Kind Of Annotation Research Articles

DiSSCover the Potential of FAIR Digital Object Annotations and How You Can Use Them!

The infrastructure for the Distributed System of Scientific Collections (DiSSCo) is in full development. Work within the DiSSCo Transition Project has been focused on building infrastructure, creating data models, and setting up Application Programming Interfaces (APIs) (Koureas et al. 2024). In the past years, DiSSCo has presented this work at different Biodiversity Information Standards (TDWG) conferences (Leeflang and Addink 2023, Leeflang et al. 2022, Addink et al. 2021). In this year’s session, we would like to focus on the human-facing application: DiSSCover. DiSSCover is the graphical user interface through which users can interact with Findable, Accessible, Interoperable and Reusable (FAIR) Digital Objects (FDOs), facilitating the curation and enhancement of specimen data (Islam 2024). Development started in 2022 and is ongoing. The interface acts as a gateway into the DiSSCo infrastructure, providing access to digital specimens and media. Extracted from the core DiSSCo API, the data is converted into an easily readable format and made discoverable through a diverse set of filters. DiSSCover’s main focus is to allow users to make annotations upon the data. Through the concept of annotations, we connect expert and machine-generated information, to create extended digital specimens (Hardisty et al. 2022), e.g, by creating linkages to other infrastructures, correcting or adding new information, or by triggering machine annotation services. Machine annotation services are automated scalable tools that run in the background and automatically curate and extend the specimen (Addink et al. 2023). Human users will remain important, as all annotations made by machine annotation services can be reviewed by a trusted person. Annotations are Fair Digital Objects and target a specific part of a specimen, be it a data fragment or an associated media file. At the heart of DiSSCover lies the Open Digital Specimen data specification (Leeflang and Addink 2023). It tries to harmonise multiple data standards into one generic specification based on the new Global Biodiversity Information Facility (GBIF) Unified Model (Robertson et al. 2022). The data is stored as JavaScript Object Notation (JSON) based on JSON Schemas (Anonymous 2024). Annotations are linked to specific data attributes using a JSON-path as the identifier. Data attributes can be individual terms, collections of terms called classes, or the whole object. This creates a flexible but complex data structure, the basis for which we used the World Wide Web Consortium (W3C) web annotation data model (Sanderson et al. 2017). The W3C Web annotation data model contains two main components: the target and body. The target specifies which data attribute the annotation is made on, for example, the term: ‘ods:specimenName’. This is a local term within the open Digital Specimen namespace (ods), which holds the accepted name of the digital specimen. The annotation body holds the value(s) that are appended to the digital specimen, and differ based upon the annotation motivation. DiSSCo recognises five different annotation motivations: addition, modification, comment, assessment and deletion, each of which has its own unique function. This creates a flexible structure that should be able to handle any information the user wants to add to the object. The challenge of DiSSCover is to preserve the complex structure of annotations, whilst making it convenient for users to work with. The session will provide a look at the different kinds of annotations and their use from a practical perspective. A demonstration of DiSSCover will show how users can create annotations, providing knowledge about the process that will give shape to DiSSCo’s main goal of enriching natural history data.

Towards more reliable evaluation in pedestrian detection by rethinking “ignore regions”

It remains a challenging task to detect pedestrians in crowds and it needs more efforts to understand why the detectors fail. When we perform an error analysis based on the traditional evaluation strategy, we find that it produces many misleading false positives, which in fact cover occluded pedestrians. The reason for this is that we usually have two kinds of annotations in the dataset: regular pedestrians (detection targets) labeled by full-body boxes and ignored pedestrians (NOT detection targets) labeled by visible boxes. Ignored pedestrians are labeled as an additional category termed the “ignore region”. Nevertheless, our detectors always predict a full-body box for each pedestrian. This gap results in the following case: when a detector successfully predicts a full-body box for those ignored pedestrians, a false positive is triggered due to the low overlap between the predicted full-body box and the labeled visible box for the ignored pedestrian. This becomes even more harmful as the detector improves and becomes more capable of locating occluded pedestrians. To alleviate this issue, we devise a new pedestrian detection pipeline, which considers the additional visible box at both the detection and evaluation stages. During detection, we predict an extra visible box apart from the full-body box for every instance; during evaluation, we employ visible boxes instead of full-body boxes to match the “ignore region”. We apply the new pipeline to dozens of detection methods and validate the effectiveness of our pipeline in reducing the over-reporting of false positives and providing more reliable evaluation results.

Real-Time Music Following in Score Sheet Images via Multi-Resolution Prediction

The task of real-time alignment between a music performance and the corresponding score (sheet music), also known as score following, poses a challenging multi-modal machine learning problem. Training a system that can solve this task robustly with live audio and real sheet music (i.e., scans or score images) requires precise ground truth alignments between audio and note-coordinate positions in the score sheet images. However, these kinds of annotations are difficult and costly to obtain, which is why research in this area mainly utilizes synthetic audio and sheet images to train and evaluate score following systems. In this work, we propose a method that does not solely rely on note alignments but is additionally capable of leveraging data with annotations of lower granularity, such as bar or score system alignments. This allows us to use a large collection of real-world piano performance recordings coarsely aligned to scanned score sheet images and, as a consequence, improve over current state-of-the-art approaches.

The Influence of Different Forms of Lexical Annotation on the Incidental Vocabulary Learning of Chinese Students based on Multimedia Technology

The development of multimedia technology makes English learning more and more simple. This paper mainly studies the influence of four different annotation forms, namely Chinese, English, Chinese + pictures and English + pictures. The results showed that the Chinese annotations were more effective than the English annotations in promoting incidental vocabulary learning. The combination of text and picture annotation is more conducive to incidental vocabulary learning than the text-only annotation. Among the four kinds of annotations, the combination of Chinese and pictures is the most effective for incidental vocabulary learning. Those with higher English proficiency are significantly better than those with lower English proficiency in using annotations to learn vocabulary and maintain word memory.

Europäische Diskursgemeinschaft.

Europe is a unique framework of communication with similar issues discussed in different linguistic and cultural areas. This paper gives a detailed overview of a discourse linguistic project that analyses this multilingual discourse space. We focus on the issue of vaccination since this is a controversial issue in the media of all countries that are of interest for this study (Germany, Italy, France, UK). Methods from discourse, corpus and computer linguistics are used to identify the most relevant linguistic, argumentative, and emotional patterns in discourse. The paper discusses these methods in detail. We then show how these patterns are annotated in our corpora and how the different kinds of annotations can be analysed in correlation.

Devotional Annotations: Preserving the Family’s Memory in Arabic Manuscripts

This contribution explores a peculiar kind of annotation in Arabic multiple-text manuscripts. These manuscripts were often compiled as a personal ‘one-volume library’, containing copies and excerpts of a unique selection of texts. Further, they were often used for less guided writing activities. The owners left notes, lists and sometimes even sketches in the margins or on blank pages between the texts. Among these, lists of life dates of relatives are a valuable source for studies on domestic devotion. On the one hand, they give glimpses on the composition of households. How many people lived together and who were they? These lists inform us about names regardless of gender. On the other hand, the penning of these list is in itself a trace of a practice intricately tied to the familial and domestic spheres. These lists are usually the only place, in which the memory of those people is preserved.

AudioPairBank: towards a large-scale tag-pair-based audio content analysis

Recently, sound recognition has been used to identify sounds, such as the sound of a car, or a river. However, sounds have nuances that may be better described by adjective-noun pairs such as “slow car” and verb-noun pairs such as “flying insects,” which are underexplored. Therefore, this work investigates the relationship between audio content and both adjective-noun pairs and verb-noun pairs. Due to the lack of datasets with these kinds of annotations, we collected and processed the AudioPairBank corpus consisting of a combined total of 1123 pairs and over 33,000 audio files. In this paper, we include previously unavailable documentation of the challenges and implications of collecting audio recordings with these types of labels. We have also shown the degree of correlation between the audio content and the labels through classification experiments, which yielded 70% accuracy. The results and study in this paper encourage further exploration of the nuances in sounds and are meant to complement similar research performed on images and text in multimedia analysis.

Practical Linguistic Annotation: The Hebrew Bible

Annotation and research in the humanities are tightly coupled. Annotations can be seen as expressions of research activity which can be turned into input data for subsequent research. The digital paradigm has profoundly altered the ways in which we humans can handle the information content of our sources and it also affects the practice of annotation. We explore new ways of annotation that were not feasible before the digital times, and we list a few requirements for annotation to act as a reliable source of research information. Rather than conducting an academic discussion on the ontology of annotations, we highlight practical use cases for new kinds of annotations. We illustrate those in a concrete system for linguistic annotations to the Hebrew Bible, SHEBANQ.

Development of CAD Model Annotation System Based on Design Intent

Most of the product design on the market is variant design or adaptive design, which need to reuse existing product design knowledge. A key aspect of reusing existing CAD model is correctly define and understand the design intents behind of existing CAD model, and this paper introduces a CAD model annotation system based on design intent. Design intents contained all design information of entire life cycle from modeling, analysis to manufacturing are marked onto the CAD model using PMI module in UG to improve the readability of the CAD model. Second, given the problems such as management difficulties, no filter and retrieval functions, this paper proposes an annotation manager system based on UG redevelopment by filtration, retrieval, grouping and other functions to reduce clutter on the 3D annotations and be convenient for users to view needed all kinds of annotations. Finally, design information is represented both internally within the 3D model and externally on a XML file.

Cross-Scenario Transfer Person Reidentification

Person reidentification (Re-ID) matches images of the same person captured in disjoint camera views and at different times. To obtain a reliable similarity measurement between images, manually annotating a large amount of pairwise cross-camera-view person images is deemed necessary. However, this kind of annotation is both costly and impractical for efficiently deploying a Re-ID system to a completely new scenario, a new setting of nonoverlapping camera views between which person images are to be matched. To solve this problem, we consider utilizing other existing person images captured in other scenarios to help the Re-ID system in a target (new) scenario, provided that a few samples are captured under the new scenario. More specifically, we tackle this problem by jointly learning the similarity measurements for Re-ID in different scenarios in an asymmetric way. To model the joint learning, we consider that the Re-ID models share certain component across tasks. A distinct consideration in our multitask modeling is to extract the discriminant shared component that reduces the cross-task data overlap in the shared latent space during the joint learning, so as to enhance the target inter-class separation in the shared latent space. For this purpose, we propose to maximize the cross-task data discrepancy on the shared component during asymmetric multitask learning (MTL), along with maximizing the local inter-class variation and minimizing local intra-class variation on all tasks. We call our proposed method the constrained asymmetric multitask discriminant component analysis (cAMT-DCA). We show that cAMT-DCA can be solved by a simple eigen decomposition with a closed form, getting rid of any iterative learning used in most conventional MTL analyses. The experimental results show that the proposed transfer model gains a clear improvement against the related nontransfer and general multitask person Re-ID models.

LEARNER CORPUS ANNOTATION IN LATVIA AND LITHUANIA

Learner corpora are gaining popularity in the Baltic States as well as elsewhere in the world. The aim of the article is to discuss what kinds of annotation have been used in learner corpus research in Latvia and Lithuania so far and to describe which ones of them would be most suitable for the newly created learner corpus of the second Baltic language – Esam . A lot of learner corpus research in Latvia and Lithuania is undertaken without any annotation. The most common types of annotation are the ones based on the theory of levels of language – morphological and syntactic annotation. There is little collaboration between researchers of neighbour countries, but linguists of each country collaborate closely with each other using similar annotation schemes and creating corpora that are comparable in some aspects. The learner corpus of the second Baltic language should try to fit in the picture to some extent. Part of speech annotation and simple syntactic annotation could help in that. However, things that have not yet become so popular in learner corpus research in this region could also be useful. Therefore, error annotation and lemmatization have been chosen to be included in the annotation plan of the corpus Esam as well. DOI: http://dx.doi.org/10.7220/2335-2027.7.8

Attribute annotations and their use in C program deductive verification

In this paper, a new kind of annotations called attribute annotations and the methodology for their application in deductive program verification are proposed. A collection of annotating attributes for the C-kernel subset of the C language is described, and, on their basis, two versions of axiomatic semantics of C-kernel—forward semantics and mixed forward semantics—are presented.

Annotating Distributed Scores for Mutual Engagement in Daisyphone and Beyond

Written and drawn annotations of musical scores form a core part of the music composition process for both individuals and groups. This article reflects on the annotations made in new forms of distributed music-making wherein the score and its annotations are shared across the web. Four kinds of annotation are identified from 8 years of studies of mutual engagement through distributed music-making systems. It is suggested that new forms of web-based music-making might benefit from shared and persistent graphical annotation mechanisms.

Semantic Search based on the Online Integration of NLP Techniques

This paper introduces a framework for semantic information retrieval based on the integration of various natural language processing (NLP) techniques, each of which annotates a base text with different kinds of information extracted from the text. Instead of running the NLP modules on the fly for individual search requests, the NLP modules are applied to the text in advance and the results are indexed in a way that enables flexible and efficient integration of them. The query language is based on a variant of the region algebra, in which we can specify a sub- structure in the annotated text that may involve different kinds of annotations. Given a query, the retrieval engine searches for the sub-structure by aggregating the different kinds of annotations through a search algorithm for the extended region algebra. We demonstrate the effectiveness and flexibility of the proposed framework through experiments with TREC Genomics Track data.

Verkets förvandlingar

Transformations of the Work: Ekelöf, Bergman, and Genetic criticism
 This article discusses genetic criticism as an interdisciplinary field of study, focusing on its application in the analysis of film and literature. Genetic criticism analyses works of art as textual histories, placing particular emphasis on the creative process, rather than the “final” state of the work. The object of study is the “avant-texte”; traditionally understood as the critical reconstruction and examination of author’s drafts, manuscripts, proofs, and other kinds of annotations. Over the past few years, the application of genetic criticism has expanded to include a variety of media and art forms; this article dicusses the implications of these new interdisciplinary perspectives. The article presents a general theoretical introduction to genetic criticism, followed by two case studies involving the works of Gunnar Ekelöf and Ingmar Bergman. In both cases, the key concept of the “avant-texte” is discussed; however, in the study of film, the diachronic relation between “text” and “avant-texte” is reevaluated. Here, the intermedial dimension of the filmic text is reinforced, and issues pertaining to media materiality and technological media in film aesthetics alter the conception of “original”, “copy” and “version”.
 There are a number of similarities and differences between Ekelöf and Bergman as writers and creators. Both use older drafts and notebooks extensively and, in both cases, the process of invention seems to emerge in the very material process of writing. Yet, Bergman’s notebooks are clearly focused, and may be regarded as an open genre suggesting new forms of mediation. By contrast, Ekelöf ’s continuous drafting of the same poem may be regarded both as a method of writing and a special trait in the author’s poetics. Ekelöf and Bergman both exemplify mediaspecific processes of creation, the various aspects of the “avant-texte”, and the ways in which the “avant-texte” suggests different aesthetic approaches to the work of art and artistic creation.
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Comparison of computationally- and manually-assigned Gene Ontology annotations to improve functional characterization of gene products.

AbstractThe Gene Ontology (GO) describes molecular functions, biological processes, and cellular components of gene products using controlled-vocabulary terms that are related to each other in a structure that facilitates computing on GO annotations within and across species. Experimentally-based GO annotations that are manually curated from the literature are often used to predict the functions of related uncharacterized proteins. The accuracy of such annotations is thus critically important, particularly for a well-studied model organism such as Saccharomyces cerevisiae which is frequently used as the source of the experimental data.Comparison of experimentally-based annotations with those predicted by computational methods for the same gene products may reveal inaccuracies in curation of the experimental data, and could additionally be used to evaluate and improve the computational methods. We will present the results of an analysis at SGD that identified four major reasons for discrepancies between the two kinds of annotation. Some discrepancies revealed cases in which human error led to errors or omissions in the manual curation, prompting prioritization for review and correction. In another category, the computational annotations were not supported or were refuted by the literature, thereby suggesting ways in which the accuracy of the prediction methods could be improved. Yet another type of discrepancy resulted from issues with the GO structure, such as missing parentage for certain terms, leading to reexamination and improvement of the ontology. Finally, some discrepancies arose because the computational predictions were entirely novel, and no relevant experimental evidence was available. These cases highlight potential interesting new avenues for experimentation.

Cymobase - the Reference Database for Cytoskeletal and Motor Proteins

Motor proteins are involved in processes like cellular transport, muscle contraction, and cell division. Three motors are myosin, dynein, and kinesin. They convert chemical energy (ATP) into mechanical work (movement). Protein sequences are the bases for many biochemical and cell biological experiments, as well as bioinformatical analyses.We implemented a web application (CyMoBase) to represent all sequence related information. Since the fist publication of Pfarao (www.cymobase.org), many changes have been integrated in the database scheme and the web application. Now, it is also possible to derive information about structures and genes. Over the years, the number of data has increased considerable. Today, there are 37 proteins, 16500 sequences, 132 domains, 819 species, 599 publications and 1392 projects, with a total sequence length of over 16 million amino acids. The web application has got a new central search page including nine search modules (species names, protein classes, taxonomy, species groups, domains, sequence meta data, publications, sequence names, and genes) and eleven result tabs (sequences, publications, downloadable FASTA files, alignment viewer, phylogenetic trees, sequence stats, domain composition, complex inventory, protein inventory, molecular weights, and class composition). All search modules can be combined to filter the results.Furthermore, we provide the gene structure of all sequences as computed by WebScipio. An other viewing option is the “Complex Inventory”, which presents the existence or absence of sequence homologs of certain complexes. The aligned protein sequences are available via the “FASTA Files” result tab.The size of the database, the kind of annotation, the possibility to use and combining different search modules, and the number of information and options offered by the web interface makes Pfarao the reference database number one for cytoskeletal and motor proteins.

Annotation: A Lost Art in Cataloguing

SUMMARY Public library catalogues in early twentieth-century Britain frequently included annotations, either to clarify obscure titles or to provide further information about the subject-matter of the books they described. Two manuals giving instruction on how to do this were published at that time. Following World War I, with the decline of the printed catalogue, this kind of annotation became rarer, and was almost confined to bulletins of new books. The early issues of the British National Bibliography included some annotations in exceptional cases. Parallels are drawn with the provision of table-of-contents information in present-day OPACs.

Construction and annotation of large phylogenetic trees

Broad availability of molecular sequence data allows construction of phylogenetic trees with 1000s or even 10 000s of taxa. This paper reviews methodological, technological and empirical issues raised in phylogenetic inference at this scale. Numerous algorithmic and computational challenges have been identified surrounding the core problem of reconstructing large trees accurately from sequence data, but many other obstacles, both upstream and downstream of this step, are less well understood. Before phylogenetic analysis, data must be generated de novo or extracted from existing databases, compiled into blocks of homologous data with controlled properties, aligned, examined for the presence of gene duplications or other kinds of complicating factors, and finally, combined with other evidence via supermatrix or supertree approaches. After phylogenetic analysis, confidence assessments are usually reported, along with other kinds of annotations, such as clade names, or annotations requiring additional inference procedures, such as trait evolution or divergence time estimates. Prospects for partial automation of large-tree construction are also discussed, as well as risks associated with ‘outsourcing’ phylogenetic inference beyond the systematics community.

Counting Insatiate Countesses: The Seventeenth-Century Annotations to Marston's "The Insatiate Countess"

I n his recent book Shakespeare after Theory, David Scott Kastan reminds us that great age of theory is overand that the present task of scholarship is to assess the theoretical insights of the last generation by a thoroughgoing practice of historical scholarship.' Keeping this exhortation in mind, I am in this essay especially concerned with the need to validate the frequently stated assertion that dramatic texts possess power. On what concrete evidence can such a proposition be sustained? And what might be the measures of that power in a dramatic text in particular? From this perspective, the hitherto unpublished marginal notations on a copy of the 1631 quarto of John Marston's and William Barksted's The Insatiate Countess assume unusual significance,2 for they present a rare opportunity to assess this play's power of representation in relation to two seventeenth-century readers. Although the annotations are not extensive, they nevertheless disclose a good deal about the cultural principles governing their inscription as well as the cultural directives that shaped this early Stuart tragedy. I propose, first, to establish the dating limits of the marginalia, to distinguish the two hands involved, and to describe fully the four kinds of annotation. Then in the balance of the essay I will attempt to establish the analogical habits of reading that govern the topical applications offered by the readers and to treat the cultural significance of their practice. This copy of The Insatiate Countess, housed at the National Library of Scotland, has been annotated by two distinct hands. In both cases this obviously occurred after 1631, the publication date of the third quarto, and their annotations can be dated more precisely using other external as well as internal evidence. The