Impact of Carriage Crowding Level on Bus Dwell Time: Modelling and Analysis

This paper develops two types of estimation models to quantify the impacts of carriage crowding level on bus dwell time. The first model (model I) takes the crowding level and the number of alighting and boarding passengers into consideration and estimates the alighting time and boarding time, respectively. The second model (model II) adopts almost the same regression method, except that the impact of crowding on dwell time is neglected. The analysis was conducted along two major bus routes in Harbin, China, by collecting 640 groups of dwell times under crowded condition manually. Compared with model II, the mean absolute error (MAE) of model I is reduced by 137.51%, which indicates that the accuracy of bus dwell time estimation could be highly improved by introducing carriage crowding level into the model. Meanwhile, the MAE of model I is about 3.9 seconds, which is acceptable in travel time estimation and bus schedule

A Multi-Sensor Phenotyping System: Applications on Wheat Height Estimation and Soybean Trait Early Prediction

Phenotyping is an essential aspect for plant breeding research since it is the foundation of the plant selection process. Traditional plant phenotyping methods such as measuring and recording plant traits manually can be inefficient, laborious and prone to error. With the help of modern sensing technologies, high-throughput field phenotyping is becoming popular recently due to its ability of sensing various crop traits non-destructively with high efficiency. A multi-sensor phenotyping system equipped with red-green-blue (RGB) cameras, radiometers, ultrasonic sensors, spectrometers, a global positioning system (GPS) receiver, a pyranometer, a temperature and relative humidity probe and a light detection and ranging (LiDAR) was first constructed, and a LabVIEW program was developed for sensor controlling and data acquisition. Two studies were conducted focusing on system performance examination and data exploration respectively. The first study was to compare wheat height measurements from ultrasonic sensor and LiDAR. Canopy heights of 100 wheat plots were estimated five times over the season by the ground phenotyping system, and the results were compared to manual measurements. Overall, LiDAR provided the better estimations with root mean square error (RMSE) of 0.05 m and R2 of 0.97. Ultrasonic sensor did not perform well due to the style of our application. In conclusion LiDAR was recommended as a reliable method for wheat height evaluation. The second study was to explore the possibility of early predicting soybean traits through color and texture features of canopy images. Six thousand three hundred and eighty-three RGB images were captured at V4/V5 growth stage over 5667 soybean plots growing at four locations. One hundred and forty color features and 315 gray-level co-occurrence matrix (GLCM)-based texture features were derived from each image. Another two variables were also introduced to account for the location and timing difference between images. Cubist and Random Forests were used for regression and classification modelling respectively. Yield (RMSE=9.82, R2=0.68), Maturity (RMSE=3.70, R2=0.76) and Seed Size (RMSE=1.63, R2=0.53) were identified as potential soybean traits that might be early-predictable. Advisor: Yufeng G

Analysis of the understudied parts of the phospho-signalome using machine learning methods

Abstract Analysis of the understudied parts of the phospho-signalome using machine learning methods Borgthor Petursson In order to make decisions and respond appropriately to external stimuli, cells rely on an intricate signalling system. One of the most important and best studied components of this signalling system is the phospho-signalling network. Phosphorylation relays information through adding phosphoryl groups onto substrates such as lipids or proteins, which in turn leads to changes in substrate function. Crucial components of this system include kinases, which phosphorylate on the substrate molecule and phosphatases that remove the phosphoryl group from the substrate. To date, even though >100K phosphoproteins have been identified through high throughput experiments, the vast majority of phosphosites are of unknown function, while over a third of kinases have no known substrate (Needham et al., 2019). Furthermore, there is a large study bias in our current knowledge, demonstrated by a disproportionate number of interactions between highly cited kinases and substrates Invergo and Beltrao, 2018. The vast understudied signalling space combined with this study bias make it difficult to understand the general principles underpinning cell signalling regulation and stresses the need to research the phosphoproteomic signalling system in an unbiased manner. In this thesis the central aim is to use data-driven and unbiased approaches to study the human phosphoproteomic signalling network. The first chapter describes a project where I co-developed a machine learning model to predict signed kinase-kinase regulatory circuits based on kinase specificities and high throughput phosphoproteomics and transcriptomic data. The network was validated using independent high throughput data and used to identify novel kinase-kinase regulatory interactions. This project was done in collaboration with Brandon Invergo, a postdoc in Pedro Beltrao’s research group. In the second chapter I expand upon work done in the first chapter. I used various predictors such as: Co-expression, kinase specificities and different variables characterising kinase-substrate potential target phosphosites to predict kinase-substrate relationships and their signs. I then used independent experimental kinase-substrate predictions to validate the predictions and identify high confidence kinase-substrate relationships. I then combined the kinase-substrate predictions with the kinase-kinase regulatory circuits to identify condition-specific signalling networks. To enable easy use of my method and networks and analyses of phosphoproteomics data by non-expert users I also developed the SELPHI2 server, where the user can extract biological insight from their datasets. SELPHI2 presents a substantial improvement upon the SELPHI server, which was developed in 2015 by my supervisor, Evangelia Petsalaki. Thirdly, to study the architecture of human cell signalling networks at a whole-cell level and address the limited predictive power of the current models of cell signalling such as pathways found in KEGG (Kanehisa, 2019), Reactome (Jassal et al., 2020) and WikiPathways (Slenter et al., 2018), the third chapter aims to identify signalling modules from phosphoproteomic data. These data-extracted modules were found to have a greater predictive power for independent data sets in terms of number of significant enrichments. Furthermore, we sought to predict the probability of module co-membership from predictors such as membership within data-driven modules, co-phosphorylation and co-expression. In summary, the work presented here seeks to explore the understudied phospho-signalling systems through system-wide prediction of kinase-substrate regulation and the identification of phospho-signalling modules through data-driven means

A Multi-Sensor Phenotyping System: Applications on Wheat Height Estimation and Soybean Trait Early Prediction

Phenotyping is an essential aspect for plant breeding research since it is the foundation of the plant selection process. Traditional plant phenotyping methods such as measuring and recording plant traits manually can be inefficient, laborious and prone to error. With the help of modern sensing technologies, high-throughput field phenotyping is becoming popular recently due to its ability of sensing various crop traits non-destructively with high efficiency. A multi-sensor phenotyping system equipped with red-green-blue (RGB) cameras, radiometers, ultrasonic sensors, spectrometers, a global positioning system (GPS) receiver, a pyranometer, a temperature and relative humidity probe and a light detection and ranging (LiDAR) was first constructed, and a LabVIEW program was developed for sensor controlling and data acquisition. Two studies were conducted focusing on system performance examination and data exploration respectively. The first study was to compare wheat height measurements from ultrasonic sensor and LiDAR. Canopy heights of 100 wheat plots were estimated five times over the season by the ground phenotyping system, and the results were compared to manual measurements. Overall, LiDAR provided the better estimations with root mean square error (RMSE) of 0.05 m and R2 of 0.97. Ultrasonic sensor did not perform well due to the style of our application. In conclusion LiDAR was recommended as a reliable method for wheat height evaluation. The second study was to explore the possibility of early predicting soybean traits through color and texture features of canopy images. Six thousand three hundred and eighty-three RGB images were captured at V4/V5 growth stage over 5667 soybean plots growing at four locations. One hundred and forty color features and 315 gray-level co-occurrence matrix (GLCM)-based texture features were derived from each image. Another two variables were also introduced to account for the location and timing difference between images. Cubist and Random Forests were used for regression and classification modelling respectively. Yield (RMSE=9.82, R2=0.68), Maturity (RMSE=3.70, R2=0.76) and Seed Size (RMSE=1.63, R2=0.53) were identified as potential soybean traits that might be early-predictable. Advisor: Yufeng G

Design of Plant Protection UAV Variable Spray System Based on Neural Networks

Recently, unmanned aerial vehicles (UAVs) have rapidly emerged as a new technology in the fields of plant protection and pest control in China. Based on existing variable spray research, a plant protection UAV variable spray system integrating neural network based decision making is designed. Using the existing data on plant protection UAV operations, combined with artificial neural network (ANN) technology, an error back propagation (BP) neural network model between the factors affecting droplet deposition is trained. The factors affecting droplet deposition include ambient temperature, ambient humidity, wind speed, flight speed, flight altitude, propeller pitch, nozzles pitch and prescription value. Subsequently, the BP neural network model is combined with variable rate spray control for plant protection UAVs, and real-time information is collected by multi-sensor. The deposition rate is determined by the neural network model, and the flow rate of the spray system is regulated according to the predicted deposition amount. The amount of droplet deposition can meet the prescription requirement. The results show that the training variance of the ANN is 0.003, and thus, the model is stable and reliable. The outdoor tests show that the error between the predicted droplet deposition and actual droplet deposition is less than 20%. The ratio of droplet deposition to prescription value in each unit is approximately equal, and a variable spray operation under different conditions is realized

Design of Plant Protection UAV Variable Spray System Based on Neural Networks

Recently, unmanned aerial vehicles (UAVs) have rapidly emerged as a new technology in the fields of plant protection and pest control in China. Based on existing variable spray research, a plant protection UAV variable spray system integrating neural network based decision making is designed. Using the existing data on plant protection UAV operations, combined with artificial neural network (ANN) technology, an error back propagation (BP) neural network model between the factors affecting droplet deposition is trained. The factors affecting droplet deposition include ambient temperature, ambient humidity, wind speed, flight speed, flight altitude, propeller pitch, nozzles pitch and prescription value. Subsequently, the BP neural network model is combined with variable rate spray control for plant protection UAVs, and real-time information is collected by multi-sensor. The deposition rate is determined by the neural network model, and the flow rate of the spray system is regulated according to the predicted deposition amount. The amount of droplet deposition can meet the prescription requirement. The results show that the training variance of the ANN is 0.003, and thus, the model is stable and reliable. The outdoor tests show that the error between the predicted droplet deposition and actual droplet deposition is less than 20%. The ratio of droplet deposition to prescription value in each unit is approximately equal, and a variable spray operation under different conditions is realized

Improved shear strength prediction model of steel fiber reinforced concrete beams by adopting gene expression programming

In this study, an artificial intelligence tool called gene expression programming (GEP) has been successfully applied to develop an empirical model that can predict the shear strength of steel fiber reinforced concrete beams. The proposed genetic model incorporates all the influencing parameters such as the geometric properties of the beam, the concrete compressive strength, the shear span-to-depth ratio, and the mechanical and material properties of steel fiber. Existing empirical models ignore the tensile strength of steel fibers, which exercise a strong influence on the crack propagation of concrete matrix, thereby affecting the beam shear strength. To overcome this limitation, an improved and robust empirical model is proposed herein that incorporates the fiber tensile strength along with the other influencing factors. For this purpose, an extensive experimental database subjected to four-point loading is constructed comprising results of 488 tests drawn from the literature. The data are divided based on different shapes (hooked or straight fiber) and the tensile strength of steel fiber. The empirical model is developed using this experimental database and statistically compared with previously established empirical equations. This comparison indicates that the proposed model shows significant improvement in predicting the shear strength of steel fiber reinforced concrete beams, thus substantiating the important role of fiber tensile strength.National University of Science and Technolog

Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria

Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic DNA, it is hard to identify the key cis-regulatory elements that determine disparate patterns of gene expression. The detection of the intra- and inter-species differences among these sequences is crucial for understanding the molecular basis of both differential gene expression and evolution. Here, we address this problem by investigating the target promoters controlled by the DNA-binding PhoP protein, which governs virulence and Mg2+ homeostasis in several bacterial species. PhoP is particularly interesting; it is highly conserved in different gamma/enterobacteria, regulating not only ancestral genes but also governing the expression of dozens of horizontally acquired genes that differ from species to species. Our approach consists of decomposing the DNA binding site sequences for a given regulator into families of motifs (i.e., termed submotifs) using a machine learning method inspired by the “Divide & Conquer” strategy. By partitioning a motif into sub-patterns, computational advantages for classification were produced, resulting in the discovery of new members of a regulon, and alleviating the problem of distinguishing functional sites in chromatin immunoprecipitation and DNA microarray genome-wide analysis. Moreover, we found that certain partitions were useful in revealing biological properties of binding site sequences, including modular gains and losses of PhoP binding sites through evolutionary turnover events, as well as conservation in distant species. The high conservation of PhoP submotifs within gamma/enterobacteria, as well as the regulatory protein that recognizes them, suggests that the major cause of divergence between related species is not due to the binding sites, as was previously suggested for other regulators. Instead, the divergence may be attributed to the fast evolution of orthologous target genes and/or the promoter architectures resulting from the interaction of those binding sites with the RNA polymerase