aka partial brain emulations, aka expanded brain emulations, aka Improved [Biont|Cyborg] Encoding Protocols, aka etc
A standard Whole Brain Emulation is the basis for the process of uploading a biont mentality into a virtual form. When such a WBE is made, each neuron, synaptic potential, dendritic connection, and so on is carefully modelled to match the functionality of the original biological brain. However, the human brain is extraordinarily inefficient at a variety of tasks, and the various shortcuts it takes lead to a number of odd effects and inefficiencies such as the ones exploited by optical illusions. Therefore a large fraction of Uploaded entities have sought ways to improve the performance of their minds, as measured by whatever criteria they use.
One of the most typical rewrites is to improve efficiency. For example, instead of modelling every neuron and glial cell of a brain's visual subsystem, with the task of 'vision' being performed by cascades of neurotransmitters, the functions performed by that subsystem can be modelled directly in code, which only requires a fraction of the processing power to run.
In regions where computronium is somewhat limited, such as when a local transapient uses significant fractions of the local computronium for er own purposes, or aboard spacecraft with limited mass, this has a number of benefits - in extreme cases, such increased efficiency may be required in order for the Upload to simply continue to run at a preferred subjective clock rate, or with a desired level of sensory fidelity; while, with less severe computronium shortages, the processing power saved can then be applied for other purposes, such as for performing computations of er own, or to increase their economic viability by leveraging rental of the saved computronium.
The other most typical rewrite is to improve on the original capabilities, allowing the Upload to perform mental tasks that were unavailable in its original substrate. One of the simplest examples is allowing the emulated brain to process forms of sensory input that were not part of their biological form, ranging from simple tetrachromatism to whole new senses. A middling rewrite allows nebs to upgrade themselves to superbrights in one or more cognitive domains.
In more extreme cases, entirely new modes of thought can be implemented, creating minds that are true hybrids between Uploads and aioids; this is a common method used by bionts who wish to ascend to transavance or full transapience. Another popular form of extreme rewrite allows the upgraded sophont to access one or another system of plug-in knowledge modules.
In general, the efficiency-focussed forms of enhancement are easily removed, returning the emulated brain's model to that of the original whole brain, allowing for easy placement back into a biological body through engeneration. However, generally, capability-improvement enhancements can only be removed at a cost - such as removing those capabilities; or requiring the implantation of computronium to run such functions in the engenerated brain the Upload downloads into; or the use of a biological substrate which significantly differs from terragenic standard.
Transapients occasionally gift pieces of code to modosophonts which, while completely incomprehensible to non-transapients, offer improvements beyond what modosophonts can write for themselves. While those who accept such transapient code receive the advantages of more efficient or capable minds, acceptance of such code is often controversial. As those minds are no longer fully comprehensible to other modosophonts or even themselves, they become difficult to undo should the Upload wish to engenerate into a biological body. A subtler danger involves such code potentially containing secret functions in addition to the stated ones.
In some regions, one or more forms of these enhancements are a standard part of the Uploading process. In others, they are viewed as violating the integrity of the self of the Upload, and are heavily frowned upon.