, yaitu anak laki-laki berusia <em>middle childhood</em> dengan autisme <em>level Mild</em>. Instrumen dalam penelitian ini adalah <em>Autism Social Skills Profile dan Functional Emotional Assesment Scale</em>. Penelitian ini berlangsung selama 20 sesi intervensi yang dilaksanakan pada bulan Mei hingga Juni 2018. Sesi intervensi terdiri dari 10 sesi sensori auditori dan 10 sesi simbolik bagi masing-masing subjek. Hasil penelitian menunjukkan adanya peningkatan yang signifikan pada kapasitas emosi, tetapi kemampuan sosial kedua partisipan tidak meningkat secara signifikan. Secara kualitatif, kedua subjek menunjukkan kemampuan sosial yang lebih baik setelah mengikuti sesi intervensi, hal ini tampak dalam perilaku sehari-hari.<strong></strong></p><p><strong>Kata kunci</strong>: autisme<em>, middle childhood, </em>DIR <em>Floortime,</em> kemampuan sosial</p>


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