Sharif Digital Repository

Decades ago, scientists and researchers found out proteins are not function isolated and act in multi protein complexes as complex networks. So, they started to study about proteins and their interaction in the term of protein-protein interaction, therefore, the number of publication in this field grows rapidly. This large amount of published articles (in scientific journals or web pages or books) are unstructured and it is hard to classify them manually. Also, study and read all of these documents is difficult for one person. Hence, it’s better to find a way which could help scientists and researcher to study these unstructured or semi-structured information more easily. The best way to... 

The fundamental goal of communication networks is to transfer messages across the network between the nodes. Often, maximizing the information flow which is limited by connectivity of the network could be interesting. The concept of connectivity is divided into edge and vertex connectivity. If our focus were on the vertex-connectivity, connected dominating sets (CDS) could be a valuable tool. Obtaining (fractionally) vertex-disjoint connected dominating sets which are called fractional CDS packing presents a backbone to get an information flow matching the size of connectivity. In this thesis, we will present a distributed algorithm that is given a communication network with n nodes and... 

The rapid development of scientific areas in this modern era makes the process of finding new field of research slow and laborious for prospective scholars. Thus, having a vision of the future could be helpful to pick a right path for doing researches and ensuring that it is worth to invest in. This thesis seeks to predict research trends by using link prediction approaches on keywords network and discusses about the performance of various algorithms in different situations. Moreover, for the last part of the experiments, novel link prediction algorithms are proposed by the author, enhances the accuracy of prediction results. The data set collected from Sciencedirect and Scopus by a strong... 

Nuclear magnetic resonance is a spectroscopic method which is used to investigate characteristics of molecules with hydrogen and carbon chains. In this thesis we used, NMR spectrum extracted from 19 types of amino acids for investigating on feature generation for protein sequences. We processed NMR spectra based on Hydrogen and Carbon atoms in structure of the amino acids and after preprocessing we extracted features for each amino acid from the spectra. After that, we tried to cluster the amino acids with Fuzzy Clustering Method (FCM) then we generated feature vectors by extracting special descriptor for amino acids in sequence of proteins. In addition to NMR, we used the features of... 

Complex Networks are everywhere, many complex systems can be represented as networks, such as the power grid, the road network, the airline network and the Protein-protein interaction network, delivery and distribution networks, and telephone networks. A fundamental issue concerning complex networks is the robustness of the overall system to the failure of its constituent parts. The robustness of networks against failure, targeted attacks to individuals’ components, and the impact on the performance of the system has become an important issue for practical reasons in the last few years. The failures attacks or errors on networks are not limited to the deletion of vertex, for common... 

A drug can be defined as a substance made to prevent disease, cure a specific symptom, relieve pain, and reduce anomalies in the body. The process of drug designing is so laborious, complex, costly, and time-consuming that chance of failure during the lab experiment stages is high. These challenges have persuaded researchers to find new usage for existing drugs, referred to as drug repurposing, with the main advantage of reducing cost, risk, and time. To this aim, computational methods have been applied to discover hidden pharmaceutical capabilities of drugs in terms of predicting whether a particular drug can interact with a particular protein.Graph Neural Networks (GNNs) have recently... 

Predicting the evolution of viruses is vital in controlling, preventing, and treating diseases. Mutations that evade the host immune system can propagate and persist through generations, making it crucial to anticipate and combat them effectively. The 1918 H1N1 pandemic serves as an example of the devastating impact of pandemics caused by viral mutations. By predicting mutations in advance, we can identify potential future pandemics and take effective preventative measures to mitigate their impact. Proteins play a vital role in the functioning of viruses. They are involved in various processes, such as replication, transcription, and host cell invasion. Any changes in the protein sequence... 

Network methods have had profound influence in many domains and fields in the past decade. Community structure is a very important property of complex networks, but the precise definition of a community remains an unresolved problem and Community detection in complex networks has recently attracted wide attention in several research areas such as social networks, communication networks, and biological systems. Complex network studies grow by the scientific community, thanks to the increasing accessibility of real-world network data. The emphasis of use analysis on the network algorithms and community structure is one of the most important problems in the field of complex network. Many... 

In recent decades, a wide range of research has been done on the characteristics of networks in various domains. Community structure is one of the most important properties in networks. However, most community detection methods designed for unipartite networks. Bipartite networks are very important in many different fields because these networks explicitly shows conceptual connections between different types of entities, for example in bioinformatics science, business, social and economic systems. Recently, community detection in bipartite networks has risen attention by the technical community, due to the accessibility of huge bipartite network data from different domains and the spread of... 

Autism spectrum disorder (ASD) is a strong genetic perturbation that encompasses a wide range of clinical symptoms, including functional at different regions of the brain, repetitive behaviors, and interests, weaknesses in social relationships, some sensitivities to environmental factors and etc. Genetic complexity and the impact of environmental factors put the disease in the category of Level 1 complex developmental disorders.We proposed a pilot, combined, and highly effective structure to identify biomarkers in the autism spectrum disorder that could be extended to other diseases that have a similar genetic architecture with autism. We also develop a Gene-tissue interaction network to... 

Complex networks represent a wide diversity of systems in nature and human interactions. Networks are graphs that describe the structures of interacting systems and give significant information about the patterns of connections between the nodes in a particular system. In turn, having knowledge about the structure of networks and their arrangements enables one to make certain types of predictions about their behavior of network.Network methods have had profound influence in many domains and fields in the past decade. Centrality measures are very important tool for analysis complex networks, in real-world complex networks are heterogeneous structures, all their components such as nodes... 

Genetic heterogeneity within a tumor, which occurs during cancer evolution, is one of the reasons for treatment failure and increased chances of drug resistance. Cancer cells initially derive from a mutated progenitor cell, resulting in shared mutated genes. Throughout the course of tumor formation and progression, the occurrence of new mutations is possible, leading to the generation of cancer cells with various mutated genes. An appropriate approach is to identify the sequence of mutations that have occurred in the tumor, which can be inferred from single-cell sequencing data. Singlecell data provides valuable information about branching events in the evolution of a cancerous tumor. In... 

In this project, the landing process is simulated by using of multi-body dynamics commercial software. Various factors, including landing situations, aircraft structures and climate are used in this simulation. The purpose of this project is to determine the forces exerted on the aircraft landing gears in landing process in various landing conditions. For this purpose, the ADAMS multi-body dynamics software is used. At first, different scenarios based on FAR-25, including level landing, tail-down landing, crab landing are simulated. Results of dynamic simulation software with landing load factor obtained from the analytical solution are compared. Then for the level landing, different... 

Discharging treated or raw waste water in to surface water may cause lots of serious problems, including growth of algae, as a result of the presence of nutrients in waste water.algae decrease the concentration of dissolve oxygen in water.phosphorus removal from waste water is of absolute necessity. according to the standards set by the environmental organization, discharge the untreated waster water in to the surface water is not allowed. on the other hand, given manager facilities of deprived area,effort is channeled to reach the desired result through designing the simplest treatment systems. anaerobic-aerobic systems have remarkably been used for many years in the treatment of urban and... 

Secure multi-party computation (MPC) enables a group of mutually distrustful parties to compute a joint and agreed upon function of their private inputs without disclosing anything but the corresponding output. One of the most important secure computation protocols is private set intersection (PSI). In PSI, often two or several parties wish to find the intersection of their sets without revealing other non-common elements. There exist some other variants of PSI protocol like PSI cardinality or threshold PSI which in the former only the cardinality of the intersection set is revealed and in the latter the intersection set is revealed if its cardinality is greater (less) than a certain value.... 

Thermoacoustics deals with the conversion of heat energy into sound energy and vice versa. This new and emerging technology has a strong potential towards the development of sustainable and renewable energy systems by utilizing waste heat or solar energy. Although thermoacoustic devices are simple to fabricate; however, the design process is very challenging. The thermoacoustic phenomenon is discovered over a century ago; nevertheless, the rapid advancement in this field occurred during the past three decades when the theoretical understanding of the phenomenon is developed along with the prototype devices. There are several advantages of heat engines and refrigerators based on...