Are there any models of human cognition that do not depend on physicalism or materialism? Are there any models of Human Cognition that do not depend on Physicalism or materialism? Could Cognition models that say 'mind' states are actually 'brain states' and that we are therefore neuro-chemical mechanisms ; could these models miss important factors like how 'behavioral algorithms' of the 'mind-brain' are organised and how they interact and how the mind-brain 'makes new 'behavioral algorithms'. What I call Behavioral Algorithms could be called 'mental programs' or 'mental software'. So are there models of Cognition that do not focus on Physicalism ( the philosophy that everything that exist has a physical basis and nothing else like  emergent qualities or something 'intangible')?
Algorithms can be seen as rules defined on various states of the system. Thus, there must be a mapping of the physical states to the abstract states, as well as a mapping of the physical rules/transitions to the abstract rules. David Chalmers is one of the most popular philosophers who discusses the notion of when a physical system implements an abstract computational system. [1] It seems like you are asking for theories of cognition that are truly emergent, however. These do exist - for an overview, see [2]. "Models governed by simple laws, especially models that learn, can give rise to emergent patterns that were not predicted in advance and that, even after they have been observed, may not be fully comprehended by the modeler. To what extent such patterns can or ever will be fully understood remains an open question." This vision of the cognitive sciences falls under the epistemological framework of explanatory pluralism - the view that properties exist on many levels, but their physical basis is the same. However, this is still physicalism - everything supervenes on the physical. [3] Furthermore, we are often required to simulate the basic rules in order to even see the emergent properties in the first place. [4] I think the take home message of this situation is that we can't have science without physicalism. 

[1] Chalmers, David J. "A computational foundation for the study of cognition." (1993).

[2] McClelland, James L. "Emergence in cognitive science." Topics in cognitive science 2.4 (2010): 751-770.

[3] http://plato.stanford.edu/archives/fall2009/entries/physicalism/

[4] Baker, Alan. "Simulation-based definitions of emergence." Journal of Artificial Societies and Social Simulation 13.1 (2010): 9.