| 1. |
- Asim, Muhammad Nabeel, et al.
(författare)
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EL-RMLocNet : An explainable LSTM network for RNA-associated multi-compartment localization prediction
- 2022
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Ingår i: Computational and Structural Biotechnology Journal. - : Elsevier. - 2001-0370. ; 20, s. 3986-4002
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Tidskriftsartikel (refereegranskat)abstract
- Subcellular localization of Ribonucleic Acid (RNA) molecules provide significant insights into the functionality of RNAs and helps to explore their association with various diseases. Predominantly developed single-compartment localization predictors (SCLPs) lack to demystify RNA association with diverse biochemical and pathological processes mainly happen through RNA co-localization in multiple compartments. Limited multi-compartment localization predictors (MCLPs) manage to produce decent performance only for target RNA class of particular sub-type. Further, existing computational approaches have limited practical significance and potential to optimize therapeutics due to the poor degree of model explainability. The paper in hand presents an explainable Long Short-Term Memory (LSTM) network “EL-RMLocNet”, predictive performance and interpretability of which are optimized using a novel GeneticSeq2Vec statistical representation learning scheme and attention mechanism for accurate multi-compartment localization prediction of different RNAs solely using raw RNA sequences. GeneticSeq2Vec generates optimized statistical vectors of raw RNA sequences by capturing short and long range relations of nucleotide k-mers. Using sequence vectors generated by GeneticSeq2Vec scheme, Long Short Term Memory layers extract most informative features, weighting of which on the basis of discriminative potential for accurate multi-compartment localization prediction is performed using attention layer. Through reverse engineering, weights of statistical feature space are mapped to nucleotide k-mers patterns to make multi-compartment localization prediction decision making transparent and explainable for different RNA classes and species. Empirical evaluation indicates that EL-RMLocNet outperforms state-of-the-art predictor for subcellular localization prediction of 4 different RNA classes by an average accuracy figure of 8% for Homo Sapiens species and 6% for Mus Musculus species. EL-RMLocNet is freely available as a web server at (https://sds_genetic_analysis.opendfki.de/subcellular_loc/).
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| 2. |
- Asim, Muhammad Nabeel, et al.
(författare)
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A robust and precise convnet for small non-coding rna classification (rpc-snrc)
- 2021
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Ingår i: IEEE Access. - 2169-3536. ; 9, s. 19379-19390
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Tidskriftsartikel (refereegranskat)abstract
- Small non-coding RNAs (ncRNAs) are attracting increasing attention as they are now considered potentially valuable resources in the development of new drugs intended to cure several human diseases. A prerequisite for the development of drugs targeting ncRNAs or the related pathways is the identification and correct classification of such ncRNAs. State-of-the-art small ncRNA classification methodologies use secondary structural features as input. However, such feature extraction approaches only take global characteristics into account and completely ignore co-relative effects of local structures. Furthermore, secondary structure based approaches incorporate high dimensional feature space which is computationally expensive. The present paper proposes a novel Robust and Precise ConvNet (RPC-snRC) methodology which classifies small ncRNAs into relevant families by utilizing their primary sequence. RPC-snRC methodology learns hierarchical representation of features by utilizing positioning and information on the occurrence of nucleotides. To avoid exploding and vanishing gradient problems, we use an approach similar to DenseNet in which gradient can flow straight from subsequent layers to previous layers. In order to assess the effectiveness of deeper architectures for small ncRNA classification, we also adapted two ResNet architectures having a different number of layers. Experimental results on a benchmark small ncRNA dataset show that the proposed methodology does not only outperform existing small ncRNA classification approaches with a significant performance margin of 10% but it also gives better results than adapted ResNet architectures. To reproduce the results Source code and data set is available at https://github.com/muas16/small-non-coding-RNA-classification.
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| 3. |
- Asim, Muhammad Nabeel, et al.
(författare)
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BoT-Net : a lightweight bag of tricks-based neural network for efficient LncRNA–miRNA interaction prediction
- 2022
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Ingår i: Interdisciplinary Sciences: Computational Life Sciences. - : Springer. - 1913-2751 .- 1867-1462. ; 14:4, s. 841-862
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Tidskriftsartikel (refereegranskat)abstract
- Background and objective: Interactions of long non-coding ribonucleic acids (lncRNAs) with micro-ribonucleic acids (miRNAs) play an essential role in gene regulation, cellular metabolic, and pathological processes. Existing purely sequence based computational approaches lack robustness and efficiency mainly due to the high length variability of lncRNA sequences. Hence, the prime focus of the current study is to find optimal length trade-offs between highly flexible length lncRNA sequences.Method: The paper at hand performs in-depth exploration of diverse copy padding, sequence truncation approaches, and presents a novel idea of utilizing only subregions of lncRNA sequences to generate fixed-length lncRNA sequences. Furthermore, it presents a novel bag of tricks-based deep learning approach “Bot-Net” which leverages a single layer long-short-term memory network regularized through DropConnect to capture higher order residue dependencies, pooling to retain most salient features, normalization to prevent exploding and vanishing gradient issues, learning rate decay, and dropout to regularize precise neural network for lncRNA–miRNA interaction prediction.Results: BoT-Net outperforms the state-of-the-art lncRNA–miRNA interaction prediction approach by 2%, 8%, and 4% in terms of accuracy, specificity, and matthews correlation coefficient. Furthermore, a case study analysis indicates that BoT-Net also outperforms state-of-the-art lncRNA–protein interaction predictor on a benchmark dataset by accuracy of 10%, sensitivity of 19%, specificity of 6%, precision of 14%, and matthews correlation coefficient of 26%.Conclusion: In the benchmark lncRNA–miRNA interaction prediction dataset, the length of the lncRNA sequence varies from 213 residues to 22,743 residues and in the benchmark lncRNA–protein interaction prediction dataset, lncRNA sequences vary from 15 residues to 1504 residues. For such highly flexible length sequences, fixed length generation using copy padding introduces a significant level of bias which makes a large number of lncRNA sequences very much identical to each other and eventually derail classifier generalizeability. Empirical evaluation reveals that within 50 residues of only the starting region of long lncRNA sequences, a highly informative distribution for lncRNA–miRNA interaction prediction is contained, a crucial finding exploited by the proposed BoT-Net approach to optimize the lncRNA fixed length generation process.
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| 4. |
- Asim, Muhammad Nabeel, et al.
(författare)
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L2S-MirLoc : A Lightweight Two Stage MiRNA Sub-Cellular Localization Prediction Framework
- 2021
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Ingår i: Proceedings of the International Joint Conference on Neural Networks. - : IEEE. - 9780738133669 - 9781665439008 - 9781665445979
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Konferensbidrag (refereegranskat)abstract
- A comprehensive understanding of miRNA sub-cellular localization may leads towards better understanding of physiological processes and support the fixation of diverse irregularities present in a variety of organisms. To date, diverse computational methodologies have been proposed to automatically infer sub-cellular localization of miR-NAs solely using sequence information, however, existing approaches lack in performance. Considering the success of data transformation approaches in Natural Language Processing which primarily transform multi-label classification problem into multi-class classification problem, here, we introduce three different data transformation approaches namely binary relevance, label power set, and classifier chains. Using data transformation approaches, at 1st stage, multi-label miRNA sub-cellular localization problem is transformed into multi-class problem. Then, at 2nd stage, 3 different machine learning classifiers are used to estimate which classifier performs better with what data transformation approach for hand on task. Empirical evaluation on independent test set indicates that L2S-MirLoc selected combination based on binary relevance and deep random forest outperforms state-of-the-art performance values by significant margin.
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| 5. |
- Asim, Muhammad Nabeel, et al.
(författare)
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MirLocPredictor : A ConvNet-Based Multi-Label MicroRNA Subcellular Localization Predictor by Incorporating k-Mer Positional Information
- 2020
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Ingår i: Genes. - : MDPI. - 2073-4425 .- 2073-4425. ; 11:12
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Tidskriftsartikel (refereegranskat)abstract
- MicroRNAs (miRNA) are small noncoding RNA sequences consisting of about 22 nucleotides that are involved in the regulation of almost 60% of mammalian genes. Presently, there are very limited approaches for the visualization of miRNA locations present inside cells to support the elucidation of pathways and mechanisms behind miRNA function, transport, and biogenesis. MIRLocator, a state-of-the-art tool for the prediction of subcellular localization of miRNAs makes use of a sequence-to-sequence model along with pretrained k-mer embeddings. Existing pretrained k-mer embedding generation methodologies focus on the extraction of semantics of k-mers. However, in RNA sequences, positional information of nucleotides is more important because distinct positions of the four nucleotides define the function of an RNA molecule. Considering the importance of the nucleotide position, we propose a novel approach (kmerPR2vec) which is a fusion of positional information of k-mers with randomly initialized neural k-mer embeddings. In contrast to existing k-mer-based representation, the proposed kmerPR2vec representation is much more rich in terms of semantic information and has more discriminative power. Using novel kmerPR2vec representation, we further present an end-to-end system (MirLocPredictor) which couples the discriminative power of kmerPR2vec with Convolutional Neural Networks (CNNs) for miRNA subcellular location prediction. The effectiveness of the proposed kmerPR2vec approach is evaluated with deep learning-based topologies (i.e., Convolutional Neural Networks (CNN) and Recurrent Neural Network (RNN)) and by using 9 different evaluation measures. Analysis of the results reveals that MirLocPredictor outperform state-of-the-art methods with a significant margin of 18% and 19% in terms of precision and recall.
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| 6. |
- 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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| 7. |
- Asim Ibrahim, Muhammad, et al.
(författare)
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Early detection of deep-seated smouldering fires in wood waste storage using ERT
- 2024
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Ingår i: Waste Management. - 0956-053X .- 1879-2456. ; 182, s. 215-224
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Tidskriftsartikel (refereegranskat)abstract
- Incidents of waste and biofuel fires are common at all stages of the waste recycling chain and have grave implications for business, employees, firefighters, society, and environment. An early detection of waste and biofuel fires in the smouldering stage could save precious lives, resources, and our environment. Existing fire detection methodologies e.g. handheld temperature sensors, IR cameras, gas sensors, and video and satellite-based monitoring techniques have inherent limitations to efficiently detect smouldering fires. An attempt was made to explore the potential of electrical resistivity tomography (ERT) as an alternate tool to address the problem. In the experiments an externally powered resistive wire was employed to initiate the smouldering fire inside the test material (wood pellets, wood shavings, wood fines). Time series of ERT that followed the initiation and development of smouldering were recorded using an automated monitoring instrument setup. The actual geometry of the experimental sample container and electrode setup was integrated in the 3D finite element method (FEM) model grid to perform inverse numerical modelling (inversion) and to develop resistivity tomographic images. The study shows a sharp increase in ratio of resistivity (?/?? ≥ 50 %) in the test material in the region of smouldering hotspot and demonstrates the potential use of ERT technique for the detection of smouldering hotspots in silos and pile storage of organic material such as wood-based fuels, wood waste, coal, municipal solid waste (MSW), recyclables etc. More research is however required for enabling the use of this technique at the practical scale for different storage conditions.
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