scholarly journals Word and sentence embedding tools to measure semantic similarity of Gene Ontology terms by their definitions

2017 ◽  
Author(s):  
Dat Duong ◽  
Wasi Uddin Ahmad ◽  
Eleazar Eskin ◽  
Kai-Wei Chang ◽  
Jingyi Jessica Li
Keyword(s):  
Neural Network ◽  
Gene Ontology ◽  
Language Processing ◽  
Classification Accuracy ◽  
Dimensional Space ◽  
Similarity Score ◽  
Biological Functions ◽  
Word Similarity ◽  
True Protein ◽  
Go Terms

AbstractThe Gene Ontology (GO) database contains GO terms that describe biological functions of genes. Previous methods for comparing GO terms have relied on the fact that GO terms are organized into a tree structure. In this paradigm, the locations of two GO terms in the tree dictate their similarity score. In this paper, we introduce two new solutions for this problem, by focusing instead on the definitions of the GO terms. We apply neural network based techniques from the natural language processing (NLP) domain. The first method does not rely on the GO tree, whereas the second indirectly depends on the GO tree. In our first approach, we compare two GO definitions by treating them as two unordered sets of words. The word similarity is estimated by a word embedding model that maps words into an N-dimensional space. In our second approach, we account for the word-ordering within a sentence. We use a sentence encoder to embed GO definitions into vectors and estimate how likely one definition entails another. We validate our methods in two ways. In the first experiment, we test the model’s ability to differentiate a true protein-protein network from a randomly generated network. In the second experiment, we test the model in identifying orthologs from randomly-matched genes in human, mouse, and fly. In both experiments, a hybrid of NLP and GO-tree based method achieves the best classification accuracy.Availabilitygithub.com/datduong/NLPMethods2CompareGOterms

A GRAPH-BASED SEMANTIC SIMILARITY MEASURE FOR THE GENE ONTOLOGY

2011 ◽  
Vol 09 (06) ◽  
pp. 681-695 ◽  
Author(s):  
MARCO A. ALVAREZ ◽  
CHANGHUI YAN
Keyword(s):  
Gene Ontology ◽  
Semantic Similarity ◽  
Common Ancestor ◽  
State Of The Art ◽  
Sequence Similarity ◽  
Similarity Score ◽  
Gene Products ◽  
Semantic Similarity Measure ◽  
Similarity Algorithm ◽  
Go Terms

Existing methods for calculating semantic similarities between pairs of Gene Ontology (GO) terms and gene products often rely on external databases like Gene Ontology Annotation (GOA) that annotate gene products using the GO terms. This dependency leads to some limitations in real applications. Here, we present a semantic similarity algorithm (SSA), that relies exclusively on the GO. When calculating the semantic similarity between a pair of input GO terms, SSA takes into account the shortest path between them, the depth of their nearest common ancestor, and a novel similarity score calculated between the definitions of the involved GO terms. In our work, we use SSA to calculate semantic similarities between pairs of proteins by combining pairwise semantic similarities between the GO terms that annotate the involved proteins. The reliability of SSA was evaluated by comparing the resulting semantic similarities between proteins with the functional similarities between proteins derived from expert annotations or sequence similarity. Comparisons with existing state-of-the-art methods showed that SSA is highly competitive with the other methods. SSA provides a reliable measure for semantics similarity independent of external databases of functional-annotation observations.

scholarly journals Image Classification: A Survey

2020 ◽  
Vol 1 (2) ◽  
pp. 1-9
Author(s):  
Ankita Singh ◽  
◽  
Pawan Singh
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Image Classification ◽  
Convolutional Neural Networks ◽  
Language Processing ◽  
Classification Accuracy ◽  
Deep Neural Network ◽  
Learning Ability ◽  
Final Decision

The Classification of images is a paramount topic in artificial vision systems which have drawn a notable amount of interest over the past years. This field aims to classify an image, which is an input, based on its visual content. Currently, most people relied on hand-crafted features to describe an image in a particular way. Then, using classifiers that are learnable, such as random forest, and decision tree was applied to the extract features to come to a final decision. The problem arises when large numbers of photos are concerned. It becomes a too difficult problem to find features from them. This is one of the reasons that the deep neural network model has been introduced. Owing to the existence of Deep learning, it can become feasible to represent the hierarchical nature of features using a various number of layers and corresponding weight with them. The existing image classification methods have been gradually applied in real-world problems, but then there are various problems in its application processes, such as unsatisfactory effect and extremely low classification accuracy or then and weak adaptive ability. Models using deep learning concepts have robust learning ability, which combines the feature extraction and the process of classification into a whole which then completes an image classification task, which can improve the image classification accuracy effectively. Convolutional Neural Networks are a powerful deep neural network technique. These networks preserve the spatial structure of a problem and were built for object recognition tasks such as classifying an image into respective classes. Neural networks are much known because people are getting a state-of-the-art outcome on complex computer vision and natural language processing tasks. Convolutional neural networks have been extensively used.

scholarly journals Evaluating Representations for Gene Ontology Terms

2019 ◽  
Author(s):  
Dat Duong ◽  
Ankith Uppunda ◽  
Lisa Gai ◽  
Chelsea Ju ◽  
James Zhang ◽  
...  
Keyword(s):  
Neural Network ◽  
Gene Ontology ◽  
Network Models ◽  
Language Models ◽  
Future Research ◽  
Model Parameters ◽  
Neural Network Models ◽  
Go Annotation ◽  
Go Terms ◽  
Similarity Scores

AbstractProtein functions can be described by the Gene Ontology (GO) terms, allowing us to compare the functions of two proteins by measuring the similarity of the terms assigned to them. Recent works have applied neural network models to derive the vector representations for GO terms and compute similarity scores for these terms by comparing their vector embeddings. There are two typical ways to embed GO terms into vectors; a model can either embed the definitions of the terms or the topology of the terms in the ontology. In this paper, we design three tasks to critically evaluate the GO embeddings of two recent neural network models, and further introduce additional models for embedding GO terms, adapted from three popular neural network frameworks: Graph Convolution Network (GCN), Embeddings from Language Models (ELMo), and Bidirectional Encoder Representations from Transformers (BERT), which have not yet been explored in previous works. Task 1 studies edge cases where the GO embeddings may not provide meaningful similarity scores for GO terms. We find that all neural network based methods fail to produce high similarity scores for related terms when these terms have low Information Content values. Task 2 is a canonical task which estimates how well GO embeddings can compare functions of two orthologous genes or two interacting proteins. The best neural network methods for this task are those that embed GO terms using their definitions, and the differences among such methods are small. Task 3 evaluates how GO embeddings affect the performance of GO annotation methods, which predict whether a protein should be labeled by certain GO terms. When the annotation datasets contain many samples for each GO label, GO embeddings do not improve the classification accuracy. Machine learning GO annotation methods often remove rare GO labels from the training datasets so that the model parameters can be efficiently trained. We evaluate whether GO embeddings can improve prediction of rare labels unseen in the training datasets, and find that GO embeddings based on the BERT framework achieve the best results in this setting. We present our embedding methods and three evaluation tasks as the basis for future research on this topic.

scholarly journals Annotating Gene Ontology terms for protein sequences with the Transformer model

2020 ◽  
Author(s):  
Dat Duong ◽  
Lisa Gai ◽  
Ankith Uppunda ◽  
Don Le ◽  
Eleazar Eskin ◽  
...  
Keyword(s):  
Neural Network ◽  
Amino Acids ◽  
Gene Ontology ◽  
Amino Acid ◽  
3D Structure ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Training Dataset ◽  
Go Annotation ◽  
Go Terms

AbstractPredicting functions for novel amino acid sequences is a long-standing research problem. The Uniprot database which contains protein sequences annotated with Gene Ontology (GO) terms, is one commonly used training dataset for this problem. Predicting protein functions can then be viewed as a multi-label classification problem where the input is an amino acid sequence and the output is a set of GO terms. Recently, deep convolutional neural network (CNN) models have been introduced to annotate GO terms for protein sequences. However, the CNN architecture can only model close-range interactions between amino acids in a sequence. In this paper, first, we build a novel GO annotation model based on the Transformer neural network. Unlike the CNN architecture, the Transformer models all pairwise interactions for the amino acids within a sequence, and so can capture more relevant information from the sequences. Indeed, we show that our adaptation of Transformer yields higher classification accuracy when compared to the recent CNN-based method DeepGO. Second, we modify our model to take motifs in the protein sequences found by BLAST as additional input features. Our strategy is different from other ensemble approaches that average the outcomes of BLAST-based and machine learning predictors. Third, we integrate into our Transformer the metadata about the protein sequences such as 3D structure and protein-protein interaction (PPI) data. We show that such information can greatly improve the prediction accuracy, especially for rare GO labels.

scholarly journals Distributional Similarity for Chinese: Exploiting Characters and Radicals

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Peng Jin ◽  
John Carroll ◽  
Yunfang Wu ◽  
Diana McCarthy
Keyword(s):  
Language Processing ◽  
Gold Standard ◽  
Chinese Language ◽  
Similarity Score ◽  
Content Word ◽  
Word Similarity ◽  
Similar Word ◽  
Distributional Similarity ◽  
Similarity Computation ◽  
Large Corpus

Distributional Similarity has attracted considerable attention in the field of natural language processing as an automatic means of countering the ubiquitous problem of sparse data. As a logographic language, Chinese words consist of characters and each of them is composed of one or more radicals. The meanings of characters are usually highly related to the words which contain them. Likewise, radicals often make a predictable contribution to the meaning of a character: characters that have the same components tend to have similar or related meanings. In this paper, we utilize these properties of the Chinese language to improve Chinese word similarity computation. Given a content word, we first extract similar words based on a large corpus and a similarity score for ranking. This rank is then adjusted according to the characters and components shared between the similar word and the target word. Experiments on two gold standard datasets show that the adjusted rank is superior and closer to human judgments than the original rank. In addition to quantitative evaluation, we examine the reasons behind errors drawing on linguistic phenomena for our explanations.

Fast Neural Network Engine for Natural Science Language Processing: A Drug-Search Case.

2020 ◽  
Author(s):  
Vadim V. Korolev ◽  
Artem Mitrofanov ◽  
Kirill Karpov ◽  
Valery Tkachenko
Keyword(s):  
Neural Network ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Natural Science ◽  
Therapeutic Agent ◽  
Semantic Relations ◽  
Chemical Data ◽  
Processing Methods ◽  
Modern Natural

The main advantage of modern natural language processing methods is a possibility to turn an amorphous human-readable task into a strict mathematic form. That allows to extract chemical data and insights from articles and to find new semantic relations. We propose a universal engine for processing chemical and biological texts. We successfully tested it on various use-cases and applied to a case of searching a therapeutic agent for a COVID-19 disease by analyzing PubMed archive.

Simulation and Performance Analysis of Tilted Time Window and Support Vector Machine Based Learning Object Ranking Method

2020 ◽  
Vol 13 (2) ◽  
pp. 153-164
Author(s):  
Narina Thakur ◽  
Deepti Mehrotra ◽  
Abhay Bansal ◽  
Manju Bala
Keyword(s):  
Support Vector Machine ◽  
Classification Accuracy ◽  
Time Window ◽  
Optimal Solution ◽  
Similarity Score ◽  
Learning Objects ◽  
Retrieval Algorithm ◽  
Support Vector ◽  
Computationally Efficient ◽  
User Query

Objective: Since the adequacy of Learning Objects (LO) is a dynamic concept and changes in its use, needs and evolution, it is important to consider the importance of LO in terms of time to assess its relevance as the main objective of the proposed research. Another goal is to increase the classification accuracy and precision. Methods: With existing IR and ranking algorithms, MAP optimization either does not lead to a comprehensively optimal solution or is expensive and time - consuming. Nevertheless, Support Vector Machine learning competently leads to a globally optimal solution. SVM is a powerful classifier method with its high classification accuracy and the Tilted time window based model is computationally efficient. Results: This paper proposes and implements the LO ranking and retrieval algorithm based on the Tilted Time window and the Support Vector Machine, which uses the merit of both methods. The proposed model is implemented for the NCBI dataset and MAT Lab. Conclusion: The experiments have been carried out on the NCBI dataset, and LO weights are assigned to be relevant and non - relevant for a given user query according to the Tilted Time series and the Cosine similarity score. Results showed that the model proposed has much better accuracy.

Improving Sentiment Analysis using Hybrid Deep Learning Model

2020 ◽  
Vol 13 (4) ◽  
pp. 627-640 ◽  
Author(s):  
Avinash Chandra Pandey ◽  
Dharmveer Singh Rajpoot
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Classification Accuracy ◽  
Short Term Memory ◽  
Computational Cost ◽  
Extraction Process ◽  
Learning Model ◽  
Sentiment Classification ◽  
Deep Learning Model

Background: Sentiment analysis is a contextual mining of text which determines viewpoint of users with respect to some sentimental topics commonly present at social networking websites. Twitter is one of the social sites where people express their opinion about any topic in the form of tweets. These tweets can be examined using various sentiment classification methods to find the opinion of users. Traditional sentiment analysis methods use manually extracted features for opinion classification. The manual feature extraction process is a complicated task since it requires predefined sentiment lexicons. On the other hand, deep learning methods automatically extract relevant features from data hence; they provide better performance and richer representation competency than the traditional methods. Objective: The main aim of this paper is to enhance the sentiment classification accuracy and to reduce the computational cost. Method: To achieve the objective, a hybrid deep learning model, based on convolution neural network and bi-directional long-short term memory neural network has been introduced. Results: The proposed sentiment classification method achieves the highest accuracy for the most of the datasets. Further, from the statistical analysis efficacy of the proposed method has been validated. Conclusion: Sentiment classification accuracy can be improved by creating veracious hybrid models. Moreover, performance can also be enhanced by tuning the hyper parameters of deep leaning models.

scholarly journals Estimation of the influence of spiking neural network parameters on classification accuracy using a genetic algorithm

2018 ◽  
Vol 145 ◽  
pp. 488-494 ◽  
Author(s):  
Aleksandr Sboev ◽  
Alexey Serenko ◽  
Roman Rybka ◽  
Danila Vlasov ◽  
Andrey Filchenkov
Keyword(s):  
Neural Network ◽  
Genetic Algorithm ◽  
Classification Accuracy ◽  
Spiking Neural Network ◽  
Network Parameters

scholarly journals Identifying protein subcellular localisation in scientific literature using bidirectional deep recurrent neural network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rakesh David ◽  
Rhys-Joshua D. Menezes ◽  
Jan De Klerk ◽  
Ian R. Castleden ◽  
Cornelia M. Hooper ◽  
...  
Keyword(s):  
Neural Network ◽  
Language Processing ◽  
Data Dissemination ◽  
Short Term Memory ◽  
Biological Data ◽  
Experimental Methodology ◽  
Subcellular Localisation ◽  
Crop Species ◽  
Deep Recurrent Neural Network ◽  
Functional Features

AbstractThe increased diversity and scale of published biological data has to led to a growing appreciation for the applications of machine learning and statistical methodologies to gain new insights. Key to achieving this aim is solving the Relationship Extraction problem which specifies the semantic interaction between two or more biological entities in a published study. Here, we employed two deep neural network natural language processing (NLP) methods, namely: the continuous bag of words (CBOW), and the bi-directional long short-term memory (bi-LSTM). These methods were employed to predict relations between entities that describe protein subcellular localisation in plants. We applied our system to 1700 published Arabidopsis protein subcellular studies from the SUBA manually curated dataset. The system combines pre-processing of full-text articles in a machine-readable format with relevant sentence extraction for downstream NLP analysis. Using the SUBA corpus, the neural network classifier predicted interactions between protein name, subcellular localisation and experimental methodology with an average precision, recall rate, accuracy and F1 scores of 95.1%, 82.8%, 89.3% and 88.4% respectively (n = 30). Comparable scoring metrics were obtained using the CropPAL database as an independent testing dataset that stores protein subcellular localisation in crop species, demonstrating wide applicability of prediction model. We provide a framework for extracting protein functional features from unstructured text in the literature with high accuracy, improving data dissemination and unlocking the potential of big data text analytics for generating new hypotheses.

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