An Overview of Biological Data Mining

Biotechnology ◽  
2019 ◽  
pp. 120-139
Author(s):  
Seetharaman Balaji
Keyword(s):  
Data Mining ◽  
Information Retrieval ◽  
Biological Networks ◽  
Web Mining ◽  
Biological Data ◽  
Biological Research ◽  
Digital Repository ◽  
Domain Specific ◽  
Novice Learner ◽  
Integration Data

The largest digital repository of information, the World Wide Web keeps growing exponentially and calls for data mining services to provide tailored web experiences. This chapter discusses the overview of information retrieval, knowledge discovery and data mining. It reviews the different stages of data mining and introduces the wide spread biological databanks, their explosion, integration, data warehousing, information retrieval, text mining, text repositories for biological research publications, domain specific search engines, web mining, biological networks and visualization, ontology and systems biology. This chapter also illustrates some technical jargon with picture analogy for a novice learner to understand the concepts clearly.

An Overview of Biological Data Mining

2017 ◽  
pp. 130-154
Author(s):  
Seetharaman Balaji
Keyword(s):  
Data Mining ◽  
Information Retrieval ◽  
Biological Networks ◽  
Web Mining ◽  
Biological Data ◽  
Biological Research ◽  
Digital Repository ◽  
Domain Specific ◽  
Novice Learner ◽  
Integration Data

The largest digital repository of information, the World Wide Web keeps growing exponentially and calls for data mining services to provide tailored web experiences. This chapter discusses the overview of information retrieval, knowledge discovery and data mining. It reviews the different stages of data mining and introduces the wide spread biological databanks, their explosion, integration, data warehousing, information retrieval, text mining, text repositories for biological research publications, domain specific search engines, web mining, biological networks and visualization, ontology and systems biology. This chapter also illustrates some technical jargon with picture analogy for a novice learner to understand the concepts clearly.

A Comprehensive Guideline for Bengali Sentiment Annotation

2022 ◽  
Vol 21 (2) ◽  
pp. 1-19
Author(s):  
Md. Saddam Hossain Mukta ◽  
Md. Adnanul Islam ◽  
Faisal Ahamed Khan ◽  
Afjal Hossain ◽  
Shuvanon Razik ◽  
...  
Keyword(s):  
Data Mining ◽  
Information Retrieval ◽  
Sentiment Analysis ◽  
Computational Linguistics ◽  
Language Processing ◽  
Web Mining ◽  
English Language ◽  
Research Work ◽  
Bengali Language

Sentiment Analysis (SA) is a Natural Language Processing (NLP) and an Information Extraction (IE) task that primarily aims to obtain the writer’s feelings expressed in positive or negative by analyzing a large number of documents. SA is also widely studied in the fields of data mining, web mining, text mining, and information retrieval. The fundamental task in sentiment analysis is to classify the polarity of a given content as Positive, Negative, or Neutral . Although extensive research has been conducted in this area of computational linguistics, most of the research work has been carried out in the context of English language. However, Bengali sentiment expression has varying degree of sentiment labels, which can be plausibly distinct from English language. Therefore, sentiment assessment of Bengali language is undeniably important to be developed and executed properly. In sentiment analysis, the prediction potential of an automatic modeling is completely dependent on the quality of dataset annotation. Bengali sentiment annotation is a challenging task due to diversified structures (syntax) of the language and its different degrees of innate sentiments (i.e., weakly and strongly positive/negative sentiments). Thus, in this article, we propose a novel and precise guideline for the researchers, linguistic experts, and referees to annotate Bengali sentences immaculately with a view to building effective datasets for automatic sentiment prediction efficiently.

Review of the Applications of Deep Learning in Bioinformatics

2021 ◽  
Vol 15 (8) ◽  
pp. 898-911
Author(s):  
Yongqing Zhang ◽  
Jianrong Yan ◽  
Siyu Chen ◽  
Meiqin Gong ◽  
Dongrui Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Biomedical Imaging ◽  
State Of The Art ◽  
Black Box ◽  
Medical Data ◽  
Biological Data ◽  
High Dimensional ◽  
Biological Research ◽  
Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

scholarly journals Dynamic model updating (DMU) approach for statistical learning model building with missing data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rahi Jain ◽  
Wei Xu
Keyword(s):  
Missing Data ◽  
Dynamic Model ◽  
Statistical Models ◽  
Missing Values ◽  
Model Building ◽  
Model Updating ◽  
Biological Data ◽  
Bayesian Regression ◽  
Biological Research ◽  
Original Dataset

Abstract Background Developing statistical and machine learning methods on studies with missing information is a ubiquitous challenge in real-world biological research. The strategy in literature relies on either removing the samples with missing values like complete case analysis (CCA) or imputing the information in the samples with missing values like predictive mean matching (PMM) such as MICE. Some limitations of these strategies are information loss and closeness of the imputed values with the missing values. Further, in scenarios with piecemeal medical data, these strategies have to wait to complete the data collection process to provide a complete dataset for statistical models. Method and results This study proposes a dynamic model updating (DMU) approach, a different strategy to develop statistical models with missing data. DMU uses only the information available in the dataset to prepare the statistical models. DMU segments the original dataset into small complete datasets. The study uses hierarchical clustering to segment the original dataset into small complete datasets followed by Bayesian regression on each of the small complete datasets. Predictor estimates are updated using the posterior estimates from each dataset. The performance of DMU is evaluated by using both simulated data and real studies and show better results or at par with other approaches like CCA and PMM. Conclusion DMU approach provides an alternative to the existing approaches of information elimination and imputation in processing the datasets with missing values. While the study applied the approach for continuous cross-sectional data, the approach can be applied to longitudinal, categorical and time-to-event biological data.

scholarly journals BioNetLink - An Architecture for Working with Network Data

2014 ◽  
Vol 11 (2) ◽  
pp. 68-79
Author(s):  
Matthias Klapperstück ◽  
Falk Schreiber
Keyword(s):  
Experimental Data ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Large Data ◽  
Biological Data ◽  
Network Data ◽  
Data Sets ◽  
Dynamic Views ◽  
Gene Regulatory ◽  
Multiple Network

Summary The visualization of biological data gained increasing importance in the last years. There is a large number of methods and software tools available that visualize biological data including the combination of measured experimental data and biological networks. With growing size of networks their handling and exploration becomes a challenging task for the user. In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction networks. Therefore, fast access, abstract and dynamic views, and intuitive exploratory methods should be provided to search and extract information from the networks. This paper will introduce a conceptual framework for handling and combining multiple network sources that enables abstract viewing and exploration of large data sets including additional experimental data. It will introduce a three-tier structure that links network data to multiple network views, discuss a proof of concept implementation, and shows a specific visualization method for combining metabolic and gene regulatory networks in an example.

Application of Data Pre-Processing Method in Web Mining

2014 ◽  
Vol 687-691 ◽  
pp. 1592-1595
Author(s):  
Yun Peng Duan ◽  
Chun Xi Zhao ◽  
Ying Shi
Keyword(s):  
Data Mining ◽  
Web Mining ◽  
Early Stage ◽  
Data Preprocessing ◽  
Web Technology ◽  
Processing Method ◽  
Web Log Mining ◽  
Web Log ◽  
User Access ◽  
Log Mining

With the widely application of the WWW and the emergence of Web technology, make the research of data mining has entered a new stage. Web log mining is based on the idea of data mining to analyze the server log processing. Paper aimed at the early stage of the data mining is put forward based on log data preprocessing methods, the purpose is to divide server logs into multiple unique user access sequence at a time, and to give a good algorithm.

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