Natural products(NPs)have long held a significant position in various fields such as medicine,food,agriculture,and materials.The chemical space covered by NPs is extensive but often underexplored.Therefore,high-throug...Natural products(NPs)have long held a significant position in various fields such as medicine,food,agriculture,and materials.The chemical space covered by NPs is extensive but often underexplored.Therefore,high-throughput and efficient methodologies for the annotation and discovery of NPs are desired to address the complexity and diversity of NP-based systems.Mass spectrometry(MS)has emerged as a powerful platform for the annotation and discovery of NPs.MS databases provide vital support for the structural characterization of NPs by integrating extensive mass spectral data and sample information.Additionally,the released annotation methodologies,based on a variety of informatics tools,continuously improve the ability to annotate the structure and properties of compounds.This review examines the current mainstream databases and annotation methodologies,focusing on their advantages and limitations.Prospects for future technological advancements are then discussed in terms of novel applications and research objectives.Through a systematic overview,this review aims to provide valuable insights and a reference for MS-based NPs annotation,thereby promoting the discovery of novel natural entities.展开更多
Glaucoma is an eye disease characterized by pathologically elevated intraocular pressure,optic nerve atrophy,and visual field defects,which can lead to irreversible vision loss.In recent years,the rapid development of...Glaucoma is an eye disease characterized by pathologically elevated intraocular pressure,optic nerve atrophy,and visual field defects,which can lead to irreversible vision loss.In recent years,the rapid development of artificial intelligence(AI)technology has provided new approaches for the early diagnosis and management of glaucoma.By classifying and annotating glaucoma-related images,AI models can learn and recognize the specific pathological features of glaucoma,thereby achieving automated imaging analysis and classification.Research on glaucoma imaging classification and annotation mainly involves color fundus photography(CFP),optical coherence tomography(OCT),anterior segment optical coherence tomography(AS-OCT),and ultrasound biomicroscopy(UBM)images.CFP is primarily used for the annotation of the optic cup and disc,while OCT is used for measuring and annotating the thickness of the retinal nerve fiber layer,and AS-OCT and UBM focus on the annotation of the anterior chamber angle structure and the measurement of anterior segment structural parameters.To standardize the classification and annotation of glaucoma images,enhance the quality and consistency of annotated data,and promote the clinical application of intelligent ophthalmology,this guideline has been developed.This guideline systematically elaborates on the principles,methods,processes,and quality control requirements for the classification and annotation of glaucoma images,providing standardized guidance for the classification and annotation of glaucoma images.展开更多
Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding.However,the lack of comprehensive functional genomic annotations in animals limits the effectiveness of mos...Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding.However,the lack of comprehensive functional genomic annotations in animals limits the effectiveness of most variant function assessment methods.In this study,we gather 1030 raw epigenomic datasets from 10 animal species and systematically annotate 7 types of key regulatory regions,creating a comprehensive functional annotation map of animal genomic variants.Our findings demonstrate that integrating variants with regulatory annotations can identify tissues and cell types underlying economic traits,underscoring the utility of these annotations in functional variant discovery.Using our functional annotations,we rank the functional potential of genetic variants and classify over 127 million candidate variants into 5 functional confidence categories,with high-confidence variants significantly enriched in eQTLs and trait-associated SNPs.Incorporating these variants into genomic prediction models can improve estimated breeding value accuracy,demonstrating their practical utility in breeding programs.To facilitate the use of our results,we develop the Integrated Functional Mutation(IFmut:http://www.ifmutants.com:8212)platform,enabling researchers to explore regulatory annotations and assess the functional potential of animal variants efficiently.Our study provides a robust framework for functional genomic annotations in farm animals,enhancing variant function assessment and breeding precision.展开更多
Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summariza...Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summarization is described. Three kernel descriptors such as gradient, shape, and color are extracted, respectively. Feature late-fusion is executed in turn by the multiple kernel learning model to obtain more discriminant image features. Absolute rank and relative rank of the tag-rank model are used to boost the key words＇ weights. A new word integration algorithm named word sequence blocks building （WSBB） is designed to create N-gram word sequences. Sentences are generated according to the N-gram word sequences and predefined templates. Experimental results show that both the BLEU-1 scores and BLEU-2 scores of the sentences are superior to those of the state-of-art baselines.展开更多
The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical research.Comprehensive reference genome annotation for both mRNA and long non-coding R...The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical research.Comprehensive reference genome annotation for both mRNA and long non-coding RNA(lncRNA)is crucial for developing animal models using this species.In the current study,we collected a total of 234 high-quality RNA sequencing(RNA-seq)datasets and two long-read isoform sequencing(ISO-seq)datasets and improved the annotation of our previously assembled high-quality chromosomelevel tree shrew genome.We obtained a total of 3514 newly annotated coding genes and 50576 lncRNA genes.We also characterized the tissuespecific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome.We identified 144 tree shrew-specific gene families,including interleukin 6(IL6)and STT3 oligosaccharyltransferase complex catalytic subunit B(STT3B),which underwent significant changes in size.Comparison of the overall expression patterns in tissues and pathways across four species(human,rhesus monkey,tree shrew,and mouse)indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level.Notably,the newly annotated purine rich element binding protein A(PURA)gene and the STT3B gene family showed dysregulation upon viral infection.The updated version of the tree shrew genome annotation(KIZ version 3:TS_3.0)is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.展开更多
The abundant entities and entity-attribute relations in medical websites are important data resources for medical research.However,the medical websites are usually characterized of storing entity and attribute values ...The abundant entities and entity-attribute relations in medical websites are important data resources for medical research.However,the medical websites are usually characterized of storing entity and attribute values in different pages.To extract those data records efficiently,we propose an automatic extraction system which is related to entity and attribute relations（attributes and values）of separate storage.Our system includes following modules：（1）rich-information interactive annotation page rendering;（2）separate storage attribute relations annotating;（3）annotated relations for pattern generating and data records extracting.This paper presents the relations about the attributes which are stored in many pages by effective annotation,then generates rules for data records extraction.The experiments show that the system can not only complete attribute relations of separate storage extraction,but also be compatible with regular relation extraction,while maintaining high accuracy.展开更多
Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple t...Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.展开更多
In industry,it is becoming common to detect and recognize industrial workpieces using deep learning methods.In this field,the lack of datasets is a big problem,and collecting and annotating datasets in this field is v...In industry,it is becoming common to detect and recognize industrial workpieces using deep learning methods.In this field,the lack of datasets is a big problem,and collecting and annotating datasets in this field is very labor intensive.The researchers need to perform dataset annotation if a dataset is generated by themselves.It is also one of the restrictive factors that the current method based on deep learning cannot expand well.At present,there are very few workpiece datasets for industrial fields,and the existing datasets are generated from ideal workpiece computer aided design(CAD)models,for which few actual workpiece images were collected and utilized.We propose an automatic industrial workpiece dataset generation method and an automatic ground truth annotation method.Included in our methods are three algorithms that we proposed:a point cloud based spatial plane segmentation algorithm to segment the workpieces in the real scene and to obtain the annotation information of the workpieces in the images captured in the real scene;a random multiple workpiece generation algorithm to generate abundant composition datasets with random rotation workpiece angles and positions;and a tangent vector based contour tracking and completion algorithm to get improved contour images.With our procedures,annotation information can be obtained using the algorithms proposed in this paper.Upon completion of the annotation process,a json format file is generated.Faster R-CNN(Faster R-convolutional neural network),SSD(single shot multibox detector)and YOLO(you only look once:unified,real-time object detection)are trained using the datasets proposed in this paper.The experimental results show the effectiveness and integrity of this dataset generation and annotation method.展开更多
In recent years it has been recognized that not only total amount of fat,but also fat distribution plays an important role in metabolism.Visceral adipose tissue(VAT),the most important component of central obesity,is ...In recent years it has been recognized that not only total amount of fat,but also fat distribution plays an important role in metabolism.Visceral adipose tissue(VAT),the most important component of central obesity,is closely related to insulin resistance and hyperlipidemia.It is hypothesized that an overflow展开更多
Commentary Most would agree that providing comprehensive detail in scientific reporting is critical for the development of mean- ingful therapies and treatments for diseases. Such stellar practices 1） allow for repro...Commentary Most would agree that providing comprehensive detail in scientific reporting is critical for the development of mean- ingful therapies and treatments for diseases. Such stellar practices 1） allow for reproduction of experiments to con- firm results, 2） promote thorough analyses of data, and 3） foster the incremental advancement of valid approaches. Unfortunately, most would also agree we have far to go to reach this vital goal （Hackam and Redelmeier, 2006; Prinz et al., 2011; Baker et al., 2014）.展开更多
The success of deep transfer learning in fault diagnosis is attributed to the collection of high-quality labeled data from the source domain.However,in engineering scenarios,achieving such high-quality label annotatio...The success of deep transfer learning in fault diagnosis is attributed to the collection of high-quality labeled data from the source domain.However,in engineering scenarios,achieving such high-quality label annotation is difficult and expensive.The incorrect label annotation produces two negative effects:1)the complex decision boundary of diagnosis models lowers the generalization performance on the target domain,and2)the distribution of target domain samples becomes misaligned with the false-labeled samples.To overcome these negative effects,this article proposes a solution called the label recovery and trajectory designable network(LRTDN).LRTDN consists of three parts.First,a residual network with dual classifiers is to learn features from cross-domain samples.Second,an annotation check module is constructed to generate a label anomaly indicator that could modify the abnormal labels of false-labeled samples in the source domain.With the training of relabeled samples,the complexity of diagnosis model is reduced via semi-supervised learning.Third,the adaptation trajectories are designed for sample distributions across domains.This ensures that the target domain samples are only adapted with the pure-labeled samples.The LRTDN is verified by two case studies,in which the diagnosis knowledge of bearings is transferred across different working conditions as well as different yet related machines.The results show that LRTDN offers a high diagnosis accuracy even in the presence of incorrect annotation.展开更多
Automatic image annotation has been an active topic of research in computer vision and pattern recognition for decades.A two stage automatic image annotation method based on Gaussian mixture model(GMM) and random walk...Automatic image annotation has been an active topic of research in computer vision and pattern recognition for decades.A two stage automatic image annotation method based on Gaussian mixture model(GMM) and random walk model(abbreviated as GMM-RW) is presented.To start with,GMM fitted by the rival penalized expectation maximization(RPEM) algorithm is employed to estimate the posterior probabilities of each annotation keyword.Subsequently,a random walk process over the constructed label similarity graph is implemented to further mine the potential correlations of the candidate annotations so as to capture the refining results,which plays a crucial role in semantic based image retrieval.The contributions exhibited in this work are multifold.First,GMM is exploited to capture the initial semantic annotations,especially the RPEM algorithm is utilized to train the model that can determine the number of components in GMM automatically.Second,a label similarity graph is constructed by a weighted linear combination of label similarity and visual similarity of images associated with the corresponding labels,which is able to avoid the phenomena of polysemy and synonym efficiently during the image annotation process.Third,the random walk is implemented over the constructed label graph to further refine the candidate set of annotations generated by GMM.Conducted experiments on the standard Corel5 k demonstrate that GMM-RW is significantly more effective than several state-of-the-arts regarding their effectiveness and efficiency in the task of automatic image annotation.展开更多
A novel image auto-annotation method is presented based on probabilistic latent semantic analysis(PLSA) model and multiple Markov random fields(MRF).A PLSA model with asymmetric modalities is first constructed to esti...A novel image auto-annotation method is presented based on probabilistic latent semantic analysis(PLSA) model and multiple Markov random fields(MRF).A PLSA model with asymmetric modalities is first constructed to estimate the joint probability between images and semantic concepts,then a subgraph is extracted served as the corresponding structure of Markov random fields and inference over it is performed by the iterative conditional modes so as to capture the final annotation for the image.The novelty of our method mainly lies in two aspects:exploiting PLSA to estimate the joint probability between images and semantic concepts as well as multiple MRF to further explore the semantic context among keywords for accurate image annotation.To demonstrate the effectiveness of this approach,an experiment on the Corel5 k dataset is conducted and its results are compared favorably with the current state-of-the-art approaches.展开更多
As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinfor...As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.展开更多
This paper presents a new method for refining image annotation by integrating probabilistic la- tent semantic analysis （PLSA） with conditional random field （CRF）. First a PLSA model with asymmetric modalities is c...This paper presents a new method for refining image annotation by integrating probabilistic la- tent semantic analysis （PLSA） with conditional random field （CRF）. First a PLSA model with asymmetric modalities is constructed to predict a candidate set of annotations with confidence scores, and then model semantic relationship among the candidate annotations by leveraging conditional ran- dom field. In CRF, the confidence scores generated lay the PLSA model and the Fliekr distance be- tween pairwise candidate annotations are considered as local evidences and contextual potentials re- spectively. The novelty of our method mainly lies in two aspects ： exploiting PLSA to predict a candi- date set of annotations with confidence scores as well as CRF to further explore the semantic context among candidate annotations for precise image annotation. To demonstrate the effectiveness of the method proposed in this paper, an experiment is conducted on the standard Corel dataset and its re- sults are ＇compared favorably with several state-of-the-art approaches.展开更多
This paper investigates the Italian firms＇ disclosure in response to the new guidance on the management commentary （MC） contained in the International Financial Reporting Standard （IFRS） practice statement issued...This paper investigates the Italian firms＇ disclosure in response to the new guidance on the management commentary （MC） contained in the International Financial Reporting Standard （IFRS） practice statement issued by International Accounting Standards Board （IASB） in 2010. The study is organized as follows. After reviewing the relevant literature on financial disclosure and MC, this paper examines the content of the Italian management＇s report-----known as ＂Relazione sulla Gestione＂ and that of the recent IASB＇s IFRS practice statement. Hence, it applies a self-constructed disclosure index and a multiple correspondence analysis （MCA） on MC of a sample of 66 Italian non-financial listed firms. The results show that the level of disclosures provided by the Italian listed firms does not seem to be affected by the IASB＇s guidelines. However, the survey highlights large differences in the level and type of disclosure provided in MC among the sectors and firms. This paper aims to contribute to the financial reporting debate by understanding the IASB＇s guidelines and their impacts on the voluntary disclosure practices of Italian listed firms.展开更多
The application of whole genome sequencing is expanding in clinical diagnostics across various genetic disorders, and the significance of non-coding variants in penetrant diseases is increasingly being demonstrated. T...The application of whole genome sequencing is expanding in clinical diagnostics across various genetic disorders, and the significance of non-coding variants in penetrant diseases is increasingly being demonstrated. Therefore, it is urgent to improve the diagnostic yield by exploring the pathogenic mechanisms of variants in non-coding regions. However, the interpretation of non-coding variants remains a significant challenge, due to the complex functional regulatory mechanisms of non-coding regions and the current limitations of available databases and tools. Hence, we develop the non-coding variant annotation database (NCAD, http://www.ncawdb.net/), encompassing comprehensive insights into 665,679,194 variants, regulatory elements, and element interaction details. Integrating data from 96 sources, spanning both GRCh37 and GRCh38 versions, NCAD v1.0 provides vital information to support the genetic diagnosis of non-coding variants, including allele frequencies of 12 diverse populations, with a particular focus on the population frequency information for 230,235,698 variants in 20,964 Chinese individuals. Moreover, it offers prediction scores for variant functionality, five categories of regulatory elements, and four types of non-coding RNAs. With its rich data and comprehensive coverage, NCAD serves as a valuable platform, empowering researchers and clinicians with profound insights into non-coding regulatory mechanisms while facilitating the interpretation of non-coding variants.展开更多
In order to bridge the semantic gap exists in image retrieval, this paper propose an approach combining generative and discriminative learning to accomplish the task of automatic image annotation and retrieval. We fir...In order to bridge the semantic gap exists in image retrieval, this paper propose an approach combining generative and discriminative learning to accomplish the task of automatic image annotation and retrieval. We firstly present continuous probabilistic latent semantic analysis (PLSA) to model continuous quantity. Furthermore, we propose a hybrid framework which employs continuous PLSA to model visual features of images in generative learning stage and uses ensembles of classifier chains to classify the multi-label data in discriminative learning stage. Since the framework combines the advantages of generative and discriminative learning, it can predict semantic annotation precisely for unseen images. Finally, we conduct a series of experiments on a standard Corel dataset. The experiment results show that our approach outperforms many state-of-the-art approaches.展开更多
●AIM:To investigate a pioneering framework for the segmentation of meibomian glands(MGs),using limited annotations to reduce the workload on ophthalmologists and enhance the efficiency of clinical diagnosis.●METHODS...●AIM:To investigate a pioneering framework for the segmentation of meibomian glands(MGs),using limited annotations to reduce the workload on ophthalmologists and enhance the efficiency of clinical diagnosis.●METHODS:Totally 203 infrared meibomian images from 138 patients with dry eye disease,accompanied by corresponding annotations,were gathered for the study.A rectified scribble-supervised gland segmentation(RSSGS)model,incorporating temporal ensemble prediction,uncertainty estimation,and a transformation equivariance constraint,was introduced to address constraints imposed by limited supervision information inherent in scribble annotations.The viability and efficacy of the proposed model were assessed based on accuracy,intersection over union(IoU),and dice coefficient.●RESULTS:Using manual labels as the gold standard,RSSGS demonstrated outcomes with an accuracy of 93.54%,a dice coefficient of 78.02%,and an IoU of 64.18%.Notably,these performance metrics exceed the current weakly supervised state-of-the-art methods by 0.76%,2.06%,and 2.69%,respectively.Furthermore,despite achieving a substantial 80%reduction in annotation costs,it only lags behind fully annotated methods by 0.72%,1.51%,and 2.04%.●CONCLUSION:An innovative automatic segmentation model is developed for MGs in infrared eyelid images,using scribble annotation for training.This model maintains an exceptionally high level of segmentation accuracy while substantially reducing training costs.It holds substantial utility for calculating clinical parameters,thereby greatly enhancing the diagnostic efficiency of ophthalmologists in evaluating meibomian gland dysfunction.展开更多
基金supported by the National Natural Science Foundation of China(Nos.82274064,82374026,and 82204591)。
文摘Natural products(NPs)have long held a significant position in various fields such as medicine,food,agriculture,and materials.The chemical space covered by NPs is extensive but often underexplored.Therefore,high-throughput and efficient methodologies for the annotation and discovery of NPs are desired to address the complexity and diversity of NP-based systems.Mass spectrometry(MS)has emerged as a powerful platform for the annotation and discovery of NPs.MS databases provide vital support for the structural characterization of NPs by integrating extensive mass spectral data and sample information.Additionally,the released annotation methodologies,based on a variety of informatics tools,continuously improve the ability to annotate the structure and properties of compounds.This review examines the current mainstream databases and annotation methodologies,focusing on their advantages and limitations.Prospects for future technological advancements are then discussed in terms of novel applications and research objectives.Through a systematic overview,this review aims to provide valuable insights and a reference for MS-based NPs annotation,thereby promoting the discovery of novel natural entities.
基金Supported by Guangdong Basic and Applied Basic Research Foundation(No.2025A1515011627)San Ming Project of Medicine in Shenzhen(No.SZSM202311012).
文摘Glaucoma is an eye disease characterized by pathologically elevated intraocular pressure,optic nerve atrophy,and visual field defects,which can lead to irreversible vision loss.In recent years,the rapid development of artificial intelligence(AI)technology has provided new approaches for the early diagnosis and management of glaucoma.By classifying and annotating glaucoma-related images,AI models can learn and recognize the specific pathological features of glaucoma,thereby achieving automated imaging analysis and classification.Research on glaucoma imaging classification and annotation mainly involves color fundus photography(CFP),optical coherence tomography(OCT),anterior segment optical coherence tomography(AS-OCT),and ultrasound biomicroscopy(UBM)images.CFP is primarily used for the annotation of the optic cup and disc,while OCT is used for measuring and annotating the thickness of the retinal nerve fiber layer,and AS-OCT and UBM focus on the annotation of the anterior chamber angle structure and the measurement of anterior segment structural parameters.To standardize the classification and annotation of glaucoma images,enhance the quality and consistency of annotated data,and promote the clinical application of intelligent ophthalmology,this guideline has been developed.This guideline systematically elaborates on the principles,methods,processes,and quality control requirements for the classification and annotation of glaucoma images,providing standardized guidance for the classification and annotation of glaucoma images.
基金supported by the National Natural Science Foundation of China(32341051)the grant from Department of Agriculture and Rural Affairs of Hubei Province(HBZY2023B006-02)+2 种基金the National Funding(2023ZD04050)the National Natural Science Foundation of China Outstanding Youth(32125035)the National Key R&D Young Scientists Project(2022YFD1302000).
文摘Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding.However,the lack of comprehensive functional genomic annotations in animals limits the effectiveness of most variant function assessment methods.In this study,we gather 1030 raw epigenomic datasets from 10 animal species and systematically annotate 7 types of key regulatory regions,creating a comprehensive functional annotation map of animal genomic variants.Our findings demonstrate that integrating variants with regulatory annotations can identify tissues and cell types underlying economic traits,underscoring the utility of these annotations in functional variant discovery.Using our functional annotations,we rank the functional potential of genetic variants and classify over 127 million candidate variants into 5 functional confidence categories,with high-confidence variants significantly enriched in eQTLs and trait-associated SNPs.Incorporating these variants into genomic prediction models can improve estimated breeding value accuracy,demonstrating their practical utility in breeding programs.To facilitate the use of our results,we develop the Integrated Functional Mutation(IFmut:http://www.ifmutants.com:8212)platform,enabling researchers to explore regulatory annotations and assess the functional potential of animal variants efficiently.Our study provides a robust framework for functional genomic annotations in farm animals,enhancing variant function assessment and breeding precision.
基金The National Natural Science Foundation of China(No.61133012)the Humanity and Social Science Foundation of the Ministry of Education(No.12YJCZH274)+1 种基金the Humanity and Social Science Foundation of Jiangxi Province(No.XW1502,TQ1503)the Science and Technology Project of Jiangxi Science and Technology Department(No.20121BBG70050,20142BBG70011)
文摘Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summarization is described. Three kernel descriptors such as gradient, shape, and color are extracted, respectively. Feature late-fusion is executed in turn by the multiple kernel learning model to obtain more discriminant image features. Absolute rank and relative rank of the tag-rank model are used to boost the key words＇ weights. A new word integration algorithm named word sequence blocks building （WSBB） is designed to create N-gram word sequences. Sentences are generated according to the N-gram word sequences and predefined templates. Experimental results show that both the BLEU-1 scores and BLEU-2 scores of the sentences are superior to those of the state-of-art baselines.
基金This study was supported by the National Natural Science Foundation of China(U1902215 to Y.G.Y.and 31970542 to Y.F.)Chinese Academy of Sciences(Light of West China Program xbzg-zdsys-201909 to Y.G.Y.)Yunnan Province(202001AS070023 and 2018FB046 to D.D.Y.and 202002AA100007 to Y.G.Y.)。
文摘The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical research.Comprehensive reference genome annotation for both mRNA and long non-coding RNA(lncRNA)is crucial for developing animal models using this species.In the current study,we collected a total of 234 high-quality RNA sequencing(RNA-seq)datasets and two long-read isoform sequencing(ISO-seq)datasets and improved the annotation of our previously assembled high-quality chromosomelevel tree shrew genome.We obtained a total of 3514 newly annotated coding genes and 50576 lncRNA genes.We also characterized the tissuespecific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome.We identified 144 tree shrew-specific gene families,including interleukin 6(IL6)and STT3 oligosaccharyltransferase complex catalytic subunit B(STT3B),which underwent significant changes in size.Comparison of the overall expression patterns in tissues and pathways across four species(human,rhesus monkey,tree shrew,and mouse)indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level.Notably,the newly annotated purine rich element binding protein A(PURA)gene and the STT3B gene family showed dysregulation upon viral infection.The updated version of the tree shrew genome annotation(KIZ version 3:TS_3.0)is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.
基金Supported by the Natural Science Foundation of Hubei Province(2013CFB334)
文摘The abundant entities and entity-attribute relations in medical websites are important data resources for medical research.However,the medical websites are usually characterized of storing entity and attribute values in different pages.To extract those data records efficiently,we propose an automatic extraction system which is related to entity and attribute relations（attributes and values）of separate storage.Our system includes following modules：（1）rich-information interactive annotation page rendering;（2）separate storage attribute relations annotating;（3）annotated relations for pattern generating and data records extracting.This paper presents the relations about the attributes which are stored in many pages by effective annotation,then generates rules for data records extraction.The experiments show that the system can not only complete attribute relations of separate storage extraction,but also be compatible with regular relation extraction,while maintaining high accuracy.
基金supported by funds from the National Key R&D Program of China (2016YFC0901603)the China 863 Program (2015AA020108)+1 种基金the State Key Laboratory of Protein and Plant Gene Researchsupported in part by the National Program for Support of Top-notch Young Professionals
文摘Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites （TFBSs） are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential ＂interference＂ among multiple variants within the same TFBS. In this study, we presented COPE-TFBS （Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site）, a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression （GTEx） Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants.
文摘In industry,it is becoming common to detect and recognize industrial workpieces using deep learning methods.In this field,the lack of datasets is a big problem,and collecting and annotating datasets in this field is very labor intensive.The researchers need to perform dataset annotation if a dataset is generated by themselves.It is also one of the restrictive factors that the current method based on deep learning cannot expand well.At present,there are very few workpiece datasets for industrial fields,and the existing datasets are generated from ideal workpiece computer aided design(CAD)models,for which few actual workpiece images were collected and utilized.We propose an automatic industrial workpiece dataset generation method and an automatic ground truth annotation method.Included in our methods are three algorithms that we proposed:a point cloud based spatial plane segmentation algorithm to segment the workpieces in the real scene and to obtain the annotation information of the workpieces in the images captured in the real scene;a random multiple workpiece generation algorithm to generate abundant composition datasets with random rotation workpiece angles and positions;and a tangent vector based contour tracking and completion algorithm to get improved contour images.With our procedures,annotation information can be obtained using the algorithms proposed in this paper.Upon completion of the annotation process,a json format file is generated.Faster R-CNN(Faster R-convolutional neural network),SSD(single shot multibox detector)and YOLO(you only look once:unified,real-time object detection)are trained using the datasets proposed in this paper.The experimental results show the effectiveness and integrity of this dataset generation and annotation method.
文摘In recent years it has been recognized that not only total amount of fat,but also fat distribution plays an important role in metabolism.Visceral adipose tissue(VAT),the most important component of central obesity,is closely related to insulin resistance and hyperlipidemia.It is hypothesized that an overflow
文摘Commentary Most would agree that providing comprehensive detail in scientific reporting is critical for the development of mean- ingful therapies and treatments for diseases. Such stellar practices 1） allow for reproduction of experiments to con- firm results, 2） promote thorough analyses of data, and 3） foster the incremental advancement of valid approaches. Unfortunately, most would also agree we have far to go to reach this vital goal （Hackam and Redelmeier, 2006; Prinz et al., 2011; Baker et al., 2014）.
基金the National Key R&D Program of China(2022YFB3402100)the National Science Fund for Distinguished Young Scholars of China(52025056)+4 种基金the National Natural Science Foundation of China(52305129)the China Postdoctoral Science Foundation(2023M732789)the China Postdoctoral Innovative Talents Support Program(BX20230290)the Open Foundation of Hunan Provincial Key Laboratory of Health Maintenance for Mechanical Equipment(2022JXKF JJ01)the Fundamental Research Funds for Central Universities。
文摘The success of deep transfer learning in fault diagnosis is attributed to the collection of high-quality labeled data from the source domain.However,in engineering scenarios,achieving such high-quality label annotation is difficult and expensive.The incorrect label annotation produces two negative effects:1)the complex decision boundary of diagnosis models lowers the generalization performance on the target domain,and2)the distribution of target domain samples becomes misaligned with the false-labeled samples.To overcome these negative effects,this article proposes a solution called the label recovery and trajectory designable network(LRTDN).LRTDN consists of three parts.First,a residual network with dual classifiers is to learn features from cross-domain samples.Second,an annotation check module is constructed to generate a label anomaly indicator that could modify the abnormal labels of false-labeled samples in the source domain.With the training of relabeled samples,the complexity of diagnosis model is reduced via semi-supervised learning.Third,the adaptation trajectories are designed for sample distributions across domains.This ensures that the target domain samples are only adapted with the pure-labeled samples.The LRTDN is verified by two case studies,in which the diagnosis knowledge of bearings is transferred across different working conditions as well as different yet related machines.The results show that LRTDN offers a high diagnosis accuracy even in the presence of incorrect annotation.
基金Supported by the National Basic Research Program of China(No.2013CB329502)the National Natural Science Foundation of China(No.61202212)+1 种基金the Special Research Project of the Educational Department of Shaanxi Province of China(No.15JK1038)the Key Research Project of Baoji University of Arts and Sciences(No.ZK16047)
文摘Automatic image annotation has been an active topic of research in computer vision and pattern recognition for decades.A two stage automatic image annotation method based on Gaussian mixture model(GMM) and random walk model(abbreviated as GMM-RW) is presented.To start with,GMM fitted by the rival penalized expectation maximization(RPEM) algorithm is employed to estimate the posterior probabilities of each annotation keyword.Subsequently,a random walk process over the constructed label similarity graph is implemented to further mine the potential correlations of the candidate annotations so as to capture the refining results,which plays a crucial role in semantic based image retrieval.The contributions exhibited in this work are multifold.First,GMM is exploited to capture the initial semantic annotations,especially the RPEM algorithm is utilized to train the model that can determine the number of components in GMM automatically.Second,a label similarity graph is constructed by a weighted linear combination of label similarity and visual similarity of images associated with the corresponding labels,which is able to avoid the phenomena of polysemy and synonym efficiently during the image annotation process.Third,the random walk is implemented over the constructed label graph to further refine the candidate set of annotations generated by GMM.Conducted experiments on the standard Corel5 k demonstrate that GMM-RW is significantly more effective than several state-of-the-arts regarding their effectiveness and efficiency in the task of automatic image annotation.
基金Supported by the National Basic Research Priorities Program(No.2013CB329502)the National High-tech R&D Program of China(No.2012AA011003)+1 种基金National Natural Science Foundation of China(No.61035003,61072085,60933004,60903141)the National Scienceand Technology Support Program of China(No.2012BA107B02)
文摘A novel image auto-annotation method is presented based on probabilistic latent semantic analysis(PLSA) model and multiple Markov random fields(MRF).A PLSA model with asymmetric modalities is first constructed to estimate the joint probability between images and semantic concepts,then a subgraph is extracted served as the corresponding structure of Markov random fields and inference over it is performed by the iterative conditional modes so as to capture the final annotation for the image.The novelty of our method mainly lies in two aspects:exploiting PLSA to estimate the joint probability between images and semantic concepts as well as multiple MRF to further explore the semantic context among keywords for accurate image annotation.To demonstrate the effectiveness of this approach,an experiment on the Corel5 k dataset is conducted and its results are compared favorably with the current state-of-the-art approaches.
基金Supported by the National Natural Science Foundation of China( No. 3 9980 0 0 5 )
文摘As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.
基金Supported by the National Basic Research Priorities Programme(No.2013CB329502)the National High Technology Research and Development Programme of China(No.2012AA011003)+1 种基金the Natural Science Basic Research Plan in Shanxi Province of China(No.2014JQ2-6036)the Science and Technology R&D Program of Baoji City(No.203020013,2013R2-2)
文摘This paper presents a new method for refining image annotation by integrating probabilistic la- tent semantic analysis （PLSA） with conditional random field （CRF）. First a PLSA model with asymmetric modalities is constructed to predict a candidate set of annotations with confidence scores, and then model semantic relationship among the candidate annotations by leveraging conditional ran- dom field. In CRF, the confidence scores generated lay the PLSA model and the Fliekr distance be- tween pairwise candidate annotations are considered as local evidences and contextual potentials re- spectively. The novelty of our method mainly lies in two aspects ： exploiting PLSA to predict a candi- date set of annotations with confidence scores as well as CRF to further explore the semantic context among candidate annotations for precise image annotation. To demonstrate the effectiveness of the method proposed in this paper, an experiment is conducted on the standard Corel dataset and its re- sults are ＇compared favorably with several state-of-the-art approaches.
文摘This paper investigates the Italian firms＇ disclosure in response to the new guidance on the management commentary （MC） contained in the International Financial Reporting Standard （IFRS） practice statement issued by International Accounting Standards Board （IASB） in 2010. The study is organized as follows. After reviewing the relevant literature on financial disclosure and MC, this paper examines the content of the Italian management＇s report-----known as ＂Relazione sulla Gestione＂ and that of the recent IASB＇s IFRS practice statement. Hence, it applies a self-constructed disclosure index and a multiple correspondence analysis （MCA） on MC of a sample of 66 Italian non-financial listed firms. The results show that the level of disclosures provided by the Italian listed firms does not seem to be affected by the IASB＇s guidelines. However, the survey highlights large differences in the level and type of disclosure provided in MC among the sectors and firms. This paper aims to contribute to the financial reporting debate by understanding the IASB＇s guidelines and their impacts on the voluntary disclosure practices of Italian listed firms.
基金supported by the National Natural Science Foundation of China(82171836)the 1·3·5 project for disciplines of excellence,West China Hospital,Sichuan University(ZYJC20002).
文摘The application of whole genome sequencing is expanding in clinical diagnostics across various genetic disorders, and the significance of non-coding variants in penetrant diseases is increasingly being demonstrated. Therefore, it is urgent to improve the diagnostic yield by exploring the pathogenic mechanisms of variants in non-coding regions. However, the interpretation of non-coding variants remains a significant challenge, due to the complex functional regulatory mechanisms of non-coding regions and the current limitations of available databases and tools. Hence, we develop the non-coding variant annotation database (NCAD, http://www.ncawdb.net/), encompassing comprehensive insights into 665,679,194 variants, regulatory elements, and element interaction details. Integrating data from 96 sources, spanning both GRCh37 and GRCh38 versions, NCAD v1.0 provides vital information to support the genetic diagnosis of non-coding variants, including allele frequencies of 12 diverse populations, with a particular focus on the population frequency information for 230,235,698 variants in 20,964 Chinese individuals. Moreover, it offers prediction scores for variant functionality, five categories of regulatory elements, and four types of non-coding RNAs. With its rich data and comprehensive coverage, NCAD serves as a valuable platform, empowering researchers and clinicians with profound insights into non-coding regulatory mechanisms while facilitating the interpretation of non-coding variants.
文摘In order to bridge the semantic gap exists in image retrieval, this paper propose an approach combining generative and discriminative learning to accomplish the task of automatic image annotation and retrieval. We firstly present continuous probabilistic latent semantic analysis (PLSA) to model continuous quantity. Furthermore, we propose a hybrid framework which employs continuous PLSA to model visual features of images in generative learning stage and uses ensembles of classifier chains to classify the multi-label data in discriminative learning stage. Since the framework combines the advantages of generative and discriminative learning, it can predict semantic annotation precisely for unseen images. Finally, we conduct a series of experiments on a standard Corel dataset. The experiment results show that our approach outperforms many state-of-the-art approaches.
基金Supported by Natural Science Foundation of Fujian Province(No.2020J011084)Fujian Province Technology and Economy Integration Service Platform(No.2023XRH001)Fuzhou-Xiamen-Quanzhou National Independent Innovation Demonstration Zone Collaborative Innovation Platform(No.2022FX5)。
文摘●AIM:To investigate a pioneering framework for the segmentation of meibomian glands(MGs),using limited annotations to reduce the workload on ophthalmologists and enhance the efficiency of clinical diagnosis.●METHODS:Totally 203 infrared meibomian images from 138 patients with dry eye disease,accompanied by corresponding annotations,were gathered for the study.A rectified scribble-supervised gland segmentation(RSSGS)model,incorporating temporal ensemble prediction,uncertainty estimation,and a transformation equivariance constraint,was introduced to address constraints imposed by limited supervision information inherent in scribble annotations.The viability and efficacy of the proposed model were assessed based on accuracy,intersection over union(IoU),and dice coefficient.●RESULTS:Using manual labels as the gold standard,RSSGS demonstrated outcomes with an accuracy of 93.54%,a dice coefficient of 78.02%,and an IoU of 64.18%.Notably,these performance metrics exceed the current weakly supervised state-of-the-art methods by 0.76%,2.06%,and 2.69%,respectively.Furthermore,despite achieving a substantial 80%reduction in annotation costs,it only lags behind fully annotated methods by 0.72%,1.51%,and 2.04%.●CONCLUSION:An innovative automatic segmentation model is developed for MGs in infrared eyelid images,using scribble annotation for training.This model maintains an exceptionally high level of segmentation accuracy while substantially reducing training costs.It holds substantial utility for calculating clinical parameters,thereby greatly enhancing the diagnostic efficiency of ophthalmologists in evaluating meibomian gland dysfunction.
