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Code Generation in Computational Neuroscience: A Review of Tools and Techniques

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Self-modifying code

In computer science, self-modifying code (SMC or SMoC) is code that alters its own instructions while it is executing – usually to reduce the instruction path length and improve performance or simply to reduce otherwise repetitively similar code, thus simplifying maintenance. The term is usually only applied to code where the self-modification is intentional, not in situations where code accidentally modifies itself due to an error such as a buffer overflow.

Mathematical model

A mathematical model is an abstract description of a concrete system using mathematical concepts and language. The process of developing a mathematical model is termed mathematical modeling. Mathematical models are used in applied mathematics and in the natural sciences (such as physics, biology, earth science, chemistry) and engineering disciplines (such as computer science, electrical engineering), as well as in non-physical systems such as the social sciences (such as economics, psychology, sociology, political science).

Computational neuroscience

Computational neuroscience (also known as theoretical neuroscience or mathematical neuroscience) is a branch of neuroscience which employs mathematical models, computer simulations, theoretical analysis and abstractions of the brain to understand the principles that govern the development, structure, physiology and cognitive abilities of the nervous system. Computational neuroscience employs computational simulations to validate and solve mathematical models, and so can be seen as a sub-field of theoretical neuroscience; however, the two fields are often synonymous.

Biological neuron model

Biological neuron models, also known as a spiking neuron models, are mathematical descriptions of the properties of certain cells in the nervous system that generate sharp electrical potentials across their cell membrane, roughly one millisecond in duration, called action potentials or spikes (Fig. 2). Since spikes are transmitted along the axon and synapses from the sending neuron to many other neurons, spiking neurons are considered to be a major information processing unit of the nervous system.

Computational complexity theory

In theoretical computer science and mathematics, computational complexity theory focuses on classifying computational problems according to their resource usage, and relating these classes to each other. A computational problem is a task solved by a computer. A computation problem is solvable by mechanical application of mathematical steps, such as an algorithm. A problem is regarded as inherently difficult if its solution requires significant resources, whatever the algorithm used.

Code generation (compiler)

In computing, code generation is part of the process chain of a compiler and converts intermediate representation of source code into a form (e.g., machine code) that can be readily executed by the target system. Sophisticated compilers typically perform multiple passes over various intermediate forms. This multi-stage process is used because many algorithms for code optimization are easier to apply one at a time, or because the input to one optimization relies on the completed processing performed by another optimization.

Portable Executable

The Portable Executable (PE) format is a for executables, , DLLs and others used in 32-bit and 64-bit versions of Windows operating systems. The PE format is a data structure that encapsulates the information necessary for the Windows OS loader to manage the wrapped executable code. This includes dynamic library references for linking, API export and import tables, resource management data and thread-local storage (TLS) data. On NT operating systems, the PE format is used for EXE, DLL, SYS (device driver), MUI and other file types.

Computational science

Computational science, also known as scientific computing, technical computing or scientific computation (SC), is a division of science that uses advanced computing capabilities to understand and solve complex physical problems. This includes Algorithms (numerical and non-numerical): mathematical models, computational models, and computer simulations developed to solve sciences (e.

High-level programming language

In computer science, a high-level programming language is a programming language with strong abstraction from the details of the computer. In contrast to low-level programming languages, it may use natural language elements, be easier to use, or may automate (or even hide entirely) significant areas of computing systems (e.g. memory management), making the process of developing a program simpler and more understandable than when using a lower-level language. The amount of abstraction provided defines how "high-level" a programming language is.

Executable compression

Executable compression is any means of compressing an executable file and combining the compressed data with decompression code into a single executable. When this compressed executable is executed, the decompression code recreates the original code from the compressed code before executing it. In most cases this happens transparently so the compressed executable can be used in exactly the same way as the original. Executable compressors are often referred to as "runtime packers", "software packers", "software protectors" (or even "polymorphic packers" and "obfuscating tools").