Types Of Annotations Research Articles

The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers

Adenosine-to-inosine (A-to-I) RNA editing, constituting nearly 90% of all RNA editing events in humans, has been reported to contribute to the tumorigenesis in diverse cancers. However, the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient. To fill this gap, we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas. For individual candidate among ∼ 1,500,000 quantified RNA editing events, we performed diverse types of downstream functional annotations. Finally, we identified 24,236 potentially functional A-to-I RNA editing events, including the cases in APOL1, IGFBP3, GRIA2, BLCAP, and miR-589-3p. These events might play crucial roles in the scenarios of tumorigenesis, due to their tumor-related editing frequencies or probable effects on altered expression profiles, protein functions, splicing patterns, and microRNA regulations of tumor genes. Our functional A-to-I RNA editing events (https://ccsm.uth.edu/CAeditome/) will help better understand the cancer pathology from the A-to-I RNA editing aspect.

Annotating for Artificial Intelligence Applications in Digital Pathology: A Practical Guide for Pathologists and Researchers

Training machine learning models for artificial intelligence (AI) applications in pathology often requires extensive annotation by human experts, but there is little guidance on the subject. In this work, we aimed to describe our experience and provide a simple, useful, and practical guide addressing annotation strategies for AI development in computational pathology. Annotation methodology will vary significantly depending on the specific study’s objectives, but common difficulties will be present across different settings. We summarize key aspects and issue guiding principles regarding team interaction, ground-truth quality assessment, different annotation types, and available software and hardware options and address common difficulties while annotating. This guide was specifically designed for pathology annotation, intending to help pathologists, other researchers, and AI developers with this process.

HybridRNAbind: prediction of RNA interacting residues across structure-annotated and disorder-annotated proteins.

The sequence-based predictors of RNA-binding residues (RBRs) are trained on either structure-annotated or disorder-annotated binding regions. A recent study of predictors of protein-binding residues shows that they are plagued by high levels of cross-predictions (protein binding residues are predicted as nucleic acid binding) and that structure-trained predictors perform poorly for the disorder-annotated regions and vice versa. Consequently, we analyze a representative set of the structure and disorder trained predictors of RBRs to comprehensively assess quality of their predictions. Our empirical analysis that relies on a new and low-similarity benchmark dataset reveals that the structure-trained predictors of RBRs perform well for the structure-annotated proteins while the disorder-trained predictors provide accurate results for the disorder-annotated proteins. However, these methods work only modestly well on the opposite types of annotations, motivating the need for new solutions. Using an empirical approach, we design HybridRNAbind meta-model that generates accurate predictions and low amounts of cross-predictions when tested on data that combines structure and disorder-annotated RBRs. We release this meta-model as a convenient webserver which is available at https://www.csuligroup.com/hybridRNAbind/.

A Scene-Text Synthesis Engine Achieved Through Learning from Decomposed Real-World Data.

Scene-text image synthesis techniques that aim to naturally compose text instances on background scene images are very appealing for training deep neural networks due to their ability to provide accurate and comprehensive annotation information. Prior studies have explored generating synthetic text images on two-dimensional and three-dimensional surfaces using rules derived from real-world observations. Some of these studies have proposed generating scene-text images through learning; however, owing to the absence of a suitable training dataset, unsupervised frameworks have been explored to learn from existing real-world data, which might not yield reliable performance. To ease this dilemma and facilitate research on learning-based scene text synthesis, we introduce DecompST, a real-world dataset prepared from some public benchmarks, containing three types of annotations: quadrilateral-level BBoxes, stroke-level text masks, and text-erased images. Leveraging the DecompST dataset, we propose a Learning-Based Text Synthesis engine (LBTS) that includes a text location proposal network (TLPNet) and a text appearance adaptation network (TAANet). TLPNet first predicts the suitable regions for text embedding, after which TAANet adaptively adjusts the geometry and color of the text instance to match the background context. After training, those networks can be integrated and utilized to generate the synthetic dataset for scene text analysis tasks. Comprehensive experiments were conducted to validate the effectiveness of the proposed LBTS along with existing methods, and the experimental results indicate the proposed LBTS can generate better pretraining data for scene text detectors. Our dataset and code are made available at: https://github.com/iiclab/DecompST.

Volumetric memory network for interactive medical image segmentation.

Despite recent progress of automatic medical image segmentation techniques, fully automatic results usually fail to meet clinically acceptable accuracy, thus typically require further refinement. To this end, we propose a novel Volumetric Memory Network, dubbed as VMN, to enable segmentation of 3D medical images in an interactive manner. Provided by user hints on an arbitrary slice, a 2D interaction network is firstly employed to produce an initial 2D segmentation for the chosen slice. Then, the VMN propagates the initial segmentation mask bidirectionally to all slices of the entire volume. Subsequent refinement based on additional user guidance on other slices can be incorporated in the same manner. To facilitate smooth human-in-the-loop segmentation, a quality assessment module is introduced to suggest the next slice for interaction based on the segmentation quality of each slice produced in the previous round. Our VMN demonstrates two distinctive features: First, the memory-augmented network design offers our model the ability to quickly encode past segmentation information, which will be retrieved later for the segmentation of other slices; Second, the quality assessment module enables the model to directly estimate the quality of each segmentation prediction, which allows for an active learning paradigm where users preferentially label the lowest-quality slice for multi-round refinement. The proposed network leads to a robust interactive segmentation engine, which can generalize well to various types of user annotations (e.g., scribble, bounding box, extreme clicking). Extensive experiments have been conducted on three public medical image segmentation datasets (i.e., MSD, KiTS19, CVC-ClinicDB), and the results clearly confirm the superiority of our approach in comparison with state-of-the-art segmentation models. The code is made publicly available at https://github.com/0liliulei/Mem3D.

Multitype Label Noise Modeling and Uncertainty-Weighted Label Correction for Concealed Object Detection

Recently, plenty of millimeter-wave image concealed object detection models have achieved superior performance on benchmark datasets. The success of these models heavily depends on a large amount of fully annotated data. However, noisy-label data often exist in a large-scale dataset, which deteriorate the performance of models. In this article, we delve into the training of the concealed object detector with label noise, where we recognize divergent types of noisy annotations. To tackle the multitype label noise problem, we propose a unified framework, including two stages: label noise modeling and correction training. We design the region-level label noise modeling, which analyzes and models label noise via the classification branch loss curves. To correct the labels during training, we design the uncertainty-weighted loss for label correction. The experiments on a millimeter-wave security image dataset demonstrate the effectiveness of our proposed training framework, which can alleviate the negative influence of noisy annotations on network training. By introducing our framework, the object detection network can achieve a prominent performance improvement on mean average precision (0.176 on average) compared to the one trained with noisy labels.

Visualizing metabolomics data with R.

In communicating scientific results, convincing data visualization is of utmost importance. Especially in metabolomics, results based on large numbers of dimensions and variables necessitate particular attention in order to convey their message unambiguously to the reader; also, in the era of open science, traceability and reproducibility are becoming increasingly important. This article describes the use of the R programming language to visualize published metabolomics data resulting from ex vivo NMR spectroscopy and mass spectrometry experiments with a special focus on reproducibility, including example figures as well as associated R code for ease of reuse. Examples include various types of plots (bar plots, swarm plots, and violin plots; volcano plots, heatmaps, Euler diagrams, Kaplan-Meier survival plots) and annotations (groupings, intragroup line connections, significance brackets, text annotations). Advantages of code-generated plots as well as advanced techniques and best practices are discussed.

Pharos 2023: an integrated resource for the understudied human proteome.

The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for fusers to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.

JN-Logo: A Logo Database for Aesthetic Visual Analysis

Data are an important part of machine learning. In recent years, it has become increasingly common for researchers to study artificial intelligence-aided design, and rich design materials are needed to provide data support for related work. Existing aesthetic visual analysis databases contain mainly photographs and works of art. There is no true logo database, and there are few public and high-quality design material databases. Facing these challenges, this paper introduces a larger-scale logo database named JN-Logo. JN-Logo provides 14,917 logo images from three well-known websites around the world and uses the votes of 150 graduate students. JN-Logo provides three types of annotation: aesthetic, style and semantic. JN-Logo’s scoring system includes 6 scoring points, 6 style labels and 11 semantic descriptions. Aesthetic annotations are divided into 0–5 points to evaluate the visual aesthetics of a logo image: the worst is 0 points; the best is 5 points. We demonstrate five advantages of the JN-Logo database: logo images as data objects, rich human annotations, quality scores for image aesthetics, style attribute labels and semantic description of style. We establish a baseline for JN-Logo to measure the effectiveness of its performance on algorithmic models of people’s choices of logo images. We compare existing traditional handcrafted and deep-learned features in both the aesthetic scoring task and the style-labeling task, showing the advantages of deep learning features. In the logo attribute classification task, the EfficientNet _B1 model achieved the best results, reaching an accuracy of 0.524. Finally, we describe two applications of JN-Logo: generating logo design style and similarity retrieval of logo content. The database of this article will eventually be made public.

Accounting for overlapping annotations in genomic prediction models of complex traits

BackgroundIt is now widespread in livestock and plant breeding to use genotyping data to predict phenotypes with genomic prediction models. In parallel, genomic annotations related to a variety of traits are increasing in number and granularity, providing valuable insight into potentially important positions in the genome. The BayesRC model integrates this prior biological information by factorizing the genome according to disjoint annotation categories, in some cases enabling improved prediction of heritable traits. However, BayesRC is not adapted to cases where markers may have multiple annotations.ResultsWe propose two novel Bayesian approaches to account for multi-annotated markers through a cumulative (BayesRC+) or preferential (BayesRCpi) model of the contribution of multiple annotation categories. We illustrate their performance on simulated data with various genetic architectures and types of annotations. We also explore their use on data from a backcross population of growing pigs in conjunction with annotations constructed using the PigQTLdb. In both simulated and real data, we observed a modest improvement in prediction quality with our models when used with informative annotations. In addition, our results show that BayesRC+ successfully prioritizes multi-annotated markers according to their posterior variance, while BayesRCpi provides a useful interpretation of informative annotations for multi-annotated markers. Finally, we explore several strategies for constructing annotations from a public database, highlighting the importance of careful consideration of this step.ConclusionWhen used with annotations that are relevant to the trait under study, BayesRCpi and BayesRC+ allow for improved prediction and prioritization of multi-annotated markers, and can provide useful biological insight into the genetic architecture of traits.

Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data.

Single-cell RNA sequencing (scRNA-seq) provides unique insights into the pathology and cellular origin of disease. We introduce single-cell disease relevance score (scDRS), an approach that links scRNA-seq with polygenic disease risk at single-cell resolution, independent of annotated cell types. scDRS identifies cells exhibiting excess expression across disease-associated genes implicated by genome-wide association studies (GWASs). We applied scDRS to 74 diseases/traits and 1.3 million single-cell gene-expression profiles across 31 tissues/organs. Cell-type-level results broadly recapitulated known cell-type-disease associations. Individual-cell-level results identified subpopulations of disease-associated cells not captured by existing cell-type labels, including T cell subpopulations associated with inflammatory bowel disease, partially characterized by their effector-like states; neuron subpopulations associated with schizophrenia, partially characterized by their spatial locations; and hepatocyte subpopulations associated with triglyceride levels, partially characterized by their higher ploidy levels. Genes whose expression was correlated with the scDRS score across cells (reflecting coexpression with GWAS disease-associated genes) were strongly enriched for gold-standard drug target and Mendelian disease genes.

A Perceiver-Centered Approach for Representing and Annotating Prosodic Functions in Performed Music.

Musical prosody is characterized by the acoustic variations that make music expressive. However, few systematic and scalable studies exist on the function it serves or on effective tools to carry out such studies. To address this gap, we introduce a novel approach to capturing information about prosodic functions through a citizen science paradigm. In typical bottom-up approaches to studying musical prosody, acoustic properties in performed music and basic musical structures such as accents and phrases are mapped to prosodic functions, namely segmentation and prominence. In contrast, our top-down, human-centered method puts listener annotations of musical prosodic functions first, to analyze the connection between these functions, the underlying musical structures, and acoustic properties. The method is applied primarily to the exploring of segmentation and prominence in performed solo piano music. These prosodic functions are marked by means of four annotation types—boundaries, regions, note groups, and comments—in the CosmoNote web-based citizen science platform, which presents the music signal or MIDI data and related acoustic features in information layers that can be toggled on and off. Various annotation strategies are discussed and appraised: intuitive vs. analytical; real-time vs. retrospective; and, audio-based vs. visual. The end-to-end process of the data collection is described, from the providing of prosodic examples to the structuring and formatting of the annotation data for analysis, to techniques for preventing precision errors. The aim is to obtain reliable and coherent annotations that can be applied to theoretical and data-driven models of musical prosody. The outcomes include a growing library of prosodic examples with the goal of achieving an annotation convention for studying musical prosody in performed music.

Advanced Technology in Agriculture Industry by Implementing Image Annotation Technique and Deep Learning Approach: A Review

The implementation of intelligent technology in agriculture is seriously investigated as a way to increase agriculture production while reducing the amount of human labor. In agriculture, recent technology has seen image annotation utilizing deep learning techniques. Due to the rapid development of image data, image annotation has gained a lot of attention. The use of deep learning in image annotation can extract features from images and has been shown to analyze enormous amounts of data successfully. Deep learning is a type of machine learning method inspired by the structure of the human brain and based on artificial neural network concepts. Through training phases that can label a massive amount of data and connect them up with their corresponding characteristics, deep learning can conclude unlabeled data in image processing. For complicated and ambiguous situations, deep learning technology provides accurate predictions. This technology strives to improve productivity, quality and economy and minimize deficiency rates in the agriculture industry. As a result, this article discusses the application of image annotation in the agriculture industry utilizing several deep learning approaches. Various types of annotations that were used to train the images are presented. Recent publications have been reviewed on the basis of their application of deep learning with current advancement technology. Plant recognition, disease detection, counting, classification and yield estimation are among the many advancements of deep learning architecture employed in many applications in agriculture that are thoroughly investigated. Furthermore, this review helps to assist researchers to gain a deeper understanding and future application of deep learning in agriculture. According to all of the articles, the deep learning technique has successfully created significant accuracy and prediction in the model utilized. Finally, the existing challenges and future promises of deep learning in agriculture are discussed.

The RETA Benchmark for Retinal Vascular Tree Analysis

Topological and geometrical analysis of retinal blood vessels could be a cost-effective way to detect various common diseases. Automated vessel segmentation and vascular tree analysis models require powerful generalization capability in clinical applications. In this work, we constructed a novel benchmark RETA with 81 labelled vessel masks aiming to facilitate retinal vessel analysis. A semi-automated coarse-to-fine workflow was proposed for vessel annotation task. During database construction, we strived to control inter-annotator and intra-annotator variability by means of multi-stage annotation and label disambiguation on self-developed dedicated software. In addition to binary vessel masks, we obtained other types of annotations including artery/vein masks, vascular skeletons, bifurcations, trees and abnormalities. Subjective and objective quality validations of the annotated vessel masks demonstrated significantly improved quality over the existing open datasets. Our annotation software is also made publicly available serving the purpose of pixel-level vessel visualization. Researchers could develop vessel segmentation algorithms and evaluate segmentation performance using RETA. Moreover, it might promote the study of cross-modality tubular structure segmentation and analysis.

Adapter-based fine-tuning of pre-trained multilingual language models for code-mixed and code-switched text classification

Code-mixing and code-switching are frequent features in online conversations. Classification of such text is challenging if one of the languages is low-resourced. Fine-tuning pre-trained multilingual language models is a promising avenue for code-mixed text classification. In this paper, we explore adapter-based fine-tuning of PMLMs for CMCS text classification. We introduce sequential and parallel stacking of adapters, continuous fine-tuning of adapters, and training adapters without freezing the original model as novel techniques with respect to single-task CMCS text classification. We also present a newly annotated dataset for the classification of Sinhala–English code-mixed and code-switched text data, where Sinhala is a low-resourced language. Our dataset of 10000 user comments has been manually annotated for five classification tasks: sentiment analysis, humor detection, hate speech detection, language identification, and aspect identification, thus making it the first publicly available Sinhala–English CMCS dataset with the largest number of task annotation types. In addition to this dataset, we also tested our proposed techniques on Kannada–English and Hindi–English datasets. These experiments confirm that our adapter-based PMLM fine-tuning techniques outperform or are on par with the basic fine-tuning of PMLM models.

Real-Time Ground-Level Building Damage Detection Based on Lightweight and Accurate YOLOv5 Using Terrestrial Images

Real-time building damage detection effectively improves the timeliness of post-earthquake assessments. In recent years, terrestrial images from smartphones or cameras have become a rich source of disaster information that may be useful in assessing building damage at a lower cost. In this study, we present an efficient method of building damage detection based on terrestrial images in combination with an improved YOLOv5. We compiled a Ground-level Detection in Building Damage Assessment (GDBDA) dataset consisting of terrestrial images with annotations of damage types, including debris, collapse, spalling, and cracks. A lightweight and accurate YOLOv5 (LA-YOLOv5) model was used to optimize the detection efficiency and accuracy. In particular, a lightweight Ghost bottleneck was added to the backbone and neck modules of the YOLOv5 model, with the aim to reduce the model size. A Convolutional Block Attention Module (CBAM) was added to the backbone module to enhance the damage recognition effect. In addition, regarding the scale difference of building damage, the Bi-Directional Feature Pyramid Network (Bi-FPN) for multi-scale feature fusion was used in the neck module to aggregate features with different damage types. Moreover, depthwise separable convolution (DSCONV) was used in the neck module to further compress the parameters. Based on our GDBDA dataset, the proposed method not only achieved detection accuracy above 90% for different damage targets, but also had the smallest weight size and fastest detection speed, which improved by about 64% and 24%, respectively. The model performed well on datasets from different regions. The overall results indicate that the proposed model realizes rapid and accurate damage detection, and meets the requirement of lightweight embedding in the future.

HemI 2.0: an online service for heatmap illustration.

Recent high-throughput omics techniques have produced a large amount of biological data. Visualization of big omics data is essential to answer a wide range of biological problems. As a concise but comprehensive strategy, a heatmap can analyze and visualize high-dimensional and heterogeneous biomolecular expression data in an attractive artwork. In 2014, we developed a stand-alone software package, Heat map Illustrator (HemI 1.0), which implemented three clustering methods and seven distance metrics for heatmap illustration. Here, we significantly improved 1.0 and released the online service of HemI 2.0, in which 7 clustering methods and 22 types of distance metrics were implemented. In HemI 2.0, the clustering results and publication-quality heatmaps can be exported directly. For an in-depth analysis of the data, we further added an option of enrichment analysis for 12 model organisms, with 15 types of functional annotations. The enrichment results can be visualized in five idioms, including bubble chart, bar graph, coxcomb chart, pie chart and word cloud. We anticipate that HemI 2.0 can be a helpful web server for visualization of biomolecular expression data, as well as the additional enrichment analysis. HemI 2.0 is freely available for all users at: https://hemi.biocuckoo.org/.

Harnessing changes in open chromatin determined by ATAC-seq to generate insulin-responsive reporter constructs

BackgroundGene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. Studies investigating the epigenome have begun to uncover the complex mechanisms regulating transcription. Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is quickly becoming the assay of choice for many epigenomic investigations. However, whether intervention-mediated changes in accessible chromatin determined by ATAC-seq can be harnessed to generate intervention-inducible reporter constructs has not been systematically assayed.ResultsWe used the insulin signaling pathway as a model to investigate chromatin regions and gene expression changes using ATAC- and RNA-seq in insulin-treated Drosophila S2 cells. We found correlations between ATAC- and RNA-seq data, especially when stratifying differentially-accessible chromatin regions by annotated feature type. In particular, our data demonstrated a weak but significant correlation between chromatin regions annotated to enhancers (1-2 kb from the transcription start site) and downstream gene expression. We cloned candidate enhancer regions upstream of luciferase and demonstrate insulin-inducibility of several of these reporters.ConclusionsInsulin-induced chromatin accessibility determined by ATAC-seq reveals enhancer regions that drive insulin-inducible reporter gene expression.

Eliciting Confidence for Improving Crowdsourced Audio Annotations

In this work we explore confidence elicitation methods for crowdsourcing "soft" labels, e.g., probability estimates, to reduce the annotation costs for domains with ambiguous data. Machine learning research has shown that such "soft" labels are more informative and can reduce the data requirements when training supervised machine learning models. By reducing the number of required labels, we can reduce the costs of slow annotation processes such as audio annotation. In our experiments we evaluated three confidence elicitation methods: 1) "No Confidence" elicitation, 2) "Simple Confidence" elicitation, and 3) "Betting" mechanism for confidence elicitation, at both individual (i.e., per participant) and aggregate (i.e., crowd) levels. In addition, we evaluated the interaction between confidence elicitation methods, annotation types (binary, probability, and z-score derived probability), and "soft" versus "hard" (i.e., binarized) aggregate labels. Our results show that both confidence elicitation mechanisms result in higher annotation quality than the "No Confidence" mechanism for binary annotations at both participant and recording levels. In addition, when aggregating labels at the recording level, results indicate that we can achieve comparable results to those with 10-participant aggregate annotations using fewer annotators if we aggregate "soft" labels instead of "hard" labels. These results suggest that for binary audio annotation using a confidence elicitation mechanism and aggregating continuous labels we can obtain higher annotation quality, more informative labels, with quality differences more pronounced with fewer participants. Finally, we propose a way of integrating these confidence elicitation methods into a two-stage, multi-label annotation pipeline.

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021update).

DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was rebuilt to gain coverage of more organisms, which increased the taxonomy coverage from 17 399 to 55 464. All existing annotation types have been updated, if available, based on the new DAVID Gene system. Compared with the last version, the number of gene-term records for most annotation types within the updated Knowledgebase have significantly increased. Moreover, we have incorporated new annotations in the Knowledgebase including small molecule-gene interactions from PubChem, drug-gene interactions from DrugBank, tissue expression information from the Human Protein Atlas, disease information from DisGeNET, and pathways from WikiPathways and PathBank. Eight of ten subgroups split from Uniprot Keyword annotation were assigned to specific types. Finally, we added a species parameter for uploading a list of gene symbols to minimize the ambiguity between species, which increases the efficiency of the list upload and eliminates confusion for users. These current updates have significantly expanded the Knowledgebase and enhanced the discovery power of DAVID.