Applications of Support Vector Machines as a Robust tool in High Throughput Virtual Screening

Chemical space is enormously huge but not all of it is pertinent for the drug designing. Virtual screening methods act as knowledge-based filters to discover the coveted novel lead molecules possessing desired pharmacological properties. Support Vector Machines (SVM) is a reliable virtual screening tool for prioritizing molecules with the required biological activity and minimum toxicity. It has to its credit inherent advantages such as support for noisy data mainly coming from varied high-throughput biological assays, high sensitivity, specificity, prediction accuracy and reduction in false positives. SVM-based classification methods can efficiently discriminate inhibitors from non-inhibitors, actives from inactives, toxic from non-toxic and promiscuous from non-promiscuous molecules. As the principles of drug design are also applicable for agrochemicals, SVM methods are being applied for virtual screening for pesticides too. The current review discusses the basic kernels and models used for binary discrimination and also features used for developing SVM-based scoring functions, which will enhance our understanding of molecular interactions. SVM modeling has also been compared by many researchers with other statistical methods such as Artificial Neural Networks, k-nearest neighbour (kNN), decision trees, partial least squares, etc. Such studies have also been discussed in this review. Moreover, a case study involving the use of SVM method for screening molecules for cancer therapy has been carried out and the preliminary results presented here indicate that the SVM is an excellent classifier for screening the molecules

Energy-efficient hardware design based on high-level synthesis

This dissertation describes research activities broadly concerning the area of High-level synthesis (HLS), but more specifically, regarding the HLS-based design of energy-efficient hardware (HW) accelerators. HW accelerators, mostly implemented on FPGAs, are integral to the heterogeneous architectures employed in modern high performance computing (HPC) systems due to their ability to speed up the execution while dramatically reducing the energy consumption of computationally challenging portions of complex applications. Hence, the first activity was regarding an HLS-based approach to directly execute an OpenCL code on an FPGA instead of its traditional GPU-based counterpart. Modern FPGAs offer considerable computational capabilities while consuming significantly smaller power as compared to high-end GPUs. Several different implementations of the K-Nearest Neighbor algorithm were considered on both FPGA- and GPU-based platforms and their performance was compared. FPGAs were generally more energy-efficient than the GPUs in all the test cases. Eventually, we were also able to get a faster (in terms of execution time) FPGA implementation by using an FPGA-specific OpenCL coding style and utilizing suitable HLS directives. The second activity was targeted towards the development of a methodology complementing HLS to automatically derive power optimization directives (also known as "power intent") from a system-level design description and use it to drive the design steps after HLS, by producing a directive file written using the common power format (CPF) to achieve power shut-off (PSO) in case of an ASIC design. The proposed LP-HLS methodology reduces the design effort by enabling designers to infer low power information from the system-level description of a design rather than at the RTL. This methodology required a SystemC description of a generic power management module to describe the design context of a HW module also modeled in SystemC, along with the development of a tool to automatically produce the CPF file to accomplish PSO. Several test cases were considered to validate the proposed methodology and the results demonstrated its ability to correctly extract the low power information and apply it to achieve power optimization in the backend flow