1,720,973 research outputs found
Cross-organism learning method to discover new gene functionalities
No full textBACKGROUND:
Knowledge of gene and protein functions is paramount for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. Analyses for biomedical knowledge discovery greatly benefit from the availability of gene and protein functional feature descriptions expressed through controlled terminologies and ontologies, i.e., of gene and protein biomedical controlled annotations. In the last years, several databases of such annotations have become available; yet, these valuable annotations are incomplete, include errors and only some of them represent highly reliable human curated information. Computational techniques able to reliably predict new gene or protein annotations with an associated likelihood value are thus paramount.
METHODS:
Here, we propose a novel cross-organisms learning approach to reliably predict new functionalities for the genes of an organism based on the known controlled annotations of the genes of another, evolutionarily related and better studied, organism. We leverage a new representation of the annotation discovery problem and a random perturbation of the available controlled annotations to allow the application of supervised algorithms to predict with good accuracy unknown gene annotations. Taking advantage of the numerous gene annotations available for a well-studied organism, our cross-organisms learning method creates and trains better prediction models, which can then be applied to predict new gene annotations of a target organism.
RESULTS:
We tested and compared our method with the equivalent single organism approach on different gene annotation datasets of five evolutionarily related organisms (Homo sapiens, Mus musculus, Bos taurus, Gallus gallus and Dictyostelium discoideum). Results show both the usefulness of the perturbation method of available annotations for better prediction model training and a great improvement of the cross-organism models with respect to the single-organism ones, without influence of the evolutionary distance between the considered organisms. The generated ranked lists of reliably predicted annotations, which describe novel gene functionalities and have an associated likelihood value, are very valuable both to complement available annotations, for better coverage in biomedical knowledge discovery analyses, and to quicken the annotation curation process, by focusing it on the prioritized novel annotations predicted
GOTA
No full textBackground: Functional annotation of genes and gene products is a major challenge in the post-genomic era. Nowadays, gene function curation is largely based on manual assignment of Gene Ontology (GO) annotations to genes by using published literature. The annotation task is extremely time-consuming, therefore there is an increasing interest in automated tools that can assist human experts.
Results: Here we introduce GOTA, a GO term annotator for biomedical literature.The proposed approach makes use only of information that is readily available from public repositories and it is easily expandable to handle novel sources of information. We assess the classification capabilities of GOTA on a large benchmark set of publications. The overall performances are encouraging in comparison to the state of the art in multi-label classification over large taxonomies. Furthermore, the experimental tests provide some interesting insights into the potential improvement of automated annotation tools.
Conclusions: GOTA implements a flexible and expandable model for GO annotation of biomedical literature. The current version of the GOTA tool is freely available at http://gota.apice.unibo.it
A comparison of term weighting schemes for text classification and sentiment analysis with a supervised variant of tf.idf
No full textIn text analysis tasks like text classification and sentiment analysis, the careful choice of term weighting schemes can have an important impact on the effectiveness. Classic unsupervised schemes are based solely on the distribution of terms across documents, while newer supervised ones leverage the knowledge of membership of training documents to categories; these latter ones are often specifically tailored for either topic or sentiment classification. We propose here a supervised variant of the well-known tf.idf scheme, where the idf factor is computed without considering documents within the category under analysis, so that terms frequently appearing only within it are not penalized. The importance of these terms is further boosted in a second variant inspired by relevance frequency. We performed extensive experiments to compare these novel schemes to known ones, observing top performances in text categorization by topic and satisfactory results in sentiment classification
Cross-domain sentiment classification via polarity-driven state transitions in a Markov model
No full textNowadays understanding people’s opinions is the way to success, whatever the goal. Sentiment classification automates this task, assigning a positive, negative or neutral polarity to free text concerning services, products, TV programs, and so on. Learning accurate models requires a considerable effort from human experts that have to properly label text data. To reduce this burden, cross-domain approaches are advisable in real cases and transfer learning between source and target domains is usually demanded due to language heterogeneity. This paper introduces some variants of our previous work [1], where both transfer learning and sentiment classification are performed by means of a Markov model. While document splitting into sentences does not perform well on common benchmark, using polarity-bearing terms to drive the classification process shows encouraging results, given that our Markov model only considers single terms without further context information
Markov Chain based method for in-domain and cross-domain sentiment classification
No full textSentiment classification of textual opinions in positive, negative or neutral polarity, is a method to understand people thoughts about products, services, persons, organisations, and so on. Interpreting and labelling opportunely text data polarity is a costly activity if performed by human experts. To cut this labelling cost, new cross domain approaches have been developed where the goal is to automatically classify the polarity of an unlabelled target text set of a given domain, for example movie reviews, from a labelled source text set of another domain, such as book reviews. Language heterogeneity between source and target domain is the trickiest issue in cross-domain setting so that a preliminary transfer learning phase is generally required. The best performing techniques addressing this point are generally complex and require onerous parameter tuning each time a new source-target couple is involved. This paper introduces a simpler method based on the Markov chain theory to accomplish both transfer learning and sentiment classification tasks. In fact, this straightforward technique requires a lower parameter calibration effort. Experiments on popular text sets show that our approach achieves performance comparable with other works
A study on term weighting for text categorization: A novel supervised variant of tf.idf
No full textWithin text categorization and other data mining tasks, the use of suitable methods for term weighting can bring a substantial boost in effectiveness. Several term weighting methods have been presented throughout literature, based on assumptions commonly derived from observation of distribution of words in documents. For example, the idf assumption states that words appearing in many documents are usually not as important as less frequent ones. Contrarily to tf.idf and other weighting methods derived from information retrieval, schemes proposed more recently are supervised, i.e. based on knownledge of membership of training documents to categories. We propose here a supervised variant of the tf.idf scheme, based on computing the usual idf factor without considering documents of the category to be recognized, so that importance of terms frequently appearing only within it is not underestimated. A further proposed variant is additionally based on relevance frequency, considering occurrences of words within the category itself. In extensive experiments on two recurring text collections with several unsupervised and supervised weighting schemes, we show that the ones we propose generally perform better than or comparably to other ones in terms of accuracy, using two different learning methods
Job recommendation from semantic similarity of LinkedIn users' skills
No full textUntil recently job seeking has been a tricky, tedious and time consuming process, because people looking for a new position had to collect information from many different sources. Job recommendation systems have been proposed in order to automate and simplify this task, also increasing its effectiveness. However, current approaches rely on scarce manually collected data that often do not completely reveal people skills. Our work aims to find out relationships between jobs and people skills making use of data from LinkedIn users' public profiles. Semantic associations arise by applying Latent Semantic Analysis (LSA). We use the mined semantics to obtain a hierarchical clustering of job positions and to build a job recommendation system. The outcome proves the effectiveness of our method in recommending job positions. Anyway, we argue that our approach is definitely general, because the extracted semantics could be worthy not only for job recommendation systems but also for recruiting systems. Furthermore, we point out that both the hierarchical clustering and the recommendation system do not require parameters to be tuned
GOTA: GO term annotation of biomedical literature
Full text linkDetailed experimental results. Detailed results of the experimental tests over the three distinct GO categories BP, MF and CC. (PDF 293 kb
Discovering new gene functionalities from random perturbations of known gene ontological annotations
No full textIterative Refining of Category Profiles for Nearest Centroid Cross-Domain Text Classification
No full textIn cross-domain text classification, topic labels for documents of a target domain are predicted by leveraging knowledge of labeled documents of a source domain, having equal or similar topics with possibly different words. Existing methods either adapt documents of the source domain to the target or represent both domains in a common space. These methods are mostly based on advanced statistical techniques and often require tuning of parameters in order to obtain optimal performances. We propose a more straightforward approach based on nearest centroid classification: profiles of topic categories are extracted from the source domain and are then adapted by iterative refining steps using most similar documents in the target domain. Experiments on common benchmark datasets show that this approach, despite its simplicity, obtains accuracy measures better or comparable to other methods, obtained with fixed empirical values for its few parameters
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