DoubleU-NetPlus: A Novel Attention and Context Guided Dual U-Net with Multi-Scale Residual Feature Fusion Network for Semantic Segmentation of Medical Images

Accurate segmentation of the region of interest in medical images can provide an essential pathway for devising effective treatment plans for life-threatening diseases. It is still challenging for U-Net, and its state-of-the-art variants, such as CE-Net and DoubleU-Net, to effectively model the higher-level output feature maps of the convolutional units of the network mostly due to the presence of various scales of the region of interest, intricacy of context environments, ambiguous boundaries, and multiformity of textures in medical images. In this paper, we exploit multi-contextual features and several attention strategies to increase networks' ability to model discriminative feature representation for more accurate medical image segmentation, and we present a novel dual U-Net-based architecture named DoubleU-NetPlus. The DoubleU-NetPlus incorporates several architectural modifications. In particular, we integrate EfficientNetB7 as the feature encoder module, a newly designed multi-kernel residual convolution module, and an adaptive feature re-calibrating attention-based atrous spatial pyramid pooling module to progressively and precisely accumulate discriminative multi-scale high-level contextual feature maps and emphasize the salient regions. In addition, we introduce a novel triple attention gate module and a hybrid triple attention module to encourage selective modeling of relevant medical image features. Moreover, to mitigate the gradient vanishing issue and incorporate high-resolution features with deeper spatial details, the standard convolution operation is replaced with the attention-guided residual convolution operations, ...

DPCSpell: A Transformer-based Detector-Purificator-Corrector Framework for Spelling Error Correction of Bangla and Resource Scarce Indic Languages

Spelling error correction is the task of identifying and rectifying misspelled words in texts. It is a potential and active research topic in Natural Language Processing because of numerous applications in human language understanding. The phonetically or visually similar yet semantically distinct characters make it an arduous task in any language. Earlier efforts on spelling error correction in Bangla and resource-scarce Indic languages focused on rule-based, statistical, and machine learning-based methods which we found rather inefficient. In particular, machine learning-based approaches, which exhibit superior performance to rule-based and statistical methods, are ineffective as they correct each character regardless of its appropriateness. In this work, we propose a novel detector-purificator-corrector framework based on denoising transformers by addressing previous issues. Moreover, we present a method for large-scale corpus creation from scratch which in turn resolves the resource limitation problem of any left-to-right scripted language. The empirical outcomes demonstrate the effectiveness of our approach that outperforms previous state-of-the-art methods by a significant margin for Bangla spelling error correction. The models and corpus are publicly available at https://tinyurl.com/DPCSpell.

An Ensemble 1D-CNN-LSTM-GRU Model with Data Augmentation for Speech Emotion Recognition

In this paper, we propose an ensemble of deep neural networks along with data augmentation (DA) learned using effective speech-based features to recognize emotions from speech. Our ensemble model is built on three deep neural network-based models. These neural networks are built using the basic local feature acquiring blocks (LFAB) which are consecutive layers of dilated 1D Convolutional Neural networks followed by the max pooling and batch normalization layers. To acquire the long-term dependencies in speech signals further two variants are proposed by adding Gated Recurrent Unit (GRU) and Long Short Term Memory (LSTM) layers respectively. All three network models have consecutive fully connected layers before the final softmax layer for classification. The ensemble model uses a weighted average to provide the final classification. We have utilized five standard benchmark datasets: TESS, EMO-DB, RAVDESS, SAVEE, and CREMA-D for evaluation. We have performed DA by injecting Additive White Gaussian Noise, pitch shifting, and stretching the signal level to generalize the models, and thus increasing the accuracy of the models and reducing the overfitting as well. We handcrafted five categories of features: Mel-frequency cepstral coefficients, Log Mel-Scaled Spectrogram, Zero-Crossing Rate, Chromagram, and statistical Root Mean Square Energy value from each audio sample. These features are used as the input to the LFAB blocks that further extract the hidden local features which are then fed to either fully connected layers or to LSTM or GRU based on the model type to acquire the additional long-term contextual representations. LFAB followed by GRU or LSTM results in better performance compared to the baseline model. The ensemble model achieves the state-of-the-art weighted average accuracy in all the datasets.

Text2Chart: A Multi-Staged Chart Generator from Natural Language Text

Generation of scientific visualization from analytical natural language text is a challenging task. In this paper, we propose Text2Chart, a multi-staged chart generator method. Text2Chart takes natural language text as input and produce visualization as two-dimensional charts. Text2Chart approaches the problem in three stages. Firstly, it identifies the axis elements of a chart from the given text known as x and y entities. Then it finds a mapping of x-entities with its corresponding y-entities. Next, it generates a chart type suitable for the given text: bar, line or pie. Combination of these three stages is capable of generating visualization from the given analytical text. We have also constructed a dataset for this problem. Experiments show that Text2Chart achieves best performances with BERT based encodings with LSTM models in the first stage to label x and y entities, Random Forest classifier for the mapping stage and fastText embedding with LSTM for the chart type prediction. In our experiments, all the stages show satisfactory results and effectiveness considering formation of charts from analytical text, achieving a commendable overall performance.

i6mA-CNN: a convolution based computational approach towards identification of DNA N6-methyladenine sites in rice genome

DNA N6-methylation (6mA) in Adenine nucleotide is a post replication modification and is responsible for many biological functions. Experimental methods for genome wide 6mA site detection is an expensive and manual labour intensive process. Automated and accurate computational methods can help to identify 6mA sites in long genomes saving significant time and money. Our study develops a convolutional neural network based tool i6mA-CNN capable of identifying 6mA sites in the rice genome. Our model coordinates among multiple types of features such as PseAAC inspired customized feature vector, multiple one hot representations and dinucleotide physicochemical properties. It achieves area under the receiver operating characteristic curve of 0.98 with an overall accuracy of 0.94 using 5 fold cross validation on benchmark dataset. Finally, we evaluate our model on two other plant genome 6mA site identification datasets besides rice. Results suggest that our proposed tool is able to generalize its ability of 6mA site identification on plant genomes irrespective of plant species. Web tool for this research can be found at: https://cutt.ly/Co6KuWG. Supplementary data (benchmark dataset, independent test dataset, comparison purpose dataset, trained model, physicochemical property values, attention mechanism details for motif finding) are available at https://cutt.ly/PpDdeDH.

iPromoter-BnCNN: a Novel Branched CNN Based Predictor for Identifying and Classifying Sigma Promoters

Promoter is a short region of DNA which is responsible for initiating transcription of specific genes. Development of computational tools for automatic identification of promoters is in high demand. According to the difference of functions, promoters can be of different types. Promoters may have both intra and inter class variation and similarity in terms of consensus sequences. Accurate classification of various types of sigma promoters still remains a challenge. We present iPromoter-BnCNN for identification and accurate classification of six types of promoters - sigma24, sigma28, sigma32, sigma38, sigma54, sigma70. It is a Convolutional Neural Network (CNN) based classifier which combines local features related to monomer nucleotide sequence, trimer nucleotide sequence, dimer structural properties and trimer structural properties through the use of parallel branching. We conducted experiments on a benchmark dataset and compared with two state-of-the-art tools to show our supremacy on 5-fold cross-validation. Moreover, we tested our classifier on an independent test dataset. Our proposed tool iPromoter-BnCNN along with the source code is freely available at https://cutt.ly/te6XISV.

A Gray Box Interpretable Visual Debugging Approach for Deep Sequence Learning Model

Deep Learning algorithms are often used as black box type learning and they are too complex to understand. The widespread usability of Deep Learning algorithms to solve various machine learning problems demands deep and transparent understanding of the internal representation as well as decision making. Moreover, the learning models, trained on sequential data, such as audio and video data, have intricate internal reasoning process due to their complex distribution of features. Thus, a visual simulator might be helpful to trace the internal decision making mechanisms in response to adversarial input data, and it would help to debug and design appropriate deep learning models. However, interpreting the internal reasoning of deep learning model is not well studied in the literature. In this work, we have developed a visual interactive web application, namely d-DeVIS, which helps to visualize the internal reasoning of the learning model which is trained on the audio data. The proposed system allows to perceive the behavior as well as to debug the model by interactively generating adversarial audio data point. The web application of d-DeVIS is available at ddevis.herokuapp.com.

FRnet-DTI: Deep Convolutional Neural Networks with Evolutionary and Structural Features for Drug-Target Interaction

The task of drug-target interaction prediction holds significant importance in pharmacology and therapeutic drug design. In this paper, we present FRnet-DTI, an auto encoder and a convolutional classifier for feature manipulation and drug target interaction prediction. Two convolutional neural neworks are proposed where one model is used for feature manipulation and the other one for classification. Using the first method FRnet-1, we generate 4096 features for each of the instances in each of the datasets and use the second method, FRnet-2, to identify interaction probability employing those features. We have tested our method on four gold standard datasets exhaustively used by other researchers. Experimental results shows that our method significantly improves over the state-of-the-art method on three of the four drug-target interaction gold standard datasets on both area under curve for Receiver Operating Characteristic(auROC) and area under Precision Recall curve(auPR) metric. We also introduce twenty new potential drug-target pairs for interaction based on high prediction scores. Codes Available: https: // github. com/ farshidrayhanuiu/ FRnet-DTI/ Web Implementation: http: // farshidrayhan. pythonanywhere. com/ FRnet-DTI/

MEBoost: Mixing Estimators with Boosting for Imbalanced Data Classification

Class imbalance problem has been a challenging research problem in the fields of machine learning and data mining as most real life datasets are imbalanced. Several existing machine learning algorithms try to maximize the accuracy classification by correctly identifying majority class samples while ignoring the minority class. However, the concept of the minority class instances usually represents a higher interest than the majority class. Recently, several cost sensitive methods, ensemble models and sampling techniques have been used in literature in order to classify imbalance datasets. In this paper, we propose MEBoost, a new boosting algorithm for imbalanced datasets. MEBoost mixes two different weak learners with boosting to improve the performance on imbalanced datasets. MEBoost is an alternative to the existing techniques such as SMOTEBoost, RUSBoost, Adaboost, etc. The performance of MEBoost has been evaluated on 12 benchmark imbalanced datasets with state of the art ensemble methods like SMOTEBoost, RUSBoost, Easy Ensemble, EUSBoost, DataBoost. Experimental results show significant improvement over the other methods and it can be concluded that MEBoost is an effective and promising algorithm to deal with imbalance datasets. The python version of the code is available here: https://github.com/farshidrayhanuiu/

CUSBoost: Cluster-based Under-sampling with Boosting for Imbalanced Classification

Class imbalance classification is a challenging research problem in data mining and machine learning, as most of the real-life datasets are often imbalanced in nature. Existing learning algorithms maximise the classification accuracy by correctly classifying the majority class, but misclassify the minority class. However, the minority class instances are representing the concept with greater interest than the majority class instances in real-life applications. Recently, several techniques based on sampling methods (under-sampling of the majority class and over-sampling the minority class), cost-sensitive learning methods, and ensemble learning have been used in the literature for classifying imbalanced datasets. In this paper, we introduce a new clustering-based under-sampling approach with boosting (AdaBoost) algorithm, called CUSBoost, for effective imbalanced classification. The proposed algorithm provides an alternative to RUSBoost (random under-sampling with AdaBoost) and SMOTEBoost (synthetic minority over-sampling with AdaBoost) algorithms. We evaluated the performance of CUSBoost algorithm with the state-of-the-art methods based on ensemble learning like AdaBoost, RUSBoost, SMOTEBoost on 13 imbalance binary and multi-class datasets with various imbalance ratios. The experimental results show that the CUSBoost is a promising and effective approach for dealing with highly imbalanced datasets.