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XAI in Genomics with LLM Generated Explanations in Oncology. 基因组学中的XAI与LLM生成的肿瘤学解释。
CEUR workshop proceedings Pub Date : 2026-01-01
Isabelle Bichindaritz, Shazveen Saleem, Leszek Kotula
{"title":"XAI in Genomics with LLM Generated Explanations in Oncology.","authors":"Isabelle Bichindaritz, Shazveen Saleem, Leszek Kotula","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The amount of genetic data available for analysis is rapidly growing, and the importance of analyzing this type of data is paramount to the field of precision medicine, in which diagnostic and prognostic tasks rely on genetic data analysis in many fields, including in oncology. Given the high dimensionality of genomic data, AI or machine learning in genomics requires more sophisticated methods to help clinicians interpret their results, as gene-level explanations may not be sufficient to make sense of these results. Given the growing importance of XAI, a rapidly growing number of AI papers in genomics refer to XAI methods. In this paper, we present general methods for XAI in genomics and focus on how LLMs can contribute to explanations at the case level in the domain of oncology. The preliminary results obtained in this study are encouraging about the role LLM chatbots can play in the user interface to help explain machine learning results to users at the case level in conversational or visual interaction modalities.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"4255 ","pages":"10-20"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13638230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
History in the Basic Formal Ontology. 基本形式本体论中的历史。
CEUR workshop proceedings Pub Date : 2025-11-01
Werner Ceusters, Alan Ruttenberg
{"title":"<i>History</i> in the Basic Formal Ontology.","authors":"Werner Ceusters, Alan Ruttenberg","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The Basic Formal Ontology's (BFO) current approach to 'history', in contradistinction to how the referent of 'history' has been described in scholarly work upon which the BFO is built, is quite reductionist: it allows only material entities to have a history, and what contributes to their histories is restricted to what takes place in the spatiotemporal region 'occupied by' the material parts. This has as one consequence that certain processes in which a material entity participates are not part of its history. In addition, the BFO is silent about whether instances of other types of continuants have a 'history'. We explore how this situation came to be and propose two alternative versions for 'history' inclusive to all sorts of continuants currently recognized by the BFO.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"4194 Main Conf","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Towards Healthy Aging through Semantic Enrichment. 通过语义富集走向健康老龄化。
CEUR workshop proceedings Pub Date : 2025-01-01 Epub Date: 2026-03-02
John Beverley, Julie C Bowker, Hollen N Reischer, Rachel A Mavrovich, Regina Hurley, Sean Kindya, Sam Smith, Jie Zheng, Yongqun He, Damayanthi Beera, William D Duncan
{"title":"Towards Healthy Aging through Semantic Enrichment.","authors":"John Beverley, Julie C Bowker, Hollen N Reischer, Rachel A Mavrovich, Regina Hurley, Sean Kindya, Sam Smith, Jie Zheng, Yongqun He, Damayanthi Beera, William D Duncan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This paper introduces two interoperable ontologies-SOLO (Solitude Ontology) and GERO (Gerotranscendence Ontology)-developed to formalize key psychological constructs relevant to healthy aging. Grounded in the Behavioral Change Intervention Ontology, the ontologies clarify distinctions between terms such as solitude, loneliness, self-transcendence, and gerotranscendence, and encode their realization conditions across the lifespan. By integrating validated psychometric instruments and supporting structured responses to competency questions, the ontologies enable semantic reasoning, cross-disciplinary data integration, and development of ontology-driven tools for aging research and intervention design.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"4176 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13310578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148347282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analyzing Llama 3-based Approach for Axiom Translation from Ontologies. 基于Llama 3的本体公理翻译方法分析
CEUR workshop proceedings Pub Date : 2024-11-01
Xubing Hao, Licong Cui, Cui Tao, Kirk Roberts, Muhammad Amith
{"title":"Analyzing Llama 3-based Approach for Axiom Translation from Ontologies.","authors":"Xubing Hao, Licong Cui, Cui Tao, Kirk Roberts, Muhammad Amith","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Ontology development involves a top-down approach where ontology engineers and domain experts collaboratively define and evaluate ontological elements and axioms. Translating ontology axioms into natural language can significantly aid in ontology evaluation by making the content more understandable to subject matter experts who may lack a background in knowledge engineering. In this preliminary study, we investigate the potential of large language models (LLMs) in axiom translation from ontologies to facilitate ontology evaluation. We utilize Llama 3 to translate 1,192 ontology axioms across 19 distinct axiom types from five published ontologies. Results show that 163 (13.67%) of the Llama 3 translation of the axiom are accurately represented, 268 (22.48%) are not accurately represented, and 761 (63.84%) are partially accurate. Our manual evaluation of the Llama 3 translation indicates some competency in producing hierarchical natural language equivalents while revealing some limitations when translating complex axioms. Nonetheless, there are opportunities to improve the results with few-shot training or using LLMs to provide support in knowledge engineering for ontologies.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"3853 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12178606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nested Named Entity Recognition using Multilayer BERT-based Model: Notebook for the BioASQ Lab at CLEF 2024. 使用多层bert模型的嵌套命名实体识别:CLEF 2024的BioASQ实验室笔记本。
CEUR workshop proceedings Pub Date : 2024-09-01
Hasin Rehana, Benu Bansal, Nur Bengisu Çam, Jie Zheng, Yongqun He, Arzucan Özgür, Junguk Hur
{"title":"Nested Named Entity Recognition using Multilayer BERT-based Model: Notebook for the BioASQ Lab at CLEF 2024.","authors":"Hasin Rehana, Benu Bansal, Nur Bengisu Çam, Jie Zheng, Yongqun He, Arzucan Özgür, Junguk Hur","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In natural language processing, named entity recognition (NER) is a crucial task involving finding and categorizing text entities. The biomedical domain presents substantial hurdles due to the complex structure of the language and the existence of nested entities. This paper introduces an innovative method for Nested NER by utilizing a multilayer bidirectional encoder representation transformer (BERT)-based model, notably employing pretrained PubMedBERT. Our proposed model is designed to manage nested entities' complexities effectively. We combined the robust contextual embeddings from PubMedBERT with a multilayer tagging process. This approach allowed the model to precisely differentiate between overlapping items, a frequent occurrence in biomedical literature. To assess the effectiveness of our Multilayer NER Model (MultilayerNERModel), we conducted thorough experiments on the BioNNE English Dataset, a dataset for a shared task of BioASQ competition. The findings suggest that employing a multilayer approach enhances the model's ability to identify nested entities, resulting in the thorough detection of entities in biomedical texts. It earned the highest overall performance in English oriented track, with an F1 score of 67.30% and a macro F1 score of 56.36%. These results demonstrate the significant impact of utilizing a multilayer approach in Nested NER tasks, especially in the biomedical domain. The use of UMLS dictionaries, along with the MultilayerNERModel, further enhances the model's performance in biomedical entity recognition.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"3740 ","pages":"197-206"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Expanding the Ontology of Organizational Structures of Trauma Centers and Trauma Systems. 拓展创伤中心与创伤系统组织结构本体论。
CEUR workshop proceedings Pub Date : 2024-07-01
Diya Mehta, Justin M Whorton, Reza Shahriari, Eric D Ragan, Jonathan P Bona, William R Hogan, Kevin W Sexton, Mathias Brochhausen
{"title":"Expanding the Ontology of Organizational Structures of Trauma Centers and Trauma Systems.","authors":"Diya Mehta, Justin M Whorton, Reza Shahriari, Eric D Ragan, Jonathan P Bona, William R Hogan, Kevin W Sexton, Mathias Brochhausen","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A knowledge gap exists regarding the impact of organizational parameters of trauma centers and patient outcomes. This is partially due to such organizational parameters being understudied. The Ontology of Organizational Structures of Trauma Centers and Trauma Systems (OOSTT) provides a controlled vocabulary to study that specific area. It is used in tools created by the TIPTOE project to provide trauma stakeholders with novel insights on role of organizational parameters and patient outcomes. This paper reports the extension of OOSTT to cover relevant patient outcome measures.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"3939 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Privacy-Preserving Unsupervised Speaker Disentanglement Method for Depression Detection from Speech. 一种用于从语音中检测抑郁的隐私保护无监督扬声器纠错方法
CEUR workshop proceedings Pub Date : 2024-02-01
Vijay Ravi, Jinhan Wang, Jonathan Flint, Abeer Alwan
{"title":"A Privacy-Preserving Unsupervised Speaker Disentanglement Method for Depression Detection from Speech.","authors":"Vijay Ravi, Jinhan Wang, Jonathan Flint, Abeer Alwan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The proposed method focuses on speaker disentanglement in the context of depression detection from speech signals. Previous approaches require patient/speaker labels, encounter instability due to loss maximization, and introduce unnecessary parameters for adversarial domain prediction. In contrast, the proposed unsupervised approach reduces cosine similarity between latent spaces of depression and pre-trained speaker classification models. This method outperforms baseline models, matches or exceeds adversarial methods in performance, and does so without relying on speaker labels or introducing additional model parameters, leading to a reduction in model complexity. The higher the speaker de-identification score (<i>DeID</i>), the better the depression detection system is in masking a patient's identity thereby enhancing the privacy attributes of depression detection systems. On the DAIC-WOZ dataset with ComparE16 features and an LSTM-only model, our method achieves an F1-Score of 0.776 and a <i>DeID</i> score of 92.87%, outperforming its adversarial counterpart which has an F1Score of 0.762 and 68.37% <i>DeID</i>, respectively. Furthermore, we demonstrate that speaker-disentanglement methods are complementary to text-based approaches, and a score-level fusion with a Word2vec-based depression detection model further enhances the overall performance to an F1-Score of 0.830.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"3649 ","pages":"57-63"},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11034881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140875057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Learning to Generate Context-Sensitive Backchannel Smiles for Embodied AI Agents with Applications in Mental Health Dialogues. 学习在心理健康对话中为具身AI代理生成上下文敏感的反向通道微笑。
CEUR workshop proceedings Pub Date : 2024-02-01
Maneesh Bilalpur, Mert Inan, Dorsa Zeinali, Jeffrey F Cohn, Malihe Alikhani
{"title":"Learning to Generate Context-Sensitive Backchannel Smiles for Embodied AI Agents with Applications in Mental Health Dialogues.","authors":"Maneesh Bilalpur, Mert Inan, Dorsa Zeinali, Jeffrey F Cohn, Malihe Alikhani","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Addressing the critical shortage of mental health resources for effective screening, diagnosis, and treatment remains a significant challenge. This scarcity underscores the need for innovative solutions, particularly in enhancing the accessibility and efficacy of therapeutic support. Embodied agents with advanced interactive capabilities emerge as a promising and cost-effective supplement to traditional caregiving methods. Crucial to these agents' effectiveness is their ability to simulate non-verbal behaviors, like backchannels, that are pivotal in establishing rapport and understanding in therapeutic contexts but remain under-explored. To improve the rapport-building capabilities of embodied agents we annotated backchannel smiles in videos of intimate face-to-face conversations over topics such as mental health, illness, and relationships. We hypothesized that both speaker and listener behaviors affect the duration and intensity of backchannel smiles. Using cues from speech prosody and language along with the demographics of the speaker and listener, we found them to contain significant predictors of the intensity of backchannel smiles. Based on our findings, we introduce backchannel smile production in embodied agents as a generation problem. Our attention-based generative model suggests that listener information offers performance improvements over the baseline speaker-centric generation approach. Conditioned generation using the significant predictors of smile intensity provides statistically significant improvements in empirical measures of generation quality. Our user study by transferring generated smiles to an embodied agent suggests that agent with backchannel smiles is perceived to be more human-like and is an attractive alternative for non-personal conversations over agent without backchannel smiles.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"3649 ","pages":"12-22"},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11608428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142775368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Internet resources for foreign language education in primary school: challenges and opportunities 小学外语教育的网络资源:挑战与机遇
CEUR workshop proceedings Pub Date : 2023-09-12 DOI: 10.55056/ceur-ws.org/vol-3482/paper041
Inna A. Kravtsova, Alina O. Mankuta, Vita A. Hamaniuk, Olga S. Bilozir, Andrei V. Voznyak
{"title":"Internet resources for foreign language education in primary school: challenges and opportunities","authors":"Inna A. Kravtsova, Alina O. Mankuta, Vita A. Hamaniuk, Olga S. Bilozir, Andrei V. Voznyak","doi":"10.55056/ceur-ws.org/vol-3482/paper041","DOIUrl":"https://doi.org/10.55056/ceur-ws.org/vol-3482/paper041","url":null,"abstract":"The paper explores the challenges and opportunities of developing professional competence of primary school teachers in teaching foreign languages according to the New Ukrainian School concept. The paper analyzes and describes various Internet resources that can facilitate and enhance foreign language learning outcomes in primary school. The paper argues that Internet resources can help modernize foreign language education in primary school and align it with the New Ukrainian School concept. The paper also discusses the importance of training primary school teachers in the methods of organizing distance learning, which is a priority for higher education institutions in the context of continuous education.","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135935615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
YouTube as an open resource for foreign language learning: a case study of German YouTube作为外语学习的开放资源:以德语为例
CEUR workshop proceedings Pub Date : 2023-09-12 DOI: 10.55056/ceur-ws.org/vol-3482/paper116
Olha V. Chorna, Vita A. Hamaniuk, Oksana Y. Markheva, Andrei V. Voznyak
{"title":"YouTube as an open resource for foreign language learning: a case study of German","authors":"Olha V. Chorna, Vita A. Hamaniuk, Oksana Y. Markheva, Andrei V. Voznyak","doi":"10.55056/ceur-ws.org/vol-3482/paper116","DOIUrl":"https://doi.org/10.55056/ceur-ws.org/vol-3482/paper116","url":null,"abstract":"The integration of information and communication technologies (ICT) in education has increased the possibilities and expanded the boundaries of the learning process. It is also a prerequisite for implementing distance learning. Various online resources, such as e-mail, blogs, forums, online applications, and video hosting sites, can be used to create open learning and education environments. This study focuses on the use of informational educational technologies for learning foreign languages, especially German. The article presents the results of a theoretical analysis of the content of YouTube video materials in terms of their personal and didactic relevance for teaching German as a first or second foreign language in higher education, specifically at a pedagogical university. Based on the practical experience of using several popular thematic YouTube channels with a large and stable audience, a brief didactic analysis of their products is provided and suggestions are made on how to transform video content into methodological material for the practical course of German language for future teachers. The article also explores the potential of using alternative YouTube resources for distance learning with regard to the development of mediation skills as defined by the authors of the CEFR Companion Volume with New Descriptors. Four types of resources that can serve as teaching materials are identified and analyzed; some examples of their preparation and use for the training of future foreign language teachers are given. The article also discusses the open resources ONCOO and TWINE, which can be used to foster the autonomy of future foreign language teachers, and describes their features. The proposed recommendations can help to achieve the following objectives: enriching vocabulary; semanticizing phraseological units, fixed expressions, clichés; developing pronunciation skills; enhancing linguistic and ICT competencies; improving listening and speaking skills; increasing motivation to learn, etc.","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135935773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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