i4mC-GRU: Identifying DNA N4-Methylcytosine sites in mouse genomes using bidirectional gated recurrent unit and sequence-embedded features.

N4-methylcytosine (4mC) is one of the most common DNA methylation modifications found in both prokaryotic and eukaryotic genomes. Since the 4mC has various essential biological roles, determining its location helps reveal unexplored physiological and pathological pathways. In this study, we propose an effective computational method called i4mC-GRU using a gated recurrent unit and duplet sequence-embedded features to predict potential 4mC sites in mouse (Mus musculus) genomes. To fairly assess the performance of the model, we compared our method with several state-of-the-art methods using two different benchmark datasets. Our results showed that i4mC-GRU achieved area under the receiver operating characteristic curve values of 0.97 and 0.89 and area under the precision-recall curve values of 0.98 and 0.90 on the first and second benchmark datasets, respectively. Briefly, our method outperformed existing methods in predicting 4mC sites in mouse genomes. Also, we deployed i4mC-GRU as an online web server, supporting users in genomics studies.

eMIC-AntiKP: Estimating minimum inhibitory concentrations of antibiotics towards Klebsiella pneumoniae using deep learning.

Nowadays, antibiotic resistance has become one of the most concerning problems that directly affects the recovery process of patients. For years, numerous efforts have been made to efficiently use antimicrobial drugs with appropriate doses not only to exterminate microbes but also stringently constrain any chances for bacterial evolution. However, choosing proper antibiotics is not a straightforward and time-effective process because well-defined drugs can only be given to patients after determining microbic taxonomy and evaluating minimum inhibitory concentrations (MICs). Besides conventional methods, numerous computer-aided frameworks have been recently developed using computational advances and public data sources of clinical antimicrobial resistance. In this study, we introduce eMIC-AntiKP, a computational framework specifically designed to predict the MIC values of 20 antibiotics towards Klebsiella pneumoniae. Our prediction models were constructed using convolutional neural networks and k-mer counting-based features. The model for cefepime has the most limited performance with a test 1-tier accuracy of 0.49, while the model for ampicillin has the highest performance with a test 1-tier accuracy of 1.00. Most models have satisfactory performance, with test accuracies ranging from about 0.70-0.90. The significance of eMIC-AntiKP is the effective utilization of computing resources to make it a compact and portable tool for most moderately configured computers. We provide users with two options, including an online web server for basic analysis and an offline package for deeper analysis and technical modification.

A lightweight classification of adaptor proteins using transformer networks.

BACKGROUND: Adaptor proteins play a key role in intercellular signal transduction, and dysfunctional adaptor proteins result in diseases. Understanding its structure is the first step to tackling the associated conditions, spurring ongoing interest in research into adaptor proteins with bioinformatics and computational biology. Our study aims to introduce a small, new, and superior model for protein classification, pushing the boundaries with new machine learning algorithms. RESULTS: We propose a novel transformer based model which includes convolutional block and fully connected layer. We input protein sequences from a database, extract PSSM features, then process it via our deep learning model. The proposed model is efficient and highly compact, achieving state-of-the-art performance in terms of area under the receiver operating characteristic curve, Matthew's Correlation Coefficient and Receiver Operating Characteristics curve. Despite merely 20 hidden nodes translating to approximately 1% of the complexity of previous best known methods, the proposed model is still superior in results and computational efficiency. CONCLUSIONS: The proposed model is the first transformer model used for recognizing adaptor protein, and outperforms all existing methods, having PSSM profiles as inputs that comprises convolutional blocks, transformer and fully connected layers for the use of classifying adaptor proteins.

iPromoter-Seqvec: identifying promoters using bidirectional long short-term memory and sequence-embedded features.

BACKGROUND: Promoters, non-coding DNA sequences located at upstream regions of the transcription start site of genes/gene clusters, are essential regulatory elements for the initiation and regulation of transcriptional processes. Furthermore, identifying promoters in DNA sequences and genomes significantly contributes to discovering entire structures of genes of interest. Therefore, exploration of promoter regions is one of the most imperative topics in molecular genetics and biology. Besides experimental techniques, computational methods have been developed to predict promoters. In this study, we propose iPromoter-Seqvec - an efficient computational model to predict TATA and non-TATA promoters in human and mouse genomes using bidirectional long short-term memory neural networks in combination with sequence-embedded features extracted from input sequences. The promoter and non-promoter sequences were retrieved from the Eukaryotic Promoter database and then were refined to create four benchmark datasets. RESULTS: The area under the receiver operating characteristic curve (AUCROC) and the area under the precision-recall curve (AUCPR) were used as two key metrics to evaluate model performance. Results on independent test sets showed that iPromoter-Seqvec outperformed other state-of-the-art methods with AUCROC values ranging from 0.85 to 0.99 and AUCPR values ranging from 0.86 to 0.99. Models predicting TATA promoters in both species had slightly higher predictive power compared to those predicting non-TATA promoters. With a novel idea of constructing artificial non-promoter sequences based on promoter sequences, our models were able to learn highly specific characteristics discriminating promoters from non-promoters to improve predictive efficiency. CONCLUSIONS: iPromoter-Seqvec is a stable and robust model for predicting both TATA and non-TATA promoters in human and mouse genomes. Our proposed method was also deployed as an online web server with a user-friendly interface to support research communities. Links to our source codes and web server are available at https://github.com/mldlproject/2022-iPromoter-Seqvec .

Unified implementation of global high dynamic range image tone-mapping algorithms.

High dynamic range (HDR) images and video require tone-mapping for display on low dynamic range (LDR) screens. Many tone-mapping operators have been proposed to convert HDR content to LDR, but almost each has a different implementation structure and requires a different execution time. We propose a unified structure that can represent any global tone-mapping algorithm with an array of just 256 coefficients. These coefficients extracted offline for every HDR image or video frame can be used to convert them to LDR in real time using linear interpolation. The produced LDR images are identical to the images produced by the original implementation of the algorithm. This unified implementation can replicate any global tone-mapping function and requires very low and fixed execution time, which is independent of algorithm and type of content and depends only on image size. Experimental studies are presented to show the accuracy and time efficiency of the proposed implementation.

BSEResU-Net: An attention-based before-activation residual U-Net for retinal vessel segmentation.

BACKGROUND AND OBJECTIVES: Retinal vessels are a major feature used for the physician to diagnose many retinal diseases, such as cardiovascular disease and Glaucoma. Therefore, the designing of an auto-segmentation algorithm for retinal vessel draw great attention in medical field. Recently, deep learning methods, especially convolutional neural networks (CNNs) show extraordinary potential for the task of vessel segmentation. However, most of the deep learning methods only take advantage of the shallow networks with a traditional cross-entropy objective, which becomes the main obstacle to further improve the performance on a task that is imbalanced. We therefore propose a new type of residual U-Net called Before-activation Squeeze-and-Excitation ResU-Net (BSEResu-Net) to tackle the aforementioned issues. METHODS: Our BSEResU-Net can be viewed as an encoder/decoder framework that constructed by Before-activation Squeeze-and-Excitation blocks (BSE Blocks). In comparison to the current existing CNN structures, we utilize a new type of residual block structure, namely BSE block, in which the attention mechanism is combined with skip connection to boost the performance. What's more, the network could consistently gain accuracy from the increasing depth as we incorporate more residual blocks, attributing to the dropblock mechanism used in BSE blocks. A joint loss function which is based on the dice and cross-entropy loss functions is also introduced to achieve more balanced segmentation between the vessel and non-vessel pixels. RESULTS: The proposed BSEResU-Net is evaluated on the publicly available DRIVE, STARE and HRF datasets. It achieves the F1-score of 0.8324, 0.8368 and 0.8237 on DRIVE, STARE and HRF dataset, respectively. Experimental results show that the proposed BSEResU-Net outperforms current state-of-the-art algorithms. CONCLUSIONS: The proposed algorithm utilizes a new type of residual blocks called BSE residual blocks for vessel segmentation. Together with a joint loss function, it shows outstanding performance both on low and high-resolution fundus images.

An Optimized Quantization Constraints Set for Image Restoration and Its GPU Implementation.

This paper presents a novel optimized quantization constraint set, acting as an add-on to existing DCT-based image restoration algorithms. The constraint set is created based on generalized Gaussian distribution which is more accurate than the commonly used uniform, Gaussian or Laplacian distributions when modeling DCT coefficients. More importantly, the proposed constraint set is optimized for individual input images and thus it is able to enhance image quality significantly in terms of signal-to-noise ratio. Experimental results indicate that the signal-to-noise ratio is improved by at least 6.78% on top of the existing state-of-the-art methods, with a corresponding expense of only 0.38% in processing time. The proposed algorithm has also been implemented in GPU, and the processing speed increases further by 20 times over that of CPU implementation. This makes the algorithm well suited for fast image retrieval in security and quality monitoring system.

Classification of adaptor proteins using recurrent neural networks and PSSM profiles.

BACKGROUND: Adaptor proteins are carrier proteins that play a crucial role in signal transduction. They commonly consist of several modular domains, each having its own binding activity and operating by forming complexes with other intracellular-signaling molecules. Many studies determined that the adaptor proteins had been implicated in a variety of human diseases. Therefore, creating a precise model to predict the function of adaptor proteins is one of the vital tasks in bioinformatics and computational biology. Few computational biology studies have been conducted to predict the protein functions, and in most of those studies, position specific scoring matrix (PSSM) profiles had been used as the features to be fed into the neural networks. However, the neural networks could not reach the optimal result because the sequential information in PSSMs has been lost. This study proposes an innovative approach by incorporating recurrent neural networks (RNNs) and PSSM profiles to resolve this problem. RESULTS: Compared to other state-of-the-art methods which had been applied successfully in other problems, our method achieves enhancement in all of the common measurement metrics. The area under the receiver operating characteristic curve (AUC) metric in prediction of adaptor proteins in the cross-validation and independent datasets are 0.893 and 0.853, respectively. CONCLUSIONS: This study opens a research path that can promote the use of RNNs and PSSM profiles in bioinformatics and computational biology. Our approach is reproducible by scientists that aim to improve the performance results of different protein function prediction problems. Our source code and datasets are available at https://github.com/ngphubinh/adaptors.

iEnhancer-ECNN: identifying enhancers and their strength using ensembles of convolutional neural networks.

BACKGROUND: Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer identification is, therefore, more complicated than other genetic factors. To address this biological issue, several in silico studies have been done to identify and classify enhancer sequences among a myriad of DNA sequences using computational advances. Although recent studies have come up with improved performance, shortfalls in these learning models still remain. To overcome limitations of existing learning models, we introduce iEnhancer-ECNN, an efficient prediction framework using one-hot encoding and k-mers for data transformation and ensembles of convolutional neural networks for model construction, to identify enhancers and classify their strength. The benchmark dataset from Liu et al.'s study was used to develop and evaluate the ensemble models. A comparative analysis between iEnhancer-ECNN and existing state-of-the-art methods was done to fairly assess the model performance. RESULTS: Our experimental results demonstrates that iEnhancer-ECNN has better performance compared to other state-of-the-art methods using the same dataset. The accuracy of the ensemble model for enhancer identification (layer 1) and enhancer classification (layer 2) are 0.769 and 0.678, respectively. Compared to other related studies, improvements in the Area Under the Receiver Operating Characteristic Curve (AUC), sensitivity, and Matthews's correlation coefficient (MCC) of our models are remarkable, especially for the model of layer 2 with about 11.0%, 46.5%, and 65.0%, respectively. CONCLUSIONS: iEnhancer-ECNN outperforms other previously proposed methods with significant improvement in most of the evaluation metrics. Strong growths in the MCC of both layers are highly meaningful in assuring the stability of our models.

iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks.

BACKGROUND: Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a challenging task in the age of post-genomic where data on protein sequences have expanded very fast. In this study, we propose iProDNA-CapsNet - a new prediction model identifying protein-DNA binding residues using an ensemble of capsule neural networks (CapsNets) on position specific scoring matrix (PSMM) profiles. The use of CapsNets promises an innovative approach to determine the location of DNA-binding residues. In this study, the benchmark datasets introduced by Hu et al. (2017), i.e., PDNA-543 and PDNA-TEST, were used to train and evaluate the model, respectively. To fairly assess the model performance, comparative analysis between iProDNA-CapsNet and existing state-of-the-art methods was done. RESULTS: Under the decision threshold corresponding to false positive rate (FPR) ≈ 5%, the accuracy, sensitivity, precision, and Matthews's correlation coefficient (MCC) of our model is increased by about 2.0%, 2.0%, 14.0%, and 5.0% with respect to TargetDNA (Hu et al., 2017) and 1.0%, 75.0%, 45.0%, and 77.0% with respect to BindN+ (Wang et al., 2010), respectively. With regards to other methods not reporting their threshold settings, iProDNA-CapsNet also shows a significant improvement in performance based on most of the evaluation metrics. Even with different patterns of change among the models, iProDNA-CapsNets remains to be the best model having top performance in most of the metrics, especially MCC which is boosted from about 8.0% to 220.0%. CONCLUSIONS: According to all evaluation metrics under various decision thresholds, iProDNA-CapsNet shows better performance compared to the two current best models (BindN and TargetDNA). Our proposed approach also shows that CapsNet can potentially be used and adopted in other biological applications.

iPseU-NCP: Identifying RNA pseudouridine sites using random forest and NCP-encoded features.

BACKGROUND: Pseudouridine modification is most commonly found among various kinds of RNA modification occurred in both prokaryotes and eukaryotes. This biochemical event has been proved to occur in multiple types of RNAs, including rRNA, mRNA, tRNA, and nuclear/nucleolar RNA. Hence, gaining a holistic understanding of pseudouridine modification can contribute to the development of drug discovery and gene therapies. Although some laboratory techniques have come up with moderately good outcomes in pseudouridine identification, they are costly and required skilled work experience. We propose iPseU-NCP - an efficient computational framework to predict pseudouridine sites using the Random Forest (RF) algorithm combined with nucleotide chemical properties (NCP) generated from RNA sequences. The benchmark dataset collected from Chen et al. (2016) was used to develop iPseU-NCP and fairly compare its performances with other methods. RESULTS: Under the same experimental settings, comparing with three state-of-the-art methods including iPseU-CNN, PseUI, and iRNA-PseU, the Matthew's correlation coefficient (MCC) of our model increased by about 20.0%, 55.0%, and 109.0% when tested on the H. sapiens (H_200) dataset and by about 6.5%, 35.0%, and 150.0% when tested on the S. cerevisiae (S_200) dataset, respectively. This significant growth in MCC is very important since it ensures the stability and performance of our model. With those two independent test datasets, our model also presented higher accuracy with a success rate boosted by 7.0%, 13.0%, and 20.0% and 2.0%, 9.5%, and 25.0% when compared to iPseU-CNN, PseUI, and iRNA-PseU, respectively. For majority of other evaluation metrics, iPseU-NCP demonstrated superior performance as well. CONCLUSIONS: iPseU-NCP combining the RF and NPC-encoded features showed better performances than other existing state-of-the-art methods in the identification of pseudouridine sites. This also shows an optimistic view in addressing biological issues related to human diseases.

Hybrid patching for a sequence of differently exposed images with moving objects.

It is very challenging to synthesize a high dynamic range (HDR) image from multiple differently exposed low dynamic range images when there are moving objects in the images. This is due to the fact that the moving objects will cause ghosting artifacts to appear in the synthesized HDR image. To prevent such artifacts, a patching algorithm is required to correct motion regions such that all the moving objects are synchronized in the differently exposed images. In this paper, a new optimization problem is formulated to correct the motion regions of the multiple differently exposed images by considering both spatial and temporal consistencies. The resultant scheme is a hybrid patching scheme composed of a correction method which is an intensity mapping function at pixel level, and a hole-filling method that uses block-level template matching. The proposed patching scheme is not only robust to large intensity changes in these input images, but also at regions that are over- or underexposed. Experimental results show that the proposed method is able to prevent ghosting artifacts from appearing in the final synthesized HDR image.

A perceptually relevant MSE-based image quality metric.

Image quality metrics (IQMs), such as the mean squared error (MSE) and the structural similarity index (SSIM), are quantitative measures to approximate perceived visual quality. In this paper, through analyzing the relationship between the MSE and the SSIM under an additive noise distortion model, we propose a perceptually relevant MSE-based IQM, MSE-SSIM, which is expressed in terms of the variance of the source image and the MSE between the source and distorted images. Evaluations on three publicly available databases (LIVE, CSIQ, and TID2008) show that the proposed metric, despite requiring less computation, compares favourably in performance to several existing IQMs. In addition, due to its simplicity, MSE-SSIM is amenable for the use in a wide range of image and video tasks that involve solving an optimization problem. As an example, MSE-SSIM is used as the objective function in designing a Wiener filter that aims at optimizing the perceptual visual quality of the output. Experimental results show that the images filtered with a MSE-SSIM-optimal Wiener filter have better visual quality than those filtered with a MSE-optimal Wiener filter.

Alternating direction method for balanced image restoration.

This paper presents an efficient algorithm for solving a balanced regularization problem in the frame-based image restoration. The balanced regularization is usually formulated as a minimization problem, involving an l(2) data-fidelity term, an l(1) regularizer on sparsity of frame coefficients, and a penalty on distance of sparse frame coefficients to the range of the frame operator. In image restoration, the balanced regularization approach bridges the synthesis-based and analysis-based approaches, and balances the fidelity, sparsity, and smoothness of the solution. Our proposed algorithm for solving the balanced optimal problem is based on a variable splitting strategy and the classical alternating direction method. This paper shows that the proposed algorithm is fast and efficient in solving the standard image restoration with balanced regularization. More precisely, a regularized version of the Hessian matrix of the l(2) data-fidelity term is involved, and by exploiting the related fast tight Parseval frame and the special structures of the observation matrices, the regularized Hessian matrix can perform quite efficiently for the frame-based standard image restoration applications, such as circular deconvolution in image deblurring and missing samples in image inpainting. Numerical simulations illustrate the efficiency of our proposed algorithm in the frame-based image restoration with balanced regularization.

Detail-enhanced exposure fusion.

In a typical processing chain of image enhancement, an exposure fusion scheme can be used to synthesize a more detailed low dynamic range (LDR) image directly from a set of differently exposed LDR images, without generation of an intermediate high dynamic range image. In this brief, we introduce a new quadratic optimization-based method to extract fine details from a vector field. The new method extracts fine details from a set of differently exposed LDR images simultaneously. The extracted fine details are then added to an intermediate LDR image which is fused by simply using an existing exposure fusion scheme. With this, the proposed scheme can enhance fine details to produce sharper images.

Object recognition by discriminative combinations of line segments, ellipses, and appearance features.

We present a novel contour-based approach that recognizes object classes in real-world scenes using simple and generic shape primitives of line segments and ellipses. Compared to commonly used contour fragment features, these primitives support more efficient representation since their storage requirements are independent of object size. Additionally, these primitives are readily described by their geometrical properties and hence afford very efficient feature comparison. We pair these primitives as shape-tokens and learn discriminative combinations of shape-tokens. Here, we allow each combination to have a variable number of shape-tokens. This, coupled with the generic nature of primitives, enables a variety of class-specific shape structures to be learned. Building on the contour-based method, we propose a new hybrid recognition method that combines shape and appearance features. Each discriminative combination can vary in the number and the types of features, where these two degrees of variability empower the hybrid method with even more flexibility and discriminative potential. We evaluate our methods across a large number of challenging classes, and obtain very competitive results against other methods. These results show the proposed shape primitives are indeed sufficiently powerful to recognize object classes in complex real-world scenes.

A split and merge based ellipse detector with self-correcting capability.

A novel ellipse detector based upon edge following is proposed in this paper. The detector models edge connectivity by line segments and exploits these line segments to construct a set of elliptical-arcs. Disconnected elliptical-arcs which describe the same ellipse are identified and grouped together by incrementally finding optimal pairings of elliptical-arcs. We extract hypothetical ellipses of an image by fitting an ellipse to the elliptical-arcs of each group. Finally, a feedback loop is developed to sieve out low confidence hypothetical ellipses and to regenerate a better set of hypothetical ellipses. In this aspect, the proposed algorithm performs self-correction and homes in on "difficult" ellipses. Detailed evaluation on synthetic images shows that the algorithm outperforms existing methods substantially in terms of recall and precision scores under the scenarios of image cluttering, salt-and-pepper noise and partial occlusion. Additionally, we apply the detector on a set of challenging real-world images. Successful detection of ellipses present in these images is demonstrated. We are not aware of any other work that can detect ellipses from such difficult images. Therefore, this work presents a significant contribution towards ellipse detection.

Natural and seamless image composition with color control.

While the state-of-the-art image composition algorithms subtly handle the object boundary to achieve seamless image copy-and-paste, it is observed that they are unable to preserve the color fidelity of the source object, often require quite an amount of user interactions, and often fail to achieve realism when there exists salient discrepancy between the background textures in the source and destination images. These observations motivate our research towards color controlled natural and seamless image composition with least user interactions. In particular, based on the Poisson image editing framework, we first propose a variational model that considers both the gradient constraint and the color fidelity. The proposed model allows users to control the coloring effect caused by gradient domain fusion. Second, to have less user interactions, we propose a distance-enhanced random walks algorithm, through which we avoid the necessity of accurate image segmentation while still able to highlight the foreground object. Third, we propose a multiresolution framework to perform image compositions at different subbands so as to separate the texture and color components to simultaneously achieve smooth texture transition and desired color control. The experimental results demonstrate that our proposed framework achieves better and more realistic results for images with salient background color or texture differences, while providing comparable results as the state-of-the-art algorithms for images without the need of preserving the object color fidelity and without significant background texture discrepancy.