scholarly journals Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ching-Tai Chen ◽  
Jen-Hung Wang ◽  
Cheng-Wei Cheng ◽  
Wei-Che Hsu ◽  
Chu-Ling Ko ◽  
...  
Keyword(s):  
State Of The Art ◽  
Systematic Evaluation ◽  
Data Sets ◽  
Differentially Expressed Proteins ◽  
Correction Algorithm ◽  
Popular Approach ◽  
Proteomic Data ◽  
Graphical Interfaces ◽  
Sample Data ◽  
Improved Accuracy

AbstractMass spectrometry-based proteomics using isobaric labeling for multiplex quantitation has become a popular approach for proteomic studies. We present Multi-Q 2, an isobaric-labeling quantitation tool which can yield the largest quantitation coverage and improved quantitation accuracy compared to three state-of-the-art methods. Multi-Q 2 supports identification results from several popular proteomic data analysis platforms for quantitation, offering up to 12% improvement in quantitation coverage for accepting identification results from multiple search engines when compared with MaxQuant and PatternLab. It is equipped with various quantitation algorithms, including a ratio compression correction algorithm, and results in up to 336 algorithmic combinations. Systematic evaluation shows different algorithmic combinations have different strengths and are suitable for different situations. We also demonstrate that the flexibility of Multi-Q 2 in customizing algorithmic combination can lead to improved quantitation accuracy over existing tools. Moreover, the use of complementary algorithmic combinations can be an effective strategy to enhance sensitivity when searching for biomarkers from differentially expressed proteins in proteomic experiments. Multi-Q 2 provides interactive graphical interfaces to process quantitation and to display ratios at protein, peptide, and spectrum levels. It also supports a heatmap module, enabling users to cluster proteins based on their abundance ratios and to visualize the clustering results. Multi-Q 2 executable files, sample data sets, and user manual are freely available at http://ms.iis.sinica.edu.tw/COmics/Software_Multi-Q2.html.

scholarly journals Bayesian Classification of Microbial Communities Based on 16S rRNA Metagenomic Data

2018 ◽  
Author(s):  
Arghavan Bahadorinejad ◽  
Ivan Ivanov ◽  
Johanna W Lampe ◽  
Meredith AJ Hullar ◽  
Robert S Chapkin ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sample Size ◽  
Microbial Communities ◽  
State Of The Art ◽  
Metagenomic Data ◽  
Data Sets ◽  
Sequencing Data ◽  
Sample Data

AbstractWe propose a Bayesian method for the classification of 16S rRNA metagenomic profiles of bacterial abundance, by introducing a Poisson-Dirichlet-Multinomial hierarchical model for the sequencing data, constructing a prior distribution from sample data, calculating the posterior distribution in closed form; and deriving an Optimal Bayesian Classifier (OBC). The proposed algorithm is compared to state-of-the-art classification methods for 16S rRNA metagenomic data, including Random Forests and the phylogeny-based Metaphyl algorithm, for varying sample size, classification difficulty, and dimensionality (number of OTUs), using both synthetic and real metagenomic data sets. The results demonstrate that the proposed OBC method, with either noninformative or constructed priors, is competitive or superior to the other methods. In particular, in the case where the ratio of sample size to dimensionality is small, it was observed that the proposed method can vastly outperform the others.Author summaryRecent studies have highlighted the interplay between host genetics, gut microbes, and colorectal tumor initiation/progression. The characterization of microbial communities using metagenomic profiling has therefore received renewed interest. In this paper, we propose a method for classification, i.e., prediction of different outcomes, based on 16S rRNA metagenomic data. The proposed method employs a Bayesian approach, which is suitable for data sets with small ration of number of available instances to the dimensionality. Results using both synthetic and real metagenomic data show that the proposed method can outperform other state-of-the-art metagenomic classification algorithms.

Delivering Sustainable Water Systems Using Kalman Filter and Statistical Approach

2017 ◽  
Vol 4 (1) ◽  
pp. 41-52
Author(s):  
Dedy Loebis
Keyword(s):  
Kalman Filtering ◽  
Statistical Approach ◽  
Water Systems ◽  
Data Sets ◽  
Pressure Data ◽  
Burst Event ◽  
Sample Data ◽  
Other Information ◽  
Supply Systems ◽  
Frequency Features

This paper presents the results of work undertaken to develop and test contrasting data analysis approaches for the detection of bursts/leaks and other anomalies within wate r supply systems at district meter area (DMA)level. This was conducted for Yorkshire Water (YW) sample data sets from the Harrogate and Dales (H&D), Yorkshire, United Kingdom water supply network as part of Project NEPTUNE EP/E003192/1 ). A data analysissystem based on Kalman filtering and statistical approach has been developed. The system has been applied to the analysis of flow and pressure data. The system was proved for one dataset case and have shown the ability to detect anomalies in flow and pres sure patterns, by correlating with other information. It will be shown that the Kalman/statistical approach is a promising approach at detecting subtle changes and higher frequency features, it has the potential to identify precursor features and smaller l eaks and hence could be useful for monitoring the development of leaks, prior to a large volume burst event.

TrustSVD: A Novel Trust-Based Matrix Factorization Model with User Trust and Item Ratings

2017 ◽  
Vol 7 (11) ◽  
pp. 7 ◽  
Author(s):  
K Sobha Rani
Keyword(s):  
Matrix Factorization ◽  
Social Trust ◽  
State Of The Art ◽  
Data Sets ◽  
Real World Data ◽  
Recommendation Algorithm ◽  
Active User ◽  
Factorization Model ◽  
The Social ◽  
Matrix Factorization Technique

Collaborative filtering suffers from the problems of data sparsity and cold start, which dramatically degrade recommendation performance. To help resolve these issues, we propose TrustSVD, a trust-based matrix factorization technique. By analyzing the social trust data from four real-world data sets, we conclude that not only the explicit but also the implicit influence of both ratings and trust should be taken into consideration in a recommendation model. Hence, we build on top of a state-of-the-art recommendation algorithm SVD++ which inherently involves the explicit and implicit influence of rated items, by further incorporating both the explicit and implicit influence of trusted users on the prediction of items for an active user. To our knowledge, the work reported is the first to extend SVD++ with social trust information. Experimental results on the four data sets demonstrate that our approach TrustSVD achieves better accuracy than other ten counterparts, and can better handle the concerned issues.

Proteomics: Opportunities and Challenges

2011 ◽  
Vol 3 (4) ◽  
pp. 1165-1172 ◽  
Author(s):  
Parag A Pathade ◽  
Vinod A Bairagi ◽  
Yogesh S. Ahire ◽  
Neela M Bhatia
Keyword(s):  
Biomedical Research ◽  
Therapy Monitoring ◽  
Dynamic State ◽  
Data Sets ◽  
Protein Markers ◽  
Drug Target Discovery ◽  
Proteomic Data ◽  
Cell Tissue ◽  
A Cell ◽  
Analytical Tools

‘‘Proteomics’’, is the emerging technology leading to high-throughput identification and understanding of proteins. Proteomics is the protein equivalent of genomics and has captured the imagination of biomolecular scientists, worldwide. Because proteome reveals more accurately the dynamic state of a cell, tissue, or organism, much is expected from proteomics to indicate better disease markers for diagnosis and therapy monitoring. Proteomics is expected to play a major role in biomedical research, and it will have a significant impact on the development of diagnostics and therapeutics for cancer, heart ailments and infectious diseases, in future. Proteomics research leads to the identification of new protein markers for diagnostic purposes and novel molecular targets for drug discovery.  Though the potential is great, many challenges and issues remain to be solved, such as gene expression, peptides, generation of low abundant proteins, analytical tools, drug target discovery and cost. A systematic and efficient analysis of vast genomic and proteomic data sets is a major challenge for researchers, today. Nevertheless, proteomics is the groundwork for constructing and extracting useful comprehension to biomedical research. This review article covers some opportunities and challenges offered by proteomics.   

scholarly journals Efficient End-to-End Sentence-Level Lipreading with Temporal Convolutional Networks

2021 ◽  
Vol 11 (15) ◽  
pp. 6975
Author(s):  
Tao Zhang ◽  
Lun He ◽  
Xudong Li ◽  
Guoqing Feng
Keyword(s):  
Performance Improvement ◽  
State Of The Art ◽  
Error Rates ◽  
Convolutional Network ◽  
Convolutional Networks ◽  
Sentence Level ◽  
End To End ◽  
High Level ◽  
Improved Accuracy ◽  
Talking Face

Lipreading aims to recognize sentences being spoken by a talking face. In recent years, the lipreading method has achieved a high level of accuracy on large datasets and made breakthrough progress. However, lipreading is still far from being solved, and existing methods tend to have high error rates on the wild data and have the defects of disappearing training gradient and slow convergence. To overcome these problems, we proposed an efficient end-to-end sentence-level lipreading model, using an encoder based on a 3D convolutional network, ResNet50, Temporal Convolutional Network (TCN), and a CTC objective function as the decoder. More importantly, the proposed architecture incorporates TCN as a feature learner to decode feature. It can partly eliminate the defects of RNN (LSTM, GRU) gradient disappearance and insufficient performance, and this yields notable performance improvement as well as faster convergence. Experiments show that the training and convergence speed are 50% faster than the state-of-the-art method, and improved accuracy by 2.4% on the GRID dataset.

scholarly journals A novel optimal multi-pattern matching method with wildcards for DNA sequence

2021 ◽  
Vol 29 ◽  
pp. 115-124
Author(s):  
Xinlu Wang ◽  
Ahmed A.F. Saif ◽  
Dayou Liu ◽  
Yungang Zhu ◽  
Jon Atli Benediktsson
Keyword(s):  
Dna Sequence ◽  
Pattern Matching ◽  
Health Informatics ◽  
State Of The Art ◽  
Machine Language ◽  
Data Sets ◽  
Fundamental Issue ◽  
Matching Method ◽  
Dna Sequence Alignment ◽  
The Given

BACKGROUND: DNA sequence alignment is one of the most fundamental and important operation to identify which gene family may contain this sequence, pattern matching for DNA sequence has been a fundamental issue in biomedical engineering, biotechnology and health informatics. OBJECTIVE: To solve this problem, this study proposes an optimal multi pattern matching with wildcards for DNA sequence. METHODS: This proposed method packs the patterns and a sliding window of texts, and the window slides along the given packed text, matching against stored packed patterns. RESULTS: Three data sets are used to test the performance of the proposed algorithm, and the algorithm was seen to be more efficient than the competitors because its operation is close to machine language. CONCLUSIONS: Theoretical analysis and experimental results both demonstrate that the proposed method outperforms the state-of-the-art methods and is especially effective for the DNA sequence.

scholarly journals gbt-HIPS: Explaining the Classifications of Gradient Boosted Tree Ensembles

2021 ◽  
Vol 11 (6) ◽  
pp. 2511
Author(s):  
Julian Hatwell ◽  
Mohamed Medhat Gaber ◽  
R. Muhammad Atif Azad
Keyword(s):  
State Of The Art ◽  
Heuristic Method ◽  
Good Explanation ◽  
Classification Rule ◽  
Data Sets ◽  
Classification Models ◽  
Boundary Values ◽  
Class Label ◽  
Input Space ◽  
Boosted Tree

This research presents Gradient Boosted Tree High Importance Path Snippets (gbt-HIPS), a novel, heuristic method for explaining gradient boosted tree (GBT) classification models by extracting a single classification rule (CR) from the ensemble of decision trees that make up the GBT model. This CR contains the most statistically important boundary values of the input space as antecedent terms. The CR represents a hyper-rectangle of the input space inside which the GBT model is, very reliably, classifying all instances with the same class label as the explanandum instance. In a benchmark test using nine data sets and five competing state-of-the-art methods, gbt-HIPS offered the best trade-off between coverage (0.16–0.75) and precision (0.85–0.98). Unlike competing methods, gbt-HIPS is also demonstrably guarded against under- and over-fitting. A further distinguishing feature of our method is that, unlike much prior work, our explanations also provide counterfactual detail in accordance with widely accepted recommendations for what makes a good explanation.

Learning emotional word embeddings for sentiment analysis

2021 ◽  
pp. 1-13
Author(s):  
Qingtian Zeng ◽  
Xishi Zhao ◽  
Xiaohui Hu ◽  
Hua Duan ◽  
Zhongying Zhao ◽  
...  
Keyword(s):  
Sentiment Analysis ◽  
Language Processing ◽  
State Of The Art ◽  
Research Problem ◽  
Emotional Word ◽  
Classification Model ◽  
Data Sets ◽  
Word Embeddings ◽  
Real World Data ◽  
Text Documents

Word embeddings have been successfully applied in many natural language processing tasks due to its their effectiveness. However, the state-of-the-art algorithms for learning word representations from large amounts of text documents ignore emotional information, which is a significant research problem that must be addressed. To solve the above problem, we propose an emotional word embedding (EWE) model for sentiment analysis in this paper. This method first applies pre-trained word vectors to represent document features using two different linear weighting methods. Then, the resulting document vectors are input to a classification model and used to train a text sentiment classifier, which is based on a neural network. In this way, the emotional polarity of the text is propagated into the word vectors. The experimental results on three kinds of real-world data sets demonstrate that the proposed EWE model achieves superior performances on text sentiment prediction, text similarity calculation, and word emotional expression tasks compared to other state-of-the-art models.

scholarly journals Critical Aspects of Person Counting and Density Estimation

2021 ◽  
Vol 7 (2) ◽  
pp. 21
Author(s):  
Roland Perko ◽  
Manfred Klopschitz ◽  
Alexander Almer ◽  
Peter M. Roth
Keyword(s):  
Density Estimation ◽  
Network Architecture ◽  
Reference Data ◽  
State Of The Art ◽  
Limit State ◽  
Ground Truth ◽  
Data Sets ◽  
Ground Truth Generation ◽  
Baseline Approach ◽  
Critical Aspects

Many scientific studies deal with person counting and density estimation from single images. Recently, convolutional neural networks (CNNs) have been applied for these tasks. Even though often better results are reported, it is often not clear where the improvements are resulting from, and if the proposed approaches would generalize. Thus, the main goal of this paper was to identify the critical aspects of these tasks and to show how these limit state-of-the-art approaches. Based on these findings, we show how to mitigate these limitations. To this end, we implemented a CNN-based baseline approach, which we extended to deal with identified problems. These include the discovery of bias in the reference data sets, ambiguity in ground truth generation, and mismatching of evaluation metrics w.r.t. the training loss function. The experimental results show that our modifications allow for significantly outperforming the baseline in terms of the accuracy of person counts and density estimation. In this way, we get a deeper understanding of CNN-based person density estimation beyond the network architecture. Furthermore, our insights would allow to advance the field of person density estimation in general by highlighting current limitations in the evaluation protocols.

scholarly journals Towards Application of One-Class Classification Methods to Medical Data

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Itziar Irigoien ◽  
Basilio Sierra ◽  
Concepción Arenas
Keyword(s):  
State Of The Art ◽  
Gaussian Mixture ◽  
Support Vector ◽  
Support Vector Data Description ◽  
Data Sets ◽  
Biomedical Data ◽  
Vector Data ◽  
Target Class ◽  
Tumor Recognition ◽  
One Class Classification

In the problem of one-class classification (OCC) one of the classes, the target class, has to be distinguished from all other possible objects, considered as nontargets. In many biomedical problems this situation arises, for example, in diagnosis, image based tumor recognition or analysis of electrocardiogram data. In this paper an approach to OCC based on a typicality test is experimentally compared with reference state-of-the-art OCC techniques—Gaussian, mixture of Gaussians, naive Parzen, Parzen, and support vector data description—using biomedical data sets. We evaluate the ability of the procedures using twelve experimental data sets with not necessarily continuous data. As there are few benchmark data sets for one-class classification, all data sets considered in the evaluation have multiple classes. Each class in turn is considered as the target class and the units in the other classes are considered as new units to be classified. The results of the comparison show the good performance of the typicality approach, which is available for high dimensional data; it is worth mentioning that it can be used for any kind of data (continuous, discrete, or nominal), whereas state-of-the-art approaches application is not straightforward when nominal variables are present.

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