Abstract: The refractory alloys are crucial for high-temperature applications to improve performance and reduce cost. They are used in several applications such as aerospace, outer space, military and defense, nuclear powerplants, automobiles, and industry. The conventional refractory alloys show greater stability at high temperatures and in contrast they have operational limitations due to their low melting temperatures. However, there is a huge requirement to improve the refractory alloys’ operational temperatures and replace the conventional alloys. The newly emerging refractory high entropy alloys (RHEAs) could be alternative materials for conventional refractory alloys and fulfill the demands and requirements of various practical applications in the future. The RHEA TaHfNbZrTi was prepared through an arc melting process. The annealing behavior of severely deformed equiatomic RHEATaHfNbZrTi has been investigated. To obtain deformed condition, the alloy is cold-rolled to 90% thickness reduction and then subjected to an annealing process to observe recrystallization and microstructural evolution in the range of 800 °C to 1400 °C temperatures. The cold-rolled – 90% condition shows the presence of microstructural heterogeneity. The annealing microstructure of 800 °C temperature reveals that partial recrystallization and further annealing treatment carried out annealing treatment in the range of 850 °C to 1400 °C temperatures exhibits completely recrystallized microstructures, followed by coarsening with a degree of annealing temperature. The deformed and annealed conditions featured the development of body-centered cubic (BCC) fiber textures. The experimental investigation of heavy deformation and followed by high-temperature annealing up to 1400 °C temperature will contribute to the understanding of microstructure and texture evolution of emerging RHEAs.
Abstract: Multiplicative multiple criteria decision making analysis (MCDMA) method is a systematic decision support system to aid decision makers reach appropriate decisions. The application of multiplicative MCDMA in the military aircraft selection problem is significant for proper decision making process, which is the decisive factor in minimizing expenditures and increasing defense capability and capacity. Nine military fighter aircraft alternatives were evaluated by ten decision criteria to solve the decision making problem. In this study, multiplicative MCDMA model aims to evaluate and select an appropriate military fighter aircraft for the Air Force fleet planning. The ranking results of multiplicative MCDMA model were compared with the ranking results of additive MCDMA, logarithmic MCDMA, and regrettive MCDMA models under the L2 norm data normalization technique to substantiate the robustness of the proposed method. The final ranking results indicate the military fighter aircraft Su-57 as the best available solution.
Abstract: Both daily and long-term management of a heavy-duty vehicles and construction machinery fleet is an extremely complicated and hard to solve issue. This is mainly due to the diversity of the fleet vehicles – machinery, which concerns not only the vehicle types, but also their age/efficiency, as well as the fleet volume, which is often of the order of hundreds or even thousands of vehicles/machineries. In the present paper we present “InteligentLogger”, a holistic heavy-duty fleet management system covering a wide range of diverse fleet vehicles. This is based on specifically designed hardware and software for the automated vehicle health status and operational cost monitoring, for smart maintenance. InteligentLogger is characterized by high adaptability that permits to be tailored to practically any heavy-duty vehicle/machinery (of different technologies -modern or legacy- and of dissimilar uses). Contrary to conventional logistic systems, which are characterized by raised operational costs and often errors, InteligentLogger provides a cost-effective and reliable integrated solution for the e-management and e-maintenance of the fleet members. The InteligentLogger system offers the following unique features that guarantee successful heavy-duty vehicles/machineries fleet management: (a) Recording and storage of operating data of motorized construction machinery, in a reliable way and in real time, using specifically designed Internet of Things (IoT) sensor nodes that communicate through the available network infrastructures, e.g., 3G/LTE; (b) Use on any machine, regardless of its age, in a universal way; (c) Flexibility and complete customization both in terms of data collection, integration with 3rd party systems, as well as in terms of processing and drawing conclusions; (d) Validation, error reporting & correction, as well as update of the system’s database; (e) Artificial intelligence (AI) software, for processing information in real time, identifying out-of-normal behavior and generating alerts; (f) A MicroStrategy based enterprise BI, for modeling information and producing reports, dashboards, and alerts focusing on vehicles– machinery optimal usage, as well as maintenance and scraping policies; (g) Modular structure that allows low implementation costs in the basic fully functional version, but offers scalability without requiring a complete system upgrade.
Abstract: t-SNE is an embedding method that the data science community has widely used. It helps two main tasks: to display results by coloring items according to the item class or feature value; and for forensic, giving a first overview of the dataset distribution. Two interesting characteristics of t-SNE are the structure preservation property and the answer to the crowding problem, where all neighbors in high dimensional space cannot be represented correctly in low dimensional space. t-SNE preserves the local neighborhood, and similar items are nicely spaced by adjusting to the local density. These two characteristics produce a meaningful representation, where the cluster area is proportional to its size in number, and relationships between clusters are materialized by closeness on the embedding. This algorithm is non-parametric. The transformation from a high to low dimensional space is described but not learned. Two initializations of the algorithm would lead to two different embedding. In a forensic approach, analysts would like to compare two or more datasets using their embedding. A naive approach would be to embed all datasets together. However, this process is costly as the complexity of t-SNE is quadratic, and would be infeasible for too many datasets. Another approach would be to learn a parametric model over an embedding built with a subset of data. While this approach is highly scalable, points could be mapped at the same exact position, making them indistinguishable. This type of model would be unable to adapt to new outliers nor concept drift. This paper presents a methodology to reuse an embedding to create a new one, where cluster positions are preserved. The optimization process minimizes two costs, one relative to the embedding shape and the second relative to the support embedding’ match. The embedding with the support process can be repeated more than once, with the newly obtained embedding. The successive embedding can be used to study the impact of one variable over the dataset distribution or monitor changes over time. This method has the same complexity as t-SNE per embedding, and memory requirements are only doubled. For a dataset of n elements sorted and split into k subsets, the total embedding complexity would be reduced from O(n2) to O(n2/k), and the memory requirement from n2 to 2(n/k)2 which enables computation on recent laptops. The method showed promising results on a real-world dataset, allowing to observe the birth, evolution and death of clusters. The proposed approach facilitates identifying significant trends and changes, which empowers the monitoring high dimensional datasets’ dynamics.
Abstract: After 27 years, Malaysia reported polio cases in 2019 involving the children of the undocumented migrants living in Sabah. These undocumented migrants present a significant challenge in achieving the elimination of vaccine-preventable diseases (VPD). Due to the recent polio outbreak among the undocumented migrant children in Sabah, an in-depth interview was conducted among the caregivers of undocumented migrant children to identify the barriers and drivers towards vaccinating their children. Financial barriers, legal citizenship status, language barrier, the COVID-19 pandemic, and physical barriers have been the barriers to access vaccination services by undocumented migrants. Five significant drivers for undocumented migrants to vaccinate their children are social influence, fear of disease, parental trust in healthcare providers, good support, and vaccine availability. Necessary action should be taken immediately to address the problems of vaccinating the children of undocumented migrants to prevent the re-emergence of VPD.
Abstract: Sightseeing glass bridges located in steep valley area are being built on a large scale owing to the development of tourism. Consequently, their aerostatic stability is seriously affected by the wind field characteristics created by strong wind and special terrain, such as wind speed and wind attack angle. For instance, a cable-stayed pedestrian bridge without backstays comprised of a 60-m cantilever girder and the glass bridge deck is located in an abrupt valley, acting as a viewing platform. The bridge’s nonlinear aerostatic stability was analyzed by the segmental model test and numerical simulation in this paper. Based on aerostatic coefficients of the main girder measured in wind tunnel tests, nonlinear influences caused by the structure and aerostatic load, inhomogeneous distribution of torsion angle along the bridge axis, and the influence of initial attack angle were analyzed by using the incremental double iteration method. The results show that the aerostatic response varying with speed shows an obvious nonlinearity, and the aerostatic instability mode is of the characteristic of space deformation of bending-twisting coupling mode. The vertical and torsional deformation of the main girder is larger than its lateral deformation, with the wind speed approaching the critical wind speed. The flow of negative attack angle will reduce the bridges’ critical stability wind speed, but the influence of the negative attack angle on the aerostatic stability is more significant than that of the positive attack angle. The critical wind speeds of torsional divergence and lateral buckling are both larger than 200 m/s; namely, the bridge will not occur aerostatic instability under the action of various wind attack angles.
Abstract: This study is investigating the impact of ideological structures in terms of conservative and liberal on shaping immigration acceptance attitudes under the contribution of socio-economic status. According to motivated reasoning theory, political ideology is identified as a recurrent impact on the formation of attitude, while conservatives tend to express more hostility toward immigrants in comparison to liberals which are proposed to be more tolerant towards immigrants. Our finding suggests that political ideology will structure individual attitudes when citizens socio-economic vulnerability and level of education are low enough to consider immigrants as a threat. Therefore, economic vulnerability is proposed to weaken the ideological predispositions’ resistance. There has been some threats and factors such as level of education and economic condition proposed by group competition theory and labor market competition theory as fundamental factors which can strengthen or weaken the effects of political ideology on individuals’ attitudes towards immigration; those mechanisms for liberals and conservatives will be operated differently.
Abstract: This article presents a methodology that improves reliability and cyclability of 2nd-life Li-ion battery system repurposed as energy storage system (ESS). Most of the 2nd-life retired battery systems in market have module/pack-level state of health (SOH) indicator, which is utilized for guiding appropriate depth of discharge (DOD) in the application of ESS. Due to the lack of cell-level SOH indication, the different degrading behaviors among various cells cannot be identified upon reaching retired status; in the end, considering end of life (EOL) loss and pack-level DOD, the repurposed ESS has to be oversized by > 1.5 times to complement the application requirement of reliability and cyclability. This proposed battery grading algorithm, using non-invasive methodology, is able to detect outlier cells based on historical voltage data and calculate cell-level historical maximum temperature data using semi-analytic methodology. In this way, the individual battery cell in the 2nd-life battery system can be graded in terms of SOH on basis of the historical voltage fluctuation and estimated historical maximum temperature variation. These grades will have corresponding DOD grades in the application of the repurposed ESS to enhance the system reliability and cyclability. In all, this introduced battery grading algorithm is non-invasive, compatible with all kinds of retired Li-ion battery systems which lack of cell-level SOH indication, as well as potentially being embedded into battery management software for preventive maintenance and real-time cyclability optimization.
Abstract: Due to the concerns about the depletion of fossil fuel sources and the deteriorating environment, the attempt to investigate the production of renewable energy will play a crucial role as a potential to alleviate the dependency on mineral fuels. One particular area of interest is generation of bio-oil through sewage sludge (SS) pyrolysis. SS can be a potential candidate in contrast to other types of biomasses due to its availability and low cost. However, the presence of high molecular weight hydrocarbons and oxygenated compounds in the SS bio-oil hinders some of its fuel applications. In this context, catalytic pyrolysis is another attainable route to upgrade bio-oil quality. Among different catalysts (i.e., zeolites) studied for SS pyrolysis, activated chars (AC) are eco-friendly alternatives. The beneficial features of AC derived from SS comprise the comparatively large surface area, porosity, enriched surface functional groups and presence of a high amount of metal species that can improve the catalytic activity. Hence, a sludge-based AC catalyst was fabricated in a single-step pyrolysis reaction with NaOH as the activation agent and was compared with HZSM5 zeolite in this study. The thermal decomposition and kinetics were invested via thermogravimetric analysis (TGA) for guidance and control of pyrolysis and catalytic pyrolysis and the design of the pyrolysis setup. The results indicated that the pyrolysis and catalytic pyrolysis contain four obvious stages and the main decomposition reaction occurred in the range of 200-600 °C. Coats-Redfern method was applied in the 2nd and 3rd devolatilization stages to estimate the reaction order and activation energy (E) from the mass loss data. The average activation energy (Em) values for the reaction orders n = 1, 2 and 3 were in the range of 6.67-20.37 kJ/mol for SS; 1.51-6.87 kJ/mol for HZSM5; and 2.29-9.17 kJ/mol for AC, respectively. According to the results, AC and HZSM5 both were able to improve the reaction rate of SS pyrolysis by abridging the Em value. Moreover, to generate and examine the effect of the catalysts on the quality of bio-oil, a fixed-bed pyrolysis system was designed and implemented. The composition analysis of the produced bio-oil was carried out via gas chromatography/mass spectrometry (GC/MS). The selected SS to catalyst ratios were 1:1, 2:1 and 4:1. The optimum ratio in terms of cracking the long-chain hydrocarbons and removing oxygen-containing compounds was 1:1 for both catalysts. The upgraded bio-oils with HZSM5 and AC were in the total range of C4-C17 with around 72% in the range of C4-C9. The bio-oil from pyrolysis of SS contained 49.27% oxygenated compounds while the presence of HZSM5 and AC dropped to 7.3% and 13.02%, respectively. Meanwhile, generation of value-added chemicals such as light aromatic compounds were significantly improved in the catalytic process. Furthermore, the fabricated AC catalyst was characterized by BET, SEM-EDX, FT-IR and TGA techniques. Overall, this research demonstrated that AC is an efficient catalyst in the pyrolysis of SS and can be used as a cost-competitive catalyst in contrast to HZSM5.
Abstract: With the advent of complex software and increased connectivity, security of life-critical medical devices is becoming an increasing concern, particularly with their direct impact to human safety. Security is essential, but it is impossible to develop completely secure and impenetrable systems at design time. Therefore, it is important to assess the potential impact on security and safety of exploiting a vulnerability in such critical medical systems. The common vulnerability scoring system (CVSS) calculates the severity of exploitable vulnerabilities. However, for medical devices, it does not consider the unique challenges of impacts to human health and privacy. Thus, the scoring of a medical device on which a human life depends (e.g., pacemakers, insulin pumps) can score very low, while a system on which a human life does not depend (e.g., hospital archiving systems) might score very high. In this paper, we present a Medical Vulnerability Scoring System (MVSS) that extends CVSS to address the health and privacy concerns of medical devices. We propose incorporating two new parameters, namely health impact and sensitivity impact. Sensitivity refers to the type of information that can be stolen from the device, and health represents the impact to the safety of the patient if the vulnerability is exploited (e.g., potential harm, life threatening). We evaluate 15 different known vulnerabilities in medical devices and compare MVSS against two state-of-the-art medical device-oriented vulnerability scoring system and the foundational CVSS.
Abstract: This paper identifies leading triggers of deficient episodes in terms of GDP growth based on a sample of countries at different stages of development over 1994-2017. Using logit models, we build early warning systems (EWS) and our results show important differences between developing countries (DCs) and advanced economies (AEs). For AEs, the main predictors of the probability of entering in a GDP growth deficient episode are the deterioration of external imbalances and the vulnerability of fiscal position while DCs face different challenges that need to be considered. The key indicators for them are first, the low ability to pay its debts and second, their belonging or not to a common currency area. We also build homogeneous pools of countries inside AEs and DCs. For AEs, the evolution of the proportion of countries in the riskiest pool is marked first, by three distinct peaks just after the high-tech bubble burst, the global financial crisis and the European sovereign debt crisis, and second by a very low minimum level in 2006 and 2007. In contrast, the situation of DCs is characterized first by a relative stability of this proportion and then by an upward trend from 2006, that can be explained by more unfavorable socio-political environment leading to shortcomings in the fiscal consolidation.
Abstract: Modern structures such as floor systems, pedestrian bridges and high-rise buildings have become lighter in mass and more flexible with negligible damping and thus prone to vibration. In this paper, a semi-actively controlled pendulum tuned mass dampers (PTMD) is presented that uses air springs as both the restoring (resilient) and energy dissipating (damping) elements; the tuned mass damper (TMD) uses no passive dampers. The proposed PTMD can readily be fine-tuned and re-tuned, via software, without changing any hardware. Almost all existing semi-active systems have the three elements that passive TMDs have, i.e., inertia, resilient, and dissipative elements with some adjustability built into one or two of these elements. The proposed semi-active air suspended TMD, on the other hand, is made up of only inertia and resilience elements. A notable feature of this TMD is the absence of a physical damping element in its make-up. The required viscous damping is introduced into the TMD using a semi-active control scheme residing in a micro-controller which actuates a high-speed proportional valve regulating the flow of air in and out of the air springs. In addition to introducing damping into the TMD, the semi-active control scheme adjusts the stiffness of the TMD. The focus of this work has been the synthesis and analysis of the control algorithms and strategies to vary the tuning accuracy, introduce damping into air suspended PTMD, and enable the PTMD to self-tune itself. The accelerations of the main structure and PTMD as well as the pressure in the air springs are used as the feedback signals in control strategies. Numerical simulation and experimental evaluation of the proposed tuned damping system are presented in this paper.
Abstract: Cognitive Behavioral Therapy (CBT) has been proven an effective tool to address anger and anxiety issues in children and adolescents with Autism Spectrum Disorders (ASD). Robot-enhanced therapy has been used in psychosocial and educational interventions for children with ASD with promising results. Whenever CBT-based techniques were incorporated in robot-based interventions, they were mainly performed in group sessions. Objectives: The study’s main objective was the implementation and evaluation of the effectiveness of a relaxation training intervention for children with ASD, delivered by the social robot NAO. Methods: 20 children (aged 7–12 years) were randomly assigned to 16 sessions of relaxation training implemented twice a week. Two groups were formed: the NAO group (children participated in individual sessions with the support of NAO) and the control group (children participated in individual sessions with the support of the therapist only). Participants received three different relaxation scenarios of increasing difficulty (a breathing scenario, a progressive muscle relaxation scenario and a body scan medication scenario), as well as related homework sheets for practicing. Pre- and post-intervention assessments were conducted using the Child Behavior Checklist (CBCL) and the Strengths and Difficulties Questionnaire for parents (SDQ-P). Participants were also asked to complete an open-ended questionnaire to evaluate the effectiveness of the training. Parents’ satisfaction was evaluated via a questionnaire and children satisfaction was assessed by a thermometer scale. Results: The study supports the use of relaxation training with the NAO robot as instructor for children with ASD. Parents of enrolled children reported high levels of satisfaction and provided positive ratings of the training acceptability. Children in the NAO group presented greater motivation to complete homework and adopt the learned techniques at home. Conclusions: Relaxation training could be effectively integrated in robot-assisted protocols to help children with ASD regulate emotions and develop self-control.
Abstract: Higher ground-level ozone (GLO) concentration adversely affects human health, vegetations as well as activities in the ecosystem. In Malaysia, most of the analysis on GLO concentration are carried out using the average value of GLO concentration, which refers to the centre of distribution to make a prediction or estimation. However, analysis which focuses on the higher value or extreme value in GLO concentration is rarely explored. Hence, the objective of this study is to classify the tail behaviour of GLO using generalized extreme value (GEV) distribution estimation the return level using the corresponding modelling (Gumbel, Weibull, and Frechet) of GEV distribution. The results show that Weibull distribution which is also known as short tail distribution and considered as having less extreme behaviour is the best-fitted distribution for four selected air monitoring stations in Peninsular Malaysia, namely Larkin, Pelabuhan Kelang, Shah Alam, and Tanjung Malim; while Gumbel distribution which is considered as a medium tail distribution is the best-fitted distribution for Nilai station. The return level of GLO concentration in Shah Alam station is comparatively higher than other stations. Overall, return levels increase with increasing return periods but the increment depends on the type of the tail of GEV distribution’s tail. We conduct this study by using maximum likelihood estimation (MLE) method to estimate the parameters at four selected stations in Peninsular Malaysia. Next, the validation for the fitted block maxima series to GEV distribution is performed using probability plot, quantile plot and likelihood ratio test. Profile likelihood confidence interval is tested to verify the type of GEV distribution. These results are important as a guide for early notification on future extreme ozone events.
Abstract: Guided ultrasonic waves are used in Non-Destructive Testing and Structural Health Monitoring for inspection and damage detection. Recently, wireless data transmission using ultrasonic waves in solid metallic channels has gained popularity in some industrial applications such as nuclear, aerospace and smart vehicles. The idea is to find a good substitute for electromagnetic waves since they are highly attenuated near metallic components due to Faraday shielding. The proposed solution is to use ultrasonic guided waves such as Lamb waves as an information carrier due to their capability of propagation for long distances. In addition to this, valuable information about the health of the structure could be extracted simultaneously. In this work, the reliable frequency bandwidth for communication is extracted experimentally from dispersion curves at first. Then, an experimental platform for wireless communication using Lamb waves is described and built. After this, coherent demodulation algorithm used in telecommunications is tested for Amplitude Shift Keying, On-Off Keying and Binary Phase Shift Keying modulation techniques. Signal processing parameters such as threshold choice, number of cycles per bit and Bit Rate are optimized. Experimental results are compared based on the average bit error percentage. Results has shown high sensitivity to threshold selection for Amplitude Shift Keying and On-Off Keying techniques resulting a Bit Rate decrease. Binary Phase Shift Keying technique shows the highest stability and data rate between all tested modulation techniques.
Abstract: In order to understand the role of the injured party's fault in dividing liability, we studied its historical background. In common law, the traditional contributory negligence rule was a complete defense. Then the legislature and judicial procedure modified that rule to one of apportionment. In Islamic law, too, the Action rule was at first used when the injured party was the sole cause, but jurists expanded the scope of this rule, so this rule was used in cases where both the injured party's fault and that of the other party are involved. There are some popular approaches for apportionment of damages. Some common law countries like Britain had chosen ‘the causal potency approach’ and ‘fixed apportionment’. Islamic countries like Iran have chosen both ‘the relative blameworthiness’ and ‘equal apportionment’ approaches. The article concludes that both common law and Islamic law believe in the division of responsibility between a wrongdoer claimant and the defendant. In contrast, in the apportionment of responsibility, Islamic law mostly believes in equal apportionment that is way easier and saves time and money, but common law legal systems have chosen the causal potency approach which is more complicated than the rival approach but is fairer.
Abstract: The performance of a permanent magnet brushless direct current (BLDC) motor controlled by the Kalman filter based position-sensorless drive is studied in terms of its dependence from the system’s parameters variations. The effects of the system’s parameters changes on the dynamic behavior of state variables are verified. Simulated is the closed loop control scheme with Kalman filter in the feedback line. Distinguished are two separate data sampling modes in analyzing feedback output from the BLDC motor: (1) equal angular separation and (2) equal time intervals. In case (1), the data are collected via equal intervals of rotor’s angular position i, i.e. keeping = const. In case (2), the data collection time points ti are separated by equal sampling time intervals t = const. Demonstrated are the effects of the parameters changes on the sensorless control flow, in particular, reduction of the instability torque ripples, switching spikes, and torque load balancing. It is specifically shown that an efficient suppression of commutation induced instability torque ripples is an achievable selection of the sampling rate in the Kalman filter settings above a certain critical value. The computational cost of such suppression is shown to be higher for the motors with lower induction values of the windings.
Abstract: A customized two-stage model has been developed to simulate, analyse, and visualize distillation of actinides as a useful alternative low-pressure separation method in the nuclear recycling cases. Under the most optimal conditions of idealized thermodynamic equilibrium stages and under total reflux of distillate the investigated cases of chloride systems for the separation of such actinides are (A) UCl4-CsCl-PuCl3 and (B) ThCl4-NaCl-PuCl3. Simulatively, uranium tetrachloride in case A is successfully separated by distillation into a six-stage distillation column, and thorium tetrachloride from case B into an eight-stage distillation column. For this, a permissible mole fraction value of 1E-06 has been assumed for the residual impurification degree. With further separation effort of eleven to seventeen required separation stages, the monochlorides of plutonium trichloride from both systems A and B are simulatively shown to be separated as high pure distillation products.
Abstract: The use of vegetable oil (or natural ester) as an insulating fluid in electrical transformers is a trend that aims to contribute to environmental preservation since it is biodegradable and non-toxic. Besides, vegetable oil has high flash and combustion points, being considered a fire safety fluid. However, vegetable oil is usually less stable towards oxidation than mineral oil. Both insulating fluids, mineral and vegetable oils, need to be tested periodically according to specific standards. Oxidation stability can be determined by the induction period measured by conductivity method (Rancimat) by monitoring the effectivity of oil’s antioxidant additives, a methodology already developed for food application and biodiesel but still not standardized for insulating fluids. Besides adequate oxidation stability, fluids must be compatible with transformer's construction materials under normal operating conditions to ensure that damage to the oil and parts of the transformer does not occur. ASTM standard and Brazilian normative differ in parameters evaluated, which reveals the need to regulate tests for each oil type. The aim of this study was to assess oxidation stability and compatibility of vegetable oils to suggest the best way to assure a viable performance of vegetable oil as transformer insulating fluid. The determination of the induction period for several vegetable insulating oils from the local market by using Rancimat was carried out according to BS EN 14112 standard, at different temperatures (110, 120, and 130 °C). Also, the compatibility of vegetable oil was assessed according to ASTM and ABNT NBR standards. The main results showed that the best temperature for use in the Rancimat test is 130 °C, which allows a better observation of conductivity change. The compatibility test results presented differences between vegetable and mineral oil standards that should be taken into account in oil testing since materials compatibility and oxidation stability are essential for equipment reliability.
Abstract: Analysis of the human microbiome using metagenomic
sequencing data has demonstrated high ability in discriminating
various human diseases. Raw metagenomic sequencing data require
multiple complex and computationally heavy bioinformatics steps
prior to data analysis. Such data contain millions of short sequences
read from the fragmented DNA sequences and stored as fastq files.
Conventional processing pipelines consist in multiple steps including
quality control, filtering, alignment of sequences against genomic
catalogs (genes, species, taxonomic levels, functional pathways,
etc.). These pipelines are complex to use, time consuming and
rely on a large number of parameters that often provide variability
and impact the estimation of the microbiome elements. Training
Deep Neural Networks directly from raw sequencing data is a
promising approach to bypass some of the challenges associated with
mainstream bioinformatics pipelines. Most of these methods use the
concept of word and sentence embeddings that create a meaningful
and numerical representation of DNA sequences, while extracting
features and reducing the dimensionality of the data. In this paper
we present an end-to-end approach that classifies patients into disease
groups directly from raw metagenomic reads: metagenome2vec. This
approach is composed of four steps (i) generating a vocabulary of
k-mers and learning their numerical embeddings; (ii) learning DNA
sequence (read) embeddings; (iii) identifying the genome from which
the sequence is most likely to come and (iv) training a multiple
instance learning classifier which predicts the phenotype based on
the vector representation of the raw data. An attention mechanism
is applied in the network so that the model can be interpreted,
assigning a weight to the influence of the prediction for each genome.
Using two public real-life data-sets as well a simulated one, we
demonstrated that this original approach reaches high performance,
comparable with the state-of-the-art methods applied directly on
processed data though mainstream bioinformatics workflows. These
results are encouraging for this proof of concept work. We believe
that with further dedication, the DNN models have the potential to
surpass mainstream bioinformatics workflows in disease classification
tasks.