Showing papers on "Annotation published in 2012"

brat: a Web-based Tool for NLP-Assisted Text Annotation

Abstract: We introduce the brat rapid annotation tool (BRAT), an intuitive web-based tool for text annotation supported by Natural Language Processing (NLP) technology. BRAT has been developed for rich structured annotation for a variety of NLP tasks and aims to support manual curation efforts and increase annotator productivity using NLP techniques. We discuss several case studies of real-world annotation projects using pre-release versions of BRAT and present an evaluation of annotation assisted by semantic class disambiguation on a multicategory entity mention annotation task, showing a 15% decrease in total annotation time. BRAT is available under an open-source license from: http://brat.nlplab.org

The UCSC Genome Browser database: extensions and updates 2011

Abstract: The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. Further, a large number of annotation tracks have been either added, updated by contributors, or remapped to the latest human reference genome. Among these are new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced ‘track data hubs’, which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image.

A beginner's guide to eukaryotic genome annotation

Abstract: The falling cost of genome sequencing is having a marked impact on the research community with respect to which genomes are sequenced and how and where they are annotated. Genome annotation projects have generally become small-scale affairs that are often carried out by an individual laboratory. Although annotating a eukaryotic genome assembly is now within the reach of non-experts, it remains a challenging task. Here we provide an overview of the genome annotation process and the available tools and describe some best-practice approaches.

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data.

Abstract: Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated to other types of quantitative genome-wide data such as the corresponding transcriptome changes. We describe a new method, 2D annotation enrichment, which compares quantitative data from any two 'omics' types in the context of categorical annotation of the proteins or genes. Suitable genome-wide categories are membership of proteins in biochemical pathways, their annotation with gene ontology terms, sub-cellular localization, presence of protein domains or membership in protein complexes. 2D annotation enrichment detects annotation terms whose members show consistent behavior in one or both of the data dimensions. This consistent behavior can be a correlation between the two data types, such as simultaneous up- or down-regulation in both data dimensions, or a lack thereof, such as regulation in one dimension but no change in the other. For the statistical formulation of the test we introduce a two-dimensional generalization of the nonparametric two-sample test. The false discovery rate is stringently controlled by correcting for multiple hypothesis testing. We also describe one-dimensional annotation enrichment, which can be applied to single omics data. The 1D and 2D annotation enrichment algorithms are freely available as part of the Perseus software.

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.

Abstract: The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas .

The UniProt-GO Annotation database in 2011

Abstract: The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set.

Concept annotation in the CRAFT corpus

Abstract: Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml .

GeneDB—an annotation database for pathogens

Abstract: GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms.

SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update)

Abstract: Broader functional annotation of single nucleotide variations is a valuable mean for prioritizing targets in further disease studies and large-scale genotyping projects. We originally developed SNPnexus to assess the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models in order to identify the phenotypically important variants. Being committed to providing continuous support to the scientific community, we have substantially improved SNPnexus over time by incorporating a broader range of variations such as insertions/deletions, block substitutions, IUPAC codes submission and region-based analysis, expanding the query size limit, and most importantly including additional categories for the assessment of functional impact. SNPnexus provides a comprehensive set of annotations for genomic variation data by characterizing related functional consequences at the transcriptome/proteome levels of seven major annotation systems with in-depth analysis of potential deleterious effects, inferring physical and cytogenetic mapping, reporting information on HapMap genotype/allele data, finding overlaps with potential regulatory elements, structural variations and conserved elements, and retrieving links with previously reported genetic disease studies. SNPnexus has a user-friendly web interface with an improved query structure, enhanced functional annotation categories and flexible output presentation making it practically useful for biologists. SNPnexus is freely available at http://www.snp-nexus.org.

ORCAE: online resource for community annotation of eukaryotes

Abstract: of modifications is available for each locus (Supplementary Methods). This allows ORCAE to eliminate a bottleneck found in other online annotation tools, such as yrGATE5, where a curator needs to approve modifications before they become available. Indeed, in the spirit of community annotation, the quality of the presented annotation is the responsibility of the whole community. However, to ensure a certain level of quality, several automatic checks have been put in place that encompass all existing knowledge on the gene structure and functions (for example, whether a KOG or EC number exist) (Supplementary Methods). Finally, ORCAE is highly dynamic: upon modification of a gene model, all the available information is immediately updated and presented on the gene page.

Image annotation using metric learning in semantic neighbourhoods

Abstract: Automatic image annotation aims at predicting a set of textual labels for an image that describe its semantics. These are usually taken from an annotation vocabulary of few hundred labels. Because of the large vocabulary, there is a high variance in the number of images corresponding to different labels ("class-imbalance"). Additionally, due to the limitations of manual annotation, a significant number of available images are not annotated with all the relevant labels ("weak-labelling"). These two issues badly affect the performance of most of the existing image annotation models. In this work, we propose 2PKNN, a two-step variant of the classical K-nearest neighbour algorithm, that addresses these two issues in the image annotation task. The first step of 2PKNN uses "image-to-label" similarities, while the second step uses "image-to-image" similarities; thus combining the benefits of both. Since the performance of nearest-neighbour based methods greatly depends on how features are compared, we also propose a metric learning framework over 2PKNN that learns weights for multiple features as well as distances together. This is done in a large margin set-up by generalizing a well-known (single-label) classification metric learning algorithm for multi-label prediction. For scalability, we implement it by alternating between stochastic sub-gradient descent and projection steps. Extensive experiments demonstrate that, though conceptually simple, 2PKNN alone performs comparable to the current state-of-the-art on three challenging image annotation datasets, and shows significant improvements after metric learning.

Natural Language Annotation for Machine Learning

Abstract: Create your own natural language training corpus for machine learning. This example-driven book walks you through the annotation cycle, from selecting an annotation task and creating the annotation specification to designing the guidelines, creating a "gold standard" corpus, and then beginning the actual data creation with the annotation process. Systems exist for analyzing existing corpora, but making a new corpus can be extremely complex. To help you build a foundation for your own machine learning goals, this easy-to-use guide includes case studies that demonstrate four different annotation tasks in detail. You'll also learn how to use a lightweight software package for annotating texts and adjudicating the annotations. This book is a perfect companion to O'Reilly's Natural Language Processing with Python, which describes how to use existing corpora with the Natural Language Toolkit.

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

Abstract: Predicting protein function has become increasingly demanding in the era of next generation sequencing technology The task to assign a curator-reviewed function to every single sequence is impracticable Bioinformatics tools, easy to use and able to provide automatic and reliable annotations at a genomic scale, are necessary and urgent In this scenario, the Gene Ontology has provided the means to standardize the annotation classification with a structured vocabulary which can be easily exploited by computational methods Argot2 is a web-based function prediction tool able to annotate nucleic or protein sequences from small datasets up to entire genomes It accepts as input a list of sequences in FASTA format, which are processed using BLAST and HMMER searches vs UniProKB and Pfam databases respectively; these sequences are then annotated with GO terms retrieved from the UniProtKB-GOA database and the terms are weighted using the e-values from BLAST and HMMER The weighted GO terms are processed according to both their semantic similarity relations described by the Gene Ontology and their associated score The algorithm is based on the original idea developed in a previous tool called Argot The entire engine has been completely rewritten to improve both accuracy and computational efficiency, thus allowing for the annotation of complete genomes The revised algorithm has been already employed and successfully tested during in-house genome projects of grape and apple, and has proven to have a high precision and recall in all our benchmark conditions It has also been successfully compared with Blast2GO, one of the methods most commonly employed for sequence annotation The server is freely accessible at http://wwwmedcompmedicinaunipdit/Argot2

Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences

Abstract: The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced. In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the 12X version. The 8X and 12X assemblies and gene predictions of the grapevine genome were compared to answer the question, “Can we uniquely map 8X predicted genes to 12X predicted genes?” The results show that while the assemblies and gene structure predictions are too different to make a complete mapping between them, most genes (18,725) showed a one-to-one relationship between 8X predicted genes and the last version of 12X predicted genes. In addition, reshuffled genomic sequence structures appeared. These highlight regions of the genome where the gene predictions need to be taken with caution. Based on the new grapevine gene functional annotation and in-depth functional categorization, twenty eight new molecular networks have been created for VitisNet while the existing networks were updated. The outcomes of this study provide a functional annotation of the 12X genes, an update of VitisNet, the system of the grapevine molecular networks, and a new functional categorization of genes. Data are available at the VitisNet website ( http://www.sdstate.edu/ps/research/vitis/pathways.cfm ).

Announcing Prague Czech-English Dependency Treebank 2.0

Abstract: We introduce a substantial update of the Prague Czech-English Dependency Treebank, a parallel corpus manually annotated at the deep syntactic layer of linguistic representation. The English part consists of the Wall Street Journal (WSJ) section of the Penn Treebank. The Czech part was translated from the English source sentence by sentence. This paper gives a high level overview of the underlying linguistic theory (the so-called tectogrammatical annotation) with some details of the most important features like valency annotation, ellipsis reconstruction or coreference.

Quality of computationally inferred gene ontology annotations.

Abstract: Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation.

Developing a large semantically annotated corpus

Abstract: What would be a good method to provide a large collection of semantically annotated texts with formal, deep semantics rather than shallow? We argue that a bootstrapping approach comprising state-of-the-art NLP tools for parsing and semantic interpretation, in combination with a wiki-like interface for collaborative annotation of experts, and a game with a purpose for crowdsourcing, are the starting ingredients for fulfilling this enterprise. The result is a semantic resource that anyone can edit and that integrates various phenomena, including predicate-argument structure, scope, tense, thematic roles, rhetorical relations and presuppositions, into a single semantic formalism: Discourse Representation Theory. Taking texts rather than sentences as the units of annotation results in deep semantic representations that incorporate discourse structure and dependencies. To manage the various (possibly conflicting) annotations provided by experts and non-experts, we introduce a method that stores " Bits of Wisdom " in a database as stand-off annotations.

Web and Personal Image Annotation by Mining Label Correlation With Relaxed Visual Graph Embedding

Abstract: The number of digital images rapidly increases, and it becomes an important challenge to organize these resources effectively. As a way to facilitate image categorization and retrieval, automatic image annotation has received much research attention. Considering that there are a great number of unlabeled images available, it is beneficial to develop an effective mechanism to leverage unlabeled images for large-scale image annotation. Meanwhile, a single image is usually associated with multiple labels, which are inherently correlated to each other. A straightforward method of image annotation is to decompose the problem into multiple independent single-label problems, but this ignores the underlying correlations among different labels. In this paper, we propose a new inductive algorithm for image annotation by integrating label correlation mining and visual similarity mining into a joint framework. We first construct a graph model according to image visual features. A multilabel classifier is then trained by simultaneously uncovering the shared structure common to different labels and the visual graph embedded label prediction matrix for image annotation. We show that the globally optimal solution of the proposed framework can be obtained by performing generalized eigen-decomposition. We apply the proposed framework to both web image annotation and personal album labeling using the NUS-WIDE, MSRA MM 2.0, and Kodak image data sets, and the AUC evaluation metric. Extensive experiments on large-scale image databases collected from the web and personal album show that the proposed algorithm is capable of utilizing both labeled and unlabeled data for image annotation and outperforms other algorithms.

Finding Celebrities in Billions of Web Images

Abstract: In this paper, we present a face annotation system to automatically collect and label celebrity faces from the web. With the proposed system, we have constructed a large-scale dataset called “Celebrities on the Web,” which contains 2.45 million distinct images of 421 436 celebrities and is orders of magnitude larger than previous datasets. Collecting and labeling such a large-scale dataset pose great challenges on current multimedia mining methods. In this work, a two-step face annotation approach is proposed to accomplish this task. In the first step, an image annotation system is proposed to label an input image with a list of celebrities. To utilize the noisy textual data, we construct a large-scale celebrity name vocabulary to identify candidate names from the surrounding text. Moreover, we expand the scope of analysis to the surrounding text of webpages hosting near-duplicates of the input image. In the second step, the celebrity names are assigned to the faces by label propagation on a facial similarity graph. To cope with the large variance in the facial appearances, a context likelihood is proposed to constrain the name assignment process. In an evaluation on 21 735 faces, both the image annotation system and name assignment algorithm significantly outperform previous techniques.

Interactive object detection

Abstract: In recent years, the rise of digital image and video data available has led to an increasing demand for image annotation. In this paper, we propose an interactive object annotation method that incrementally trains an object detector while the user provides annotations. In the design of the system, we have focused on minimizing human annotation time rather than pure algorithm learning performance. To this end, we optimize the detector based on a realistic annotation cost model based on a user study. Since our system gives live feedback to the user by detecting objects on the fly and predicts the potential annotation costs of unseen images, data can be efficiently annotated by a single user without excessive waiting time. In contrast to popular tracking-based methods for video annotation, our method is suitable for both still images and video. We have evaluated our interactive annotation approach on three datasets, ranging from surveillance, television, to cell microscopy.

The Icelandic Parsed Historical Corpus (IcePaHC)

Abstract: The Icelandic Parsed Historical Corpus (IcePaHC) is a manually corrected treebank, parsed according to the annotation guidelines of The Penn Parsed Corpora of Historical English (PPCHE), with minor modifications that are specific to Icelandic. It consists of about 1 million words from the 12th century to the 21st. The samples in the corpus are close to being evenly distributed over this period. Most of the text consists of narratives and religious material but some samples from other genres are also included. The file format is labeled bracketing as in the Penn Treebank with a UTF-8 encoding. The corpus is released under a CC BY 4.0 license. Sogulegi islenski trjabankinn (IcePaHC) er handleiðrettur trjabanki sem er greindur samkvaemt þattunarskema sogulegu ensku Penn-trjabankanna (Penn Parsed Corpora of Historical English; PPCHE). Bankinn inniheldur um 1 milljon lesmalsorða fra 12. til 21. aldar. Gognin i malheildinni eru tiltolulega jafndreifð yfir þetta timabil. Flestir textarnir eru frasagnartextar eða truartextar en einnig er um að raeða einhver daemi um aðrar textategundir. Skraarsniðið er svigasnið (e. labeled bracketing) eins og i Penn-trjabankanum og textinn er i UTF-8 stafasetti. Malheildinni er dreift með CC BY 4.0 leyfi.

The Joy of Parallelism with CzEng 1.0

Abstract: CzEng 1.0 is an updated release of our Czech-English parallel corpus, freely available for non-commercial research or educational purposes. In this release, we approximately doubled the corpus size, reaching 15 million sentence pairs (about 200 million tokens per language). More importantly, we carefully filtered the data to reduce the amount of non-matching sentence pairs. CzEng 1.0 is automatically aligned at the level of sentences as well as words. We provide not only the plain text representation, but also automatic morphological tags, surface syntactic as well as deep syntactic dependency parse trees and automatic co-reference links in both English and Czech. This paper describes key properties of the released resource including the distribution of text domains, the corpus data formats, and a toolkit to handle the provided rich annotation. We also summarize the procedure of the rich annotation (incl. co-reference resolution) and of the automatic filtering. Finally, we provide some suggestions on exploiting such an automatically annotated sentence-parallel corpus.

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

Abstract: In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future.

Multilingual Named Entity Recognition using Parallel Data and Metadata from Wikipedia

Abstract: In this paper we propose a method to automatically label multi-lingual data with named entity tags. We build on prior work utilizing Wikipedia metadata and show how to effectively combine the weak annotations stemming from Wikipedia metadata with information obtained through English-foreign language parallel Wikipedia sentences. The combination is achieved using a novel semi-CRF model for foreign sentence tagging in the context of a parallel English sentence. The model outperforms both standard annotation projection methods and methods based solely on Wikipedia metadata.

Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning

Abstract: In the studies of Drosophila embryogenesis, a large number of two-dimensional digital images of gene expression patterns have been produced to build an atlas of spatio-temporal gene expression dynamics across developmental time. Gene expressions captured in these images have been manually annotated with anatomical and developmental ontology terms using a controlled vocabulary (CV), which are useful in research aimed at understanding gene functions, interactions, and networks. With the rapid accumulation of images, the process of manual annotation has become increasingly cumbersome, and computational methods to automate this task are urgently needed. However, the automated annotation of embryo images is challenging. This is because the annotation terms spatially correspond to local expression patterns of images, yet they are assigned collectively to groups of images and it is unknown which term corresponds to which region of which image in the group. In this paper, we address this problem using a new machine learning framework, Multi-Instance Multi-Label (MIML) learning. We first show that the underlying nature of the annotation task is a typical MIML learning problem. Then, we propose two support vector machine algorithms under the MIML framework for the task. Experimental results on the FlyExpress database (a digital library of standardized Drosophila gene expression pattern images) reveal that the exploitation of MIML framework leads to significant performance improvement over state-of-the-art approaches.

Supporting ground-truth annotation of image datasets using clustering

Abstract: As more subject-specific image datasets (medical images, birds, etc) become available, high quality labels associated with these datasets are essential for building statistical models and method evaluation. Obtaining these annotations is a time-comsuming and thus a costly business. We propose a clustering method to support this annotation task, making the task easier and more efficient to perform for users. In this paper, we provide a framework to illustrate how a clustering method can support the annotation task. A large reduction in both the time to annotate images and number of mouse clicks needed for the annotation is achieved. By investigating the quality of the annotation, we show that this framework is affected by the particular clustering method used. This, however, does not have a large influence on the overall accuracy and disappears if the data is annotated by multiple persons.

HamleDT: To Parse or Not to Parse?

Abstract: We propose HamleDT ― HArmonized Multi-LanguagE Dependency Treebank. HamleDT is a compilation of existing dependency treebanks (or dependency conversions of other treebanks), transformed so that they all conform to the same annotation style. While the license terms prevent us from directly redistributing the corpora, most of them are easily acquirable for research purposes. What we provide instead is the software that normalizes tree structures in the data obtained by the user from their original providers.