Developing a Supplementary Diagnostic Tool for Breast Cancer Risk Estimation Using Ensemble Transfer Learning.

Breast cancer is the most prevalent cancer worldwide. Thus, it is necessary to improve the efficiency of the medical workflow of the disease. Therefore, this study aims to develop a supplementary diagnostic tool for radiologists using ensemble transfer learning and digital mammograms. The digital mammograms and their associated information were collected from the department of radiology and pathology at Hospital Universiti Sains Malaysia. Thirteen pre-trained networks were selected and tested in this study. ResNet101V2 and ResNet152 had the highest mean PR-AUC, MobileNetV3Small and ResNet152 had the highest mean precision, ResNet101 had the highest mean F1 score, and ResNet152 and ResNet152V2 had the highest mean Youden J index. Subsequently, three ensemble models were developed using the top three pre-trained networks whose ranking was based on PR-AUC values, precision, and F1 scores. The final ensemble model, which consisted of Resnet101, Resnet152, and ResNet50V2, had a mean precision value, F1 score, and Youden J index of 0.82, 0.68, and 0.12, respectively. Additionally, the final model demonstrated balanced performance across mammographic density. In conclusion, this study demonstrates the good performance of ensemble transfer learning and digital mammograms in breast cancer risk estimation. This model can be utilised as a supplementary diagnostic tool for radiologists, thus reducing their workloads and further improving the medical workflow in the screening and diagnosis of breast cancer.

Enhanced Intrusion Detection with Data Stream Classification and Concept Drift Guided by the Incremental Learning Genetic Programming Combiner.

Concept drift (CD) in data streaming scenarios such as networking intrusion detection systems (IDS) refers to the change in the statistical distribution of the data over time. There are five principal variants related to CD: incremental, gradual, recurrent, sudden, and blip. Genetic programming combiner (GPC) classification is an effective core candidate for data stream classification for IDS. However, its basic structure relies on the usage of traditional static machine learning models that receive onetime training, limiting its ability to handle CD. To address this issue, we propose an extended variant of the GPC using three main components. First, we replace existing classifiers with alternatives: online sequential extreme learning machine (OSELM), feature adaptive OSELM (FA-OSELM), and knowledge preservation OSELM (KP-OSELM). Second, we add two new components to the GPC, specifically, a data balancing and a classifier update. Third, the coordination between the sub-models produces three novel variants of the GPC: GPC-KOS for KA-OSELM; GPC-FOS for FA-OSELM; and GPC-OS for OSELM. This article presents the first data stream-based classification framework that provides novel strategies for handling CD variants. The experimental results demonstrate that both GPC-KOS and GPC-FOS outperform the traditional GPC and other state-of-the-art methods, and the transfer learning and memory features contribute to the effective handling of most types of CD. Moreover, the application of our incremental variants on real-world datasets (KDD Cup '99, CICIDS-2017, CSE-CIC-IDS-2018, and ISCX '12) demonstrate improved performance (GPC-FOS in connection with CSE-CIC-IDS-2018 and CICIDS-2017; GPC-KOS in connection with ISCX2012 and KDD Cup '99), with maximum accuracy rates of 100% and 98% by GPC-KOS and GPC-FOS, respectively. Additionally, our GPC variants do not show superior performance in handling blip drift.

Over-the-Counter Breast Cancer Classification Using Machine Learning and Patient Registration Records.

This study aims to determine the feasibility of machine learning (ML) and patient registration record to be utilised to develop an over-the-counter (OTC) screening model for breast cancer risk estimation. Data were retrospectively collected from women who came to the Hospital Universiti Sains Malaysia, Malaysia for breast-related problems. Eight ML models were used: k-nearest neighbour (kNN), elastic-net logistic regression, multivariate adaptive regression splines, artificial neural network, partial least square, random forest, support vector machine (SVM), and extreme gradient boosting. Features utilised for the development of the screening models were limited to information in the patient registration form. The final model was evaluated in terms of performance across a mammographic density. Additionally, the feature importance of the final model was assessed using the model agnostic approach. kNN had the highest Youden J index, precision, and PR-AUC, while SVM had the highest F2 score. The kNN model was selected as the final model. The model had a balanced performance in terms of sensitivity, specificity, and PR-AUC across the mammographic density groups. The most important feature was the age at examination. In conclusion, this study showed that ML and patient registration information are feasible to be used as the OTC screening model for breast cancer.

Factors Influencing Mammographic Density in Asian Women: A Retrospective Cohort Study in the Northeast Region of Peninsular Malaysia.

Mammographic density is a significant risk factor for breast cancer. In this study, we identified the risk factors of mammographic density in Asian women and quantified the impact of breast density on the severity of breast cancer. We collected data from Hospital Universiti Sains Malaysia, a research- and university-based hospital located in Kelantan, Malaysia. Multivariable logistic regression was performed to analyse the data. Five significant factors were found to be associated with mammographic density: age (OR: 0.94; 95% CI: 0.92, 0.96), number of children (OR: 0.88; 95% CI: 0.81, 0.96), body mass index (OR: 0.88; 95% CI: 0.85, 0.92), menopause status (yes vs. no, OR: 0.59; 95% CI: 0.42, 0.82), and BI-RADS classification (2 vs. 1, OR: 1.87; 95% CI: 1.22, 2.84; 3 vs. 1, OR: 3.25; 95% CI: 1.86, 5.66; 4 vs. 1, OR: 3.75; 95% CI: 1.88, 7.46; 5 vs. 1, OR: 2.46; 95% CI: 1.21, 5.02; 6 vs. 1, OR: 2.50; 95% CI: 0.65, 9.56). Similarly, the average predicted probabilities were higher among BI-RADS 3 and 4 classified women. Understanding mammographic density and its influencing factors aids in accurately assessing and screening dense breast women.

Evaluating the effects of electronic health records system adoption on the performance of Malaysian health care providers.

BACKGROUND: The Ministry of Health of Malaysia has invested significant resources to implement an electronic health record (EHR) system to ensure the full automation of hospitals for coordinated care delivery. Thus, evaluating whether the system has been effectively utilized is necessary, particularly regarding how it predicts the post-implementation primary care providers' performance impact. METHODS: Convenience sampling was employed for data collection in three government hospitals for 7 months. A standardized effectiveness survey for EHR systems was administered to primary health care providers (specialists, medical officers, and nurses) as they participated in medical education programs. Empirical data were assessed by employing partial least squares-structural equation modeling for hypothesis testing. RESULTS: The results demonstrated that knowledge quality had the highest score for predicting performance and had a large effect size, whereas system compatibility was the most substantial system quality component. The findings indicated that EHR systems supported the clinical tasks and workflows of care providers, which increased system quality, whereas the increased quality of knowledge improved user performance. CONCLUSION: Given these findings, knowledge quality and effective use should be incorporated into evaluating EHR system effectiveness in health institutions. Data mining features can be integrated into current systems for efficiently and systematically generating health populations and disease trend analysis, improving clinical knowledge of care providers, and increasing their productivity. The validated survey instrument can be further tested with empirical surveys in other public and private hospitals with different interoperable EHR systems.

Multiobjective optimization to reconstruct biological networks.

Automated methods for reconstructing biological networks are becoming increasingly important in computational systems biology. Public databases containing information on biological processes for hundreds of organisms are assisting in the inference of such networks. This paper proposes a multiobjective genetic algorithm method to reconstruct networks related to metabolism and protein interaction. Such a method utilizes structural properties of scale-free networks and known biological information about individual genes and proteins to reconstruct metabolic networks represented as enzyme graph and protein interaction networks. We test our method on four commonly-used protein networks in yeast. Two are networks related to the metabolism of the yeast: KEGG and BioCyc. The other two datasets are networks from protein-protein interaction: Krogan and BioGrid. Experimental results show that the proposed method is capable of reconstructing biological networks by combining different omics data and structural characteristics of scale-free networks. However, the proposed method to reconstruct the network is time-consuming because several evaluations must be performed. We parallelized this method on GPU to overcome this limitation by parallelizing the objective functions of the presented method. The parallel method shows a significant reduction in the execution time over the GPU card which yields a 492-fold speedup.

Quantum exhaustive key search with simplified-DES as a case study.

To evaluate the security of a symmetric cryptosystem against any quantum attack, the symmetric algorithm must be first implemented on a quantum platform. In this study, a quantum implementation of a classical block cipher is presented. A quantum circuit for a classical block cipher of a polynomial size of quantum gates is proposed. The entire work has been tested on a quantum mechanics simulator called libquantum. First, the functionality of the proposed quantum cipher is verified and the experimental results are compared with those of the original classical version. Then, quantum attacks are conducted by using Grover's algorithm to recover the secret key. The proposed quantum cipher is used as a black box for the quantum search. The quantum oracle is then queried over the produced ciphertext to mark the quantum state, which consists of plaintext and key qubits. The experimental results show that for a key of n-bit size and key space of N such that [Formula: see text], the key can be recovered in [Formula: see text] computational steps.

The influence of system quality characteristics on health care providers' performance: Empirical evidence from Malaysia.

BACKGROUND: The Ministry of Health Malaysia initiated the total hospital information system (THIS) as the first national electronic health record system for use in selected public hospitals across the country. Since its implementation 15 years ago, there has been the critical requirement for a systematic evaluation to assess its effectiveness in coping with the current system, task complexity, and rapid technological changes. The study aims to assess system quality factors to predict the performance of electronic health in a single public hospital in Malaysia. METHODS: Non-probability sampling was employed for data collection among selected providers in a single hospital for two months. Data cleaning and bias checking were performed before final analysis in partial least squares-structural equation modeling. RESULTS AND CONCLUSIONS: Convergent and discriminant validity assessments were satisfied the required criterions in the reflective measurement model. The structural model output revealed that the proposed adequate infrastructure, system interoperability, security control, and system compatibility were the significant predictors, where system compatibility became the most critical characteristic to influence an individual health care provider's performance. The previous DeLone and McLean information system success models should be extended to incorporate these technological factors in the medical system research domain to examine the effectiveness of modern electronic health record systems. In this study, care providers' performance was expected when the system usage fits with patients' needs that eventually increased their productivity.

Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter.

Empirical analysis on k-mer DNA has been proven as an effective tool in finding unique patterns in DNA sequences which can lead to the discovery of potential sequence motifs. In an extensive study of empirical k-mer DNA on hundreds of organisms, the researchers found unique multi-modal k-mer spectra occur in the genomes of organisms from the tetrapod clade only which includes all mammals. The multi-modality is caused by the formation of the two lowest modes where k-mers under them are referred as the rare k-mers. The suppression of the two lowest modes (or the rare k-mers) can be attributed to the CG dinucleotide inclusions in them. Apart from that, the rare k-mers are selectively distributed in certain genomic features of CpG Island (CGI), promoter, 5' UTR, and exon. We correlated the rare k-mers with hundreds of annotated features using several bioinformatic tools, performed further intrinsic rare k-mer analyses within the correlated features, and modeled the elucidated rare k-mer clustering feature into a classifier to predict the correlated CGI and promoter features. Our correlation results show that rare k-mers are highly associated with several annotated features of CGI, promoter, 5' UTR, and open chromatin regions. Our intrinsic results show that rare k-mers have several unique topological, compositional, and clustering properties in CGI and promoter features. Finally, the performances of our RWC (rare-word clustering) method in predicting the CGI and promoter features are ranked among the top three, in eight of the CGI and promoter evaluations, among eight of the benchmarked datasets.

Fast decision tree-based method to index large DNA-protein sequence databases using hybrid distributed-shared memory programming model.

In recent times, the size of biological databases has increased significantly, with the continuous growth in the number of users and rate of queries; such that some databases have reached the terabyte size. There is therefore, the increasing need to access databases at the fastest rates possible. In this paper, the decision tree indexing model (PDTIM) was parallelised, using a hybrid of distributed and shared memory on resident database; with horizontal and vertical growth through Message Passing Interface (MPI) and POSIX Thread (PThread), to accelerate the index building time. The PDTIM was implemented using 1, 2, 4 and 5 processors on 1, 2, 3 and 4 threads respectively. The results show that the hybrid technique improved the speedup, compared to a sequential version. It could be concluded from results that the proposed PDTIM is appropriate for large data sets, in terms of index building time.

Normal forms of spiking neural P systems with anti-spikes.

Spiking neural P systems with anti-spikes (ASN P systems, for short) are a variant of spiking neural P systems, which were inspired by inhibitory impulses/spikes or inhibitory synapses. In this work, we consider normal forms of ASN P systems. Specifically, we prove that ASN P systems with pure spiking rules of categories (a, a) and (a, (a)) without forgetting rules are universal as number generating devices. In an ASN P system with spiking rules of categories (a, (a)) and ((a), a) without forgetting rules, the neurons change spikes to anti-spikes or change anti-spikes to spikes; such systems are proved to be universal. We also prove that ASN P systems with inhibitory synapses using pure spiking rules of category (a, a) and forgetting rules are universal. These results answer an open problem and improve a corresponding result from [IJCCC, IV(3), 2009, 273-282].

Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.

A comparative taxonomy of parallel algorithms for RNA secondary structure prediction.

RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting RNA secondary structure is an NP-hard problem, especially in pseudoknotted RNA structures. The detection process is also time-consuming; as a result, an alternative approach such as using parallel architectures is a desirable option. The main goal in this paper is to do an intensive investigation of parallel methods used in the literature to solve the demanding issues, related to the RNA secondary structure prediction methods. Then, we introduce a new taxonomy for the parallel RNA folding methods. Based on this proposed taxonomy, a systematic and scientific comparison is performed among these existing methods.