| 1. |
- Abbasi, Ahtisham Fazeel, et al.
(författare)
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Deep learning architectures for the prediction of YY1-mediated chromatin loops
- 2023
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Ingår i: Bioinformatics research and applications. - : Springer. - 9789819970735 - 9789819970742 ; , s. 72-84
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Konferensbidrag (refereegranskat)abstract
- YY1-mediated chromatin loops play substantial roles in basic biological processes like gene regulation, cell differentiation, and DNA replication. YY1-mediated chromatin loop prediction is important to understand diverse types of biological processes which may lead to the development of new therapeutics for neurological disorders and cancers. Existing deep learning predictors are capable to predict YY1-mediated chromatin loops in two different cell lines however, they showed limited performance for the prediction of YY1-mediated loops in the same cell lines and suffer significant performance deterioration in cross cell line setting. To provide computational predictors capable of performing large-scale analyses of YY1-mediated loop prediction across multiple cell lines, this paper presents two novel deep learning predictors. The two proposed predictors make use of Word2vec, one hot encoding for sequence representation and long short-term memory, and a convolution neural network along with a gradient flow strategy similar to DenseNet architectures. Both of the predictors are evaluated on two different benchmark datasets of two cell lines HCT116 and K562. Overall the proposed predictors outperform existing DEEPYY1 predictor with an average maximum margin of 4.65%, 7.45% in terms of AUROC, and accuracy, across both of the datases over the independent test sets and 5.1%, 3.2% over 5-fold validation. In terms of cross-cell evaluation, the proposed predictors boast maximum performance enhancements of up to 9.5% and 27.1% in terms of AUROC over HCT116 and K562 datasets.
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| 2. |
- Khalid, Nabeel, et al.
(författare)
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PACE : point annotation-based cell segmentation for efficient microscopic image analysis
- 2023
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Ingår i: Artificial Neural Networks and Machine Learning – ICANN 2023. - : Springer Nature. - 9783031442094 - 9783031442100 ; , s. 545-557
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Konferensbidrag (refereegranskat)abstract
- Cells are essential to life because they provide the functional, genetic, and communication mechanisms essential for the proper functioning of living organisms. Cell segmentation is pivotal for any biological hypothesis validation/analysis i.e., to get valuable insights into cell behavior, function, diagnosis, and treatment. Deep learning-based segmentation methods have high segmentation precision, however, need fully annotated segmentation masks for each cell annotated manually by the experts, which is very laborious and costly. Many approaches have been developed in the past to reduce the effort required to annotate the data manually and even though these approaches produce good results, there is still a noticeable difference in performance when compared to fully supervised methods. To fill that gap, a weakly supervised approach, PACE, is presented, which uses only the point annotations and the bounding box for each cell to perform cell instance segmentation. The proposed approach not only achieves 99.8% of the fully supervised performance, but it also surpasses the previous state-of-the-art by a margin of more than 4%.
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| 3. |
- Shah, Syed Qasim Ali, et al.
(författare)
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What is the role of remittance and education for environmental pollution?-Analyzing in the presence of financial inclusion and natural resource extraction
- 2023
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Ingår i: Heliyon. - : CELL PRESS. - 2405-8440. ; 9:6
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Tidskriftsartikel (refereegranskat)abstract
- This study assessed the impact of gross domestic product (GDP), education, natural resources, remittances, and financial inclusion on carbon emissions in G-11 countries from 1990 to 2021. Based on the negative impact of pollution and the need for sustainable development, this study examined factors affecting CO2 emissions in G-11 countries using non-linear panel ARDL model. The study found that a positive GDP shock increases CO2 emissions in the short and long term, while a negative shock decreases emissions in the short term and increases emissions in the long term. Education was found to increase CO2 emissions in the long term but decrease them in the short term, emphasizing the need for education on combating emissions. Natural resources were also found to increase emissions in the long term, highlighting the need for government-defined institutions to minimize extraction effects and enforce transparency and accountability. Positive changes in personal remittances and financial inclusion were found to increase emissions in both the short and long term, suggesting the need for policies that encourage renewable energy sources and energy efficiency improvement. The study concludes that policymakers should prioritize efficient resource allocation, promote renewable energy usage, and enhance environmental awareness to achieve sustainable development goals in G-11 countries. The possible applications of this study include the use of the models to investigate the asymmetric effects on CO2 emissions. This model can be applied in future studies to examine the relationship between GDP, education, natural resources, personal remittances, financial inclusion, and CO2 emissions in other countries.
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