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1.
PLoS One ; 19(8): e0308236, 2024.
Article in English | MEDLINE | ID: mdl-39106259

ABSTRACT

A fundamental computer vision task called semantic segmentation has significant uses in the understanding of medical pictures, including the segmentation of tumors in the brain. The G-Shaped Net architecture appears in this context as an innovative and promising design that combines components from many models to attain improved accuracy and efficiency. In order to improve efficiency, the G-Shaped Net architecture synergistically incorporates four fundamental components: the Self-Attention, Squeeze Excitation, Fusion, and Spatial Pyramid Pooling block structures. These factors work together to improve the precision and effectiveness of brain tumor segmentation. Self-Attention, a crucial component of G-Shaped architecture, gives the model the ability to concentrate on the image's most informative areas, enabling accurate localization of tumor boundaries. By adjusting channel-wise feature maps, Squeeze Excitation completes this by improving the model's capacity to capture fine-grained information in the medical pictures. Since the G-Shaped model's Spatial Pyramid Pooling component provides multi-scale contextual information, the model is capable of handling tumors of various sizes and complexity levels. Additionally, the Fusion block architectures combine characteristics from many sources, enabling a thorough comprehension of the image and improving the segmentation outcomes. The G-Shaped Net architecture is an asset for medical imaging and diagnostics and represents a substantial development in semantic segmentation, which is needed more and more for accurate brain tumor segmentation.


Subject(s)
Brain Neoplasms , Semantics , Humans , Brain Neoplasms/diagnostic imaging , Brain Neoplasms/pathology , Image Processing, Computer-Assisted/methods , Algorithms , Magnetic Resonance Imaging/methods , Neural Networks, Computer
2.
Sci Rep ; 14(1): 17971, 2024 08 02.
Article in English | MEDLINE | ID: mdl-39095437

ABSTRACT

Mnemonic discrimination of highly similar memory traces is affected in healthy aging via changes in hippocampal pattern separation-i.e., the ability of the hippocampus to orthogonalize highly similar neural inputs. The decline of this process leads to a loss of episodic specificity. Because previous studies have almost exclusively tested mnemonic discrimination of visuospatial stimuli (e.g., objects or scenes), less is known about age-related effects on the episodic specificity of semantically similar traces. To address this gap, we designed a task to assess mnemonic discrimination of verbal stimuli as a function of semantic similarity based on word embeddings. Forty young (Mage = 21.7 years) and 40 old adults (Mage = 69.8 years) first incidentally encoded adjective-noun phrases, then performed a surprise recognition test involving exactly repeated and highly similar lure phrases. We found that increasing semantic similarity negatively affected mnemonic discrimination in both age groups, and that compared to young adults, older adults showed worse discrimination at medium levels of semantic similarity. These results indicate that episodic specificity of semantically similar memory traces is affected in aging via less efficient mnemonic operations and strengthen the notion that mnemonic discrimination is a modality-independent process supporting memory specificity across representational domains.


Subject(s)
Healthy Aging , Semantics , Humans , Aged , Female , Male , Healthy Aging/physiology , Healthy Aging/psychology , Young Adult , Adult , Middle Aged , Recognition, Psychology/physiology , Memory/physiology , Memory, Episodic , Aging/physiology
3.
Brief Bioinform ; 25(5)2024 Jul 25.
Article in English | MEDLINE | ID: mdl-39154194

ABSTRACT

Understanding the genetic basis of disease is a fundamental aspect of medical research, as genes are the classic units of heredity and play a crucial role in biological function. Identifying associations between genes and diseases is critical for diagnosis, prevention, prognosis, and drug development. Genes that encode proteins with similar sequences are often implicated in related diseases, as proteins causing identical or similar diseases tend to show limited variation in their sequences. Predicting gene-disease association (GDA) requires time-consuming and expensive experiments on a large number of potential candidate genes. Although methods have been proposed to predict associations between genes and diseases using traditional machine learning algorithms and graph neural networks, these approaches struggle to capture the deep semantic information within the genes and diseases and are dependent on training data. To alleviate this issue, we propose a novel GDA prediction model named FusionGDA, which utilizes a pre-training phase with a fusion module to enrich the gene and disease semantic representations encoded by pre-trained language models. Multi-modal representations are generated by the fusion module, which includes rich semantic information about two heterogeneous biomedical entities: protein sequences and disease descriptions. Subsequently, the pooling aggregation strategy is adopted to compress the dimensions of the multi-modal representation. In addition, FusionGDA employs a pre-training phase leveraging a contrastive learning loss to extract potential gene and disease features by training on a large public GDA dataset. To rigorously evaluate the effectiveness of the FusionGDA model, we conduct comprehensive experiments on five datasets and compare our proposed model with five competitive baseline models on the DisGeNet-Eval dataset. Notably, our case study further demonstrates the ability of FusionGDA to discover hidden associations effectively. The complete code and datasets of our experiments are available at https://github.com/ZhaohanM/FusionGDA.


Subject(s)
Machine Learning , Humans , Computational Biology/methods , Genetic Predisposition to Disease , Semantics , Algorithms , Genetic Association Studies , Neural Networks, Computer
4.
Commun Biol ; 7(1): 926, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-39090387

ABSTRACT

A crucial aim in neuroscience is to understand how the human brain adapts to varying cognitive demands. This study investigates network reconfiguration during controlled semantic retrieval in differing contexts. We analyze brain responses to two semantic tasks of varying difficulty - global association and feature matching judgments - which are contrasted with non-semantic tasks on the cortical surface and within a whole-brain state space. Demanding semantic association tasks elicit activation in anterior prefrontal and temporal regions, while challenging semantic feature matching and non-semantic tasks predominantly activate posterior regions. Task difficulty also modulates activation along different dimensions of functional organization, suggesting different mechanisms of cognitive control. More demanding semantic association judgments engage cognitive control and default mode networks together, while feature matching and non-semantic tasks are skewed towards cognitive control networks. These findings highlight the brain's dynamic ability to tailor its networks to support diverse neurocognitive states, enriching our understanding of controlled cognition.


Subject(s)
Brain , Cognition , Magnetic Resonance Imaging , Semantics , Humans , Cognition/physiology , Brain/physiology , Male , Female , Adult , Young Adult , Brain Mapping , Nerve Net/physiology
5.
Database (Oxford) ; 20242024 Aug 08.
Article in English | MEDLINE | ID: mdl-39114977

ABSTRACT

The BioRED track at BioCreative VIII calls for a community effort to identify, semantically categorize, and highlight the novelty factor of the relationships between biomedical entities in unstructured text. Relation extraction is crucial for many biomedical natural language processing (NLP) applications, from drug discovery to custom medical solutions. The BioRED track simulates a real-world application of biomedical relationship extraction, and as such, considers multiple biomedical entity types, normalized to their specific corresponding database identifiers, as well as defines relationships between them in the documents. The challenge consisted of two subtasks: (i) in Subtask 1, participants were given the article text and human expert annotated entities, and were asked to extract the relation pairs, identify their semantic type and the novelty factor, and (ii) in Subtask 2, participants were given only the article text, and were asked to build an end-to-end system that could identify and categorize the relationships and their novelty. We received a total of 94 submissions from 14 teams worldwide. The highest F-score performances achieved for the Subtask 1 were: 77.17% for relation pair identification, 58.95% for relation type identification, 59.22% for novelty identification, and 44.55% when evaluating all of the above aspects of the comprehensive relation extraction. The highest F-score performances achieved for the Subtask 2 were: 55.84% for relation pair, 43.03% for relation type, 42.74% for novelty, and 32.75% for comprehensive relation extraction. The entire BioRED track dataset and other challenge materials are available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BC8-BioRED-track/ and https://codalab.lisn.upsaclay.fr/competitions/13377 and https://codalab.lisn.upsaclay.fr/competitions/13378. Database URL: https://ftp.ncbi.nlm.nih.gov/pub/lu/BC8-BioRED-track/https://codalab.lisn.upsaclay.fr/competitions/13377https://codalab.lisn.upsaclay.fr/competitions/13378.


Subject(s)
Data Mining , Natural Language Processing , Humans , Data Mining/methods , Databases, Factual , Semantics
6.
Sci Rep ; 14(1): 18319, 2024 08 07.
Article in English | MEDLINE | ID: mdl-39112791

ABSTRACT

Accurately assigning standardized diagnosis and procedure codes from clinical text is crucial for healthcare applications. However, this remains challenging due to the complexity of medical language. This paper proposes a novel model that incorporates extreme multi-label classification tasks to enhance International Classification of Diseases (ICD) coding. The model utilizes deformable convolutional neural networks to fuse representations from hidden layer outputs of pre-trained language models and external medical knowledge embeddings fused using a multimodal approach to provide rich semantic encodings for each code. A probabilistic label tree is constructed based on the hierarchical structure existing in ICD labels to incorporate ontological relationships between ICD codes and enable structured output prediction. Experiments on medical code prediction on the MIMIC-III database demonstrate competitive performance, highlighting the benefits of this technique for robust clinical code assignment.


Subject(s)
International Classification of Diseases , Neural Networks, Computer , Semantics , Humans , Natural Language Processing , Algorithms , Databases, Factual
7.
Sci Rep ; 14(1): 18538, 2024 08 09.
Article in English | MEDLINE | ID: mdl-39122920

ABSTRACT

All leading models of visual word recognition assume a hierarchical process that progressively converts the visual input into abstract letter and word representations. However, the results from recent behavioral studies suggest that the mental representations of words with a highly consistent visual format, such as logotypes, may comprise not only purely abstract information but also perceptual information. This hypothesis would explain why participants often misperceive transposed-letter misspellings with the original base words to a larger degree in logotypes (e.g., SASMUNG, but not SARVUNG, is perceived as SAMSUNG) than in common words. The present experiment examined the electrophysiological signature behind the identification of correctly spelled and misspelled logotypes (via letter transposition or replacement) in an ERP go/no-go semantic categorization experiment. Results showed that N400 amplitudes for transposed-letter misspelled logotypes (SASMUNG) and intact logotypes (SAMSUNG) did not differ significantly across various time windows (until 600 ms), whereas replacement-letter misspelled logotypes (SARVUNG) yielded consistently larger N400 amplitudes. These findings reveal that the mental representations of logotypes are particularly resistant to minor orthographic changes, which has important theoretical and applied (e.g., marketing) implications.


Subject(s)
Brain , Electroencephalography , Evoked Potentials , Humans , Male , Female , Brain/physiology , Young Adult , Evoked Potentials/physiology , Adult , Reading , Pattern Recognition, Visual/physiology , Semantics
8.
PeerJ ; 12: e17878, 2024.
Article in English | MEDLINE | ID: mdl-39157770

ABSTRACT

It remains uncertain whether causal structure prediction can improve comprehension in Chinese sentences and whether the position of the headword mediates the prediction effect. We conducted an experiment to explore the effect of causal prediction and headword position in Chinese sentence reading. Participants were asked to read sentences containing causal connectives with their eye movements recorded. In the experiment, we manipulated the causal structure of the sentence and the position of the headword. We found a promoting effect of causal structure on first-pass reading time and a hindering impact on total reading time. However, the effect was not mediated by the headword position. The results show that causal syntactic prediction facilitated early-stage processing and increased the integration cost in the late stage of Chinese sentence processing. These findings also support the constraint-based approach, which suggests an isolation between semantic and syntactic processing.


Subject(s)
Comprehension , Eye Movements , Reading , Semantics , Humans , Eye Movements/physiology , Comprehension/physiology , Female , Male , Young Adult , China , Language , Adult , East Asian People
9.
Cereb Cortex ; 34(8)2024 Aug 01.
Article in English | MEDLINE | ID: mdl-39123309

ABSTRACT

The functional importance of the anterior temporal lobes (ATLs) has come to prominence in two active, albeit unconnected literatures-(i) face recognition and (ii) semantic memory. To generate a unified account of the ATLs, we tested the predictions from each literature and examined the effects of bilateral versus unilateral ATL damage on face recognition, person knowledge, and semantic memory. Sixteen people with bilateral ATL atrophy from semantic dementia (SD), 17 people with unilateral ATL resection for temporal lobe epilepsy (TLE; left = 10, right = 7), and 14 controls completed tasks assessing perceptual face matching, person knowledge and general semantic memory. People with SD were impaired across all semantic tasks, including person knowledge. Despite commensurate total ATL damage, unilateral resection generated mild impairments, with minimal differences between left- and right-ATL resection. Face matching performance was largely preserved but slightly reduced in SD and right TLE. All groups displayed the familiarity effect in face matching; however, it was reduced in SD and right TLE and was aligned with the level of item-specific semantic knowledge in all participants. We propose a neurocognitive framework whereby the ATLs underpin a resilient bilateral representation system that supports semantic memory, person knowledge and face recognition.


Subject(s)
Epilepsy, Temporal Lobe , Facial Recognition , Semantics , Temporal Lobe , Humans , Male , Female , Middle Aged , Temporal Lobe/surgery , Temporal Lobe/diagnostic imaging , Temporal Lobe/pathology , Adult , Facial Recognition/physiology , Epilepsy, Temporal Lobe/surgery , Epilepsy, Temporal Lobe/psychology , Epilepsy, Temporal Lobe/physiopathology , Recognition, Psychology/physiology , Functional Laterality/physiology , Neuropsychological Tests , Memory/physiology , Aged , Face
10.
Sensors (Basel) ; 24(15)2024 Jul 26.
Article in English | MEDLINE | ID: mdl-39123907

ABSTRACT

Skeleton-based action recognition, renowned for its computational efficiency and indifference to lighting variations, has become a focal point in the realm of motion analysis. However, most current methods typically only extract global skeleton features, overlooking the potential semantic relationships among various partial limb motions. For instance, the subtle differences between actions such as "brush teeth" and "brush hair" are mainly distinguished by specific elements. Although combining limb movements provides a more holistic representation of an action, relying solely on skeleton points proves inadequate for capturing these nuances. Therefore, integrating detailed linguistic descriptions into the learning process of skeleton features is essential. This motivates us to explore integrating fine-grained language descriptions into the learning process of skeleton features to capture more discriminative skeleton behavior representations. To this end, we introduce a new Linguistic-Driven Partial Semantic Relevance Learning framework (LPSR) in this work. While using state-of-the-art large language models to generate linguistic descriptions of local limb motions and further constrain the learning of local motions, we also aggregate global skeleton point representations and textual representations (which generated from an LLM) to obtain a more generalized cross-modal behavioral representation. On this basis, we propose a cyclic attentional interaction module to model the implicit correlations between partial limb motions. Numerous ablation experiments demonstrate the effectiveness of the method proposed in this paper, and our method also obtains state-of-the-art results.


Subject(s)
Semantics , Humans , Linguistics , Movement/physiology , Pattern Recognition, Automated/methods , Algorithms , Learning/physiology
11.
J Psychiatry Neurosci ; 49(4): E252-E262, 2024.
Article in English | MEDLINE | ID: mdl-39122409

ABSTRACT

BACKGROUND: Psychosis involves a distortion of thought content, which is partly reflected in anomalous ways in which words are semantically connected into utterances in speech. We sought to explore how these linguistic anomalies are realized through putative circuit-level abnormalities in the brain's semantic network. METHODS: Using a computational large-language model, Bidirectional Encoder Representations from Transformers (BERT), we quantified the contextual expectedness of a given word sequence (perplexity) across 180 samples obtained from descriptions of 3 pictures by patients with first-episode schizophrenia (FES) and controls matched for age, parental social status, and sex, scanned with 7 T ultra-high field functional magnetic resonance imaging (fMRI). Subsequently, perplexity was used to parametrize a spectral dynamic causal model (DCM) of the effective connectivity within (intrinsic) and between (extrinsic) 4 key regions of the semantic network at rest, namely the anterior temporal lobe, the inferior frontal gyrus (IFG), the posterior middle temporal gyrus (MTG), and the angular gyrus. RESULTS: We included 60 participants, including 30 patients with FES and 30 controls. We observed higher perplexity in the FES group, indicating that speech was less predictable by the preceding context among patients. Results of Bayesian model comparisons showed that a DCM including the group by perplexity interaction best explained the underlying patterns of neural activity. We observed an increase of self-inhibitory effective connectivity within the IFG, as well as reduced self-inhibitory tone within the pMTG, in the FES group. An increase in self-inhibitory tone in the IFG correlated strongly and positively with inter-regional excitation between the IFG and posterior MTG, while self-inhibition of the posterior MTG was negatively correlated with this interregional excitation. LIMITATION: Our design did not address connectivity in the semantic network during tasks that selectively activated the semantic network, which could corroborate findings from this resting-state fMRI study. Furthermore, we do not present a replication study, which would ideally use speech in a different language. CONCLUSION: As an explanation for peculiar speech in psychosis, these results index a shift in the excitatory-inhibitory balance regulating information flow across the semantic network, confined to 2 regions that were previously linked specifically to the executive control of meaning. Based on our approach of combining a large language model with causal connectivity estimates, we propose loss in semantic control as a potential neurocognitive mechanism contributing to disorganization in psychosis.


Subject(s)
Magnetic Resonance Imaging , Psychotic Disorders , Schizophrenia , Semantics , Humans , Male , Female , Adult , Schizophrenia/diagnostic imaging , Schizophrenia/physiopathology , Young Adult , Psychotic Disorders/diagnostic imaging , Psychotic Disorders/physiopathology , Temporal Lobe/diagnostic imaging , Temporal Lobe/physiopathology , Speech/physiology , Bayes Theorem , Brain/diagnostic imaging , Brain/physiopathology , Nerve Net/diagnostic imaging , Nerve Net/physiopathology
12.
PLoS One ; 19(8): e0306812, 2024.
Article in English | MEDLINE | ID: mdl-39146270

ABSTRACT

This investigation into the effects of indoor soundscapes on learning efficiency during home-based online classes amidst the COVID-19 pandemic leveraged a questionnaire survey to gather insights from participants across 32 provinces in China. The survey findings reveal a notable preference among respondents for sounds emanating from nature and culture, alongside an acceptance of sounds inherent to lectures. A significant majority showed a preference for a tranquil soundscape or one enriched with natural and cultural elements, emphasizing that such an environment, coupled with the ability for active communication, is conducive to enhancing learning efficiency. Through semantic differential analysis, the study identified four pivotal factors that influence subjective evaluations of indoor soundscapes: the nature of online classes, relaxation, physical attributes of the soundscape, and aspects related to personal study. Additionally, the analysis delved into gender and regional differences in soundscape perceptions and their impact on learning. A key finding is that complex soundscapes negatively affect the learning process, with 45.7% of respondents reporting a perceived decrease in learning efficiency attributable to the indoor soundscape experienced during home-based online classes. Consequently, this study suggests that optimizing learning efficiency requires creating simpler, lighter, quieter, and more relaxing soundscapes. These insights hold both theoretical and practical value, offering a foundational basis for further research into indoor soundscapes and informing the development and management of online classes. The findings underscore the importance of considering the auditory environment as a critical component of effective online education, highlighting the need for strategies that mitigate auditory distractions and foster an acoustically conducive learning space.


Subject(s)
COVID-19 , Education, Distance , Learning , Humans , Male , Female , COVID-19/epidemiology , COVID-19/prevention & control , Adult , China , Education, Distance/methods , Surveys and Questionnaires , Sound , SARS-CoV-2 , Young Adult , Semantics , Pandemics , Middle Aged
13.
Phys Med Biol ; 69(17)2024 Aug 20.
Article in English | MEDLINE | ID: mdl-39094615

ABSTRACT

Objective.Automatic segmentation of prostatic zones from MRI can improve clinical diagnosis of prostate cancer as lesions in the peripheral zone (PZ) and central gland (CG) exhibit different characteristics. Existing approaches are limited in their accuracy in localizing the edges of PZ and CG. The proposed boundary-aware semantic clustering network (BASC-Net) improves segmentation performance by learning features in the vicinity of the prostate zonal boundaries, instead of only focusing on manually segmented boundaries.Approach.BASC-Net consists of two major components: the semantic clustering attention (SCA) module and the boundary-aware contrastive (BAC) loss. The SCA module implements a self-attention mechanism that extracts feature bases representing essential features of the inner body and boundary subregions and constructs attention maps highlighting each subregion. SCA is the first self-attention algorithm that utilizes ground truth masks to supervise the feature basis construction process. The features extracted from the inner body and boundary subregions of the same zone were integrated by BAC loss, which promotes the similarity of features extracted in the two subregions of the same zone. The BAC loss further promotes the difference between features extracted from different zones.Main results.BASC-Net was evaluated on the NCI-ISBI 2013 Challenge and Prostate158 datasets. An inter-dataset evaluation was conducted to evaluate the generalizability of the proposed method. BASC-Net outperformed nine state-of-the-art methods in all three experimental settings, attaining Dice similarity coefficients of 79.9% and 88.6% for PZ and CG, respectively, in the NCI-ISBI dataset, 80.5% and 89.2% for PZ and CG, respectively, in Prostate158 dataset, and 73.2% and 87.4% for PZ and CG, respectively, in the inter-dataset evaluation.Significance.As prostate lesions in PZ and CG have different characteristics, the zonal boundaries segmented by BASC-Net will facilitate prostate lesion detection.


Subject(s)
Image Processing, Computer-Assisted , Magnetic Resonance Imaging , Prostate , Semantics , Male , Humans , Magnetic Resonance Imaging/methods , Image Processing, Computer-Assisted/methods , Cluster Analysis , Prostate/diagnostic imaging , Prostatic Neoplasms/diagnostic imaging
14.
JMIR Hum Factors ; 11: e57670, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-39146009

ABSTRACT

BACKGROUND: The rapid growth of web-based medical services has highlighted the significance of smart triage systems in helping patients find the most appropriate physicians. However, traditional triage methods often rely on department recommendations and are insufficient to accurately match patients' textual questions with physicians' specialties. Therefore, there is an urgent need to develop algorithms for recommending physicians. OBJECTIVE: This study aims to develop and validate a patient-physician hybrid recommendation (PPHR) model with response metrics for better triage performance. METHODS: A total of 646,383 web-based medical consultation records from the Internet Hospital of the First Affiliated Hospital of Xiamen University were collected. Semantic features representing patients and physicians were developed to identify the set of most similar questions and semantically expand the pool of recommended physician candidates, respectively. The physicians' response rate feature was designed to improve candidate rankings. These 3 characteristics combine to create the PPHR model. Overall, 5 physicians participated in the evaluation of the efficiency of the PPHR model through multiple metrics and questionnaires as well as the performance of Sentence Bidirectional Encoder Representations from Transformers and Doc2Vec in text embedding. RESULTS: The PPHR model reaches the best recommendation performance when the number of recommended physicians is 14. At this point, the model has an F1-score of 76.25%, a proportion of high-quality services of 41.05%, and a rating of 3.90. After removing physicians' characteristics and response rates from the PPHR model, the F1-score decreased by 12.05%, the proportion of high-quality services fell by 10.87%, the average hit ratio dropped by 1.06%, and the rating declined by 11.43%. According to whether those 5 physicians were recommended by the PPHR model, Sentence Bidirectional Encoder Representations from Transformers achieved an average hit ratio of 88.6%, while Doc2Vec achieved an average hit ratio of 53.4%. CONCLUSIONS: The PPHR model uses semantic features and response metrics to enable patients to accurately find the physician who best suits their needs.


Subject(s)
Physicians , Semantics , Humans , Triage/methods , Triage/standards , Surveys and Questionnaires , Algorithms
15.
J Psycholinguist Res ; 53(5): 63, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-39147859

ABSTRACT

The present study investigated the effect of verbal working memory capacity (VWMC) on the processing of semantic information during on-line lexical ambiguity resolution of bilinguals. Seventeen Persian-English subordinate bilinguals of similar proficiency level were recruited to perform two experimental tasks: (1) a multi-load-level reading span task designed to measure their VWMC and (2) a cross-modal semantic priming task (CMPT), 24 h subsequent to the last encoding session, to assess their performance on semantic processing of L2 homographs whose subordinate readings were deemed "novel" for them. An overall 2 × 3 repeated-measures ANOVA revealed a statistically significant difference in the processing of the encoded semantic information between high and low WMC participants. The findings of the experiments lend support to the veracity of the assumptions made by Reordered Access Model in that biasing semantic context facilitates the ambiguity resolution of lexical items. Lastly, the pedagogical implications of the findings were expounded on.


Subject(s)
Memory, Short-Term , Multilingualism , Reading , Semantics , Humans , Memory, Short-Term/physiology , Young Adult , Male , Female , Adult , Psycholinguistics
16.
Database (Oxford) ; 20242024 Aug 09.
Article in English | MEDLINE | ID: mdl-39126204

ABSTRACT

The automatic recognition of biomedical relationships is an important step in the semantic understanding of the information contained in the unstructured text of the published literature. The BioRED track at BioCreative VIII aimed to foster the development of such methods by providing the participants the BioRED-BC8 corpus, a collection of 1000 PubMed documents manually curated for diseases, gene/proteins, chemicals, cell lines, gene variants, and species, as well as pairwise relationships between them which are disease-gene, chemical-gene, disease-variant, gene-gene, chemical-disease, chemical-chemical, chemical-variant, and variant-variant. Furthermore, relationships are categorized into the following semantic categories: positive correlation, negative correlation, binding, conversion, drug interaction, comparison, cotreatment, and association. Unlike most of the previous publicly available corpora, all relationships are expressed at the document level as opposed to the sentence level, and as such, the entities are normalized to the corresponding concept identifiers of the standardized vocabularies, namely, diseases and chemicals are normalized to MeSH, genes (and proteins) to National Center for Biotechnology Information (NCBI) Gene, species to NCBI Taxonomy, cell lines to Cellosaurus, and gene/protein variants to Single Nucleotide Polymorphism Database. Finally, each annotated relationship is categorized as 'novel' depending on whether it is a novel finding or experimental verification in the publication it is expressed in. This distinction helps differentiate novel findings from other relationships in the same text that provides known facts and/or background knowledge. The BioRED-BC8 corpus uses the previous BioRED corpus of 600 PubMed articles as the training dataset and includes a set of newly published 400 articles to serve as the test data for the challenge. All test articles were manually annotated for the BioCreative VIII challenge by expert biocurators at the National Library of Medicine, using the original annotation guidelines, where each article is doubly annotated in a three-round annotation process until full agreement is reached between all curators. This manuscript details the characteristics of the BioRED-BC8 corpus as a critical resource for biomedical named entity recognition and relation extraction. Using this new resource, we have demonstrated advancements in biomedical text-mining algorithm development. Database URL: https://codalab.lisn.upsaclay.fr/competitions/16381.


Subject(s)
Data Curation , Humans , Data Curation/methods , Data Mining/methods , Semantics , PubMed
17.
Neuroreport ; 35(13): 868-872, 2024 Sep 04.
Article in English | MEDLINE | ID: mdl-39101373

ABSTRACT

This study investigated whether the brain utilizes morphologically induced tones for semantic processing during online speech perception. An auditory comprehension task was conducted while measuring event-related potentials (ERPs). The study tested whether a discrepancy between contextual expectations and the tonal realizations of the target word would yield an N400 effect, indicative of semantic processing difficulty. An N400 effect was observed, reflecting integration difficulty due to semantic anomalies caused by incongruent tones. Additionally, the ERPs in the congruent conditions were modulated by the cohort entropy of the target word indicating lexical competition. The late negativity observed in this study encompasses both the N400 and preactivation negativity. This overlap underscores the brain's potential for rapidly connecting form and meaning from different sources within the word, relying on statistically based prediction in semantic processing.


Subject(s)
Electroencephalography , Semantics , Speech Perception , Humans , Male , Female , Speech Perception/physiology , Young Adult , Adult , Evoked Potentials/physiology , Acoustic Stimulation/methods , Brain/physiology , Comprehension/physiology , Evoked Potentials, Auditory/physiology , Adolescent
18.
Phys Med Biol ; 69(16)2024 Aug 02.
Article in English | MEDLINE | ID: mdl-39047770

ABSTRACT

Objective. Convolutional neural network (CNN) is developing rapidly in the field of medical image registration, and the proposed U-Net further improves the precision of registration. However, this method may discard certain important information in the process of encoding and decoding steps, consequently leading to a decline in accuracy. To solve this problem, a multi-channel semantic-aware and residual attention mechanism network (MSRA-Net) is proposed in this paper.Approach. Our proposed network achieves efficient information aggregation by cleverly extracting the features of different channels. Firstly, a context-aware module (CAM) is designed to extract valuable contextual information. And the depth-wise separable convolution is employed in the CAM to alleviate the computational burden. Then, a new multi-channel semantic-aware module (MCSAM) is designed for more comprehensive fusion of up-sampling features. Additionally, the residual attention module is introduced in the up-sampling process to extract more semantic information and minimize information loss.Main results. This study utilizes Dice score, average symmetric surface distance and negative Jacobian determinant evaluation metrics to evaluate the influence of registration. The experimental results demonstrate that our proposed MSRA-Net has the highest accuracy compared to several state-of-the-art methods. Moreover, our network has demonstrated the highest Dice score across multiple datasets, thereby indicating that the superior generalization capabilities of our model.Significance. The proposed MSRA-Net offers a novel approach to improve medical image registration accuracy, with implications for various clinical applications. Our implementation is available athttps://github.com/shy922/MSRA-Net.


Subject(s)
Imaging, Three-Dimensional , Neural Networks, Computer , Semantics , Imaging, Three-Dimensional/methods , Humans , Unsupervised Machine Learning
19.
Proc Natl Acad Sci U S A ; 121(30): e2315438121, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39028693

ABSTRACT

There is evidence from both behavior and brain activity that the way information is structured, through the use of focus, can up-regulate processing of focused constituents, likely to give prominence to the relevant aspects of the input. This is hypothesized to be universal, regardless of the different ways in which languages encode focus. In order to test this universalist hypothesis, we need to go beyond the more familiar linguistic strategies for marking focus, such as by means of intonation or specific syntactic structures (e.g., it-clefts). Therefore, in this study, we examine Makhuwa-Enahara, a Bantu language spoken in northern Mozambique, which uniquely marks focus through verbal conjugation. The participants were presented with sentences that consisted of either a semantically anomalous constituent or a semantically nonanomalous constituent. Moreover, focus on this particular constituent could be either present or absent. We observed a consistent pattern: Focused information generated a more negative N400 response than the same information in nonfocus position. This demonstrates that regardless of how focus is marked, its consequence seems to result in an upregulation of processing of information that is in focus.


Subject(s)
Language , Humans , Female , Male , Adult , Mozambique , Electroencephalography , Semantics , Brain/physiology , Young Adult , Linguistics , Evoked Potentials/physiology
20.
Cereb Cortex ; 34(7)2024 Jul 03.
Article in English | MEDLINE | ID: mdl-39011935

ABSTRACT

Companionship refers to one's being in the presence of another individual. For adults, acquiring a new language is a highly social activity that often involves learning in the context of companionship. However, the effects of companionship on new language learning have gone relatively underexplored, particularly with respect to word learning. Using a within-subject design, the current study employs electroencephalography to examine how two types of companionship (monitored and co-learning) affect word learning (semantic and lexical) in a new language. Dyads of Chinese speakers of English as a second language participated in a pseudo-word-learning task during which they were placed in monitored and co-learning companionship contexts. The results showed that exposure to co-learning companionship affected the early attention stage of word learning. Moreover, in this early stage, evidence of a higher representation similarity between co-learners showed additional support that co-learning companionship influenced attention. Observed increases in delta and theta interbrain synchronization further revealed that co-learning companionship facilitated semantic access. In all, the similar neural representations and interbrain synchronization between co-learners suggest that co-learning companionship offers important benefits for learning words in a new language.


Subject(s)
Brain , Electroencephalography , Humans , Male , Female , Young Adult , Adult , Brain/physiology , Learning/physiology , Semantics , Multilingualism , Language , Attention/physiology , Verbal Learning/physiology
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