HTM Theory Reading List

This is a community-maintained wiki. Feel free to add something but try to keep a consistent format.

Sensory Processing

HTM-related Papers



General Intelligence

Other lists of HTM related papers

From old wiki:

This page contains a list of reading materials for further self-education on neuroscience and HTM.

For those interested there is also a very useful in-depth annotated bibliography being maintained in nupic.research. If you are a Mendeley user, you can go to this link and click on the “follow” button to get updates to the list of papers.

Neuroscience Books

Introductory Books

  • Neuroscience Online, an online electronic textbook, can be found here:, provided by the Department of Neurobiology and Anatomy at The University of Texas Medical School at Houston.

    Notes: This is a nice free online introduction to Neuroscience. It covers basic cellular biology of neurons, as well as a detailed tour of sensory systems, and motor systems, and higher brain functions.

  • Kandel, Eric. Principles of Neural Science. 2013. ISBN-10: 0071390111 | ISBN-13:978-0071390118

    Notes: General neuroscience reference book. It’s a classic text book and contains a ton of material.

  • Montcastle, Vernon B. Perceptual Neuroscience: The Cerebral Cortex. 1998. ISBN-10: 0674661885 | ISBN-13: 978-0674661882.

    Notes: As suggested by Jeff Hawkins on the mailing list - “It is a beautiful book and well written. It will give you a good overview of the cortex but not a clue as to how it works.”

More specific books

  • Sherman, S. Murray, and Rainer W. Guillery. Functional Connections of Cortical Areas: A New View from the Thalamus. MIT Press, 2013. ISBN-10: 0262019302 | ISBN-13: 978-0262019309.

    Notes: For those interested in going deeper into the role of the thalamus, this is an excellent book. Suggested by Jeff, it is a well written summary of a modern view of cortico-thalamic connections. It describes, for example, the connections between every cortical region and the thalamus including the role of sub-cortical motor centers. It does require some neuroscience background but is much easier to read than many of the really dense neuroscience papers. The diagrams are also very clear.

  • O’Regan, J. Kevin. Why Red Doesn’t Sound Like a Bell. 2011. ISBN-10: 0199775222 | ISBN-13: 978-0199775224

    Notes: A book about consciousness. His 2001 paper “A sensorimotor account of vision and visual consciousness” focuses on perception and is a harder read.

Neuroscience Papers

Laminar and Columnar Structure

  • Thomson, Alex M., and A. Peter Bannister. Interlaminar connections in the neocortex. Cerebral cortex 13.1 (2003): 5-14.

  • Thomson, Alex M., and Christophe Lamy. Functional maps of neocortical local circuitry. Frontiers in neuroscience 1 (2007): 2.

    Notes: These papers by Thomson are dense but contain a lot of detailed information about the connections into, out of, and within the various cortical layers.

  • Buxhoeveden and Casanova. The minicolumn hypothesis in neuroscience. Brain (2002)

    Note from Jeff: this is the best review article I know about mini-columns. Start here.

  • Raizada, R D., Grossberg S. Towards a Theory of the Laminar Architecture of Cerebral Cortex: Computational Clues from the Visual System (2003).

    Notes: This paper reviews a laminar theory of visual cortex. It proposes a computational model for the visual system based on a lot of experimental details of laminar circuitry.

  • Constantinople CM. and Bruno RM. Deep Cortical Layers Are Activated Directly by Thalamus. Science (2013) 340:1591. DOI: 10.1126/science.1236425

    Notes: This paper showed evidence supporting the idea that superficial layers (L4->L2/3) and deeper layers (L5/6) act as parallel systems. It challenges the classical belief of sensory processing pathway along L4->L2/3->L5/6 among cortical layers.

  • Harris Kenneth D, and Mrsic-Flogel Thomas D. (2013) Cortical connectivity and sensory coding. Nature (2013) 503:51 doi:10.1038/nature12654
    Notes: This is a recent review paper on cortical connectivity and its relationship with sensory coding.

Sparse Coding

  • Olshausen, Bruno A., and David J. Field. Sparse coding with an overcomplete basis set: A strategy employed by V1?. Vision research 37.23 (1997): 3311-3325.

  • Olshausen, Bruno A., and David J. Field. Sparse coding of sensory inputs. Current opinion in neurobiology 14.4 (2004): 481-487.

    Notes: The 1997 paper is one of the first papers on sparse representations in the cortex. Their work has been very influential in the machine learning and neuroscience. The 2004 paper is shorter and easier to read, more of a review.

  • Wixted, John T., Squire, Larry R., Jang, Yoonhee, Papesh, Megan H., et al., Sparse and distributed coding of episodic memory in neurons of the human hippocampus PNAS, (2014): doi: 10.1073/pnas.1408365111

    Notes: This papers demonstrate sparse distributed neural code are used for human hippocampus episodic memory.

Sensorimotor Inference

  • Sommer, Marc A., and Wurtz, Robert H. Brain Circuits for the Internal Monitoring of Movements Annu Rev Neurosci (2008) 31:317–38

    Notes: This review paper summarizes a series of studies that established a pathway for corollary discharge signal (the motor command copy to sensory cortex), explains how predictive shifting of receptive field is constructed with CD signal, and how visual stability is achieved despite eye-movements.

  • Miall RC and Wolpert DM, Forward models for physiological motor control. Neural Networks (1996) 9:8,1265-1279

    Notes: This paper discussed sensorimotor integration from a computational perspective. The forward model concept in this paper is widely used in motor control and sensorimotor inference.

  • Keller GB, Bonhoeffer B and Hubener Mark, Sensorimotor Mismatch Signals in Primary Visual Cortex of the Behaving Mouse. Neuron (2012) 74:809–815

    Notes: This research paper demonstrated that the primary visual cortex are strongly driven by locomotion and by mismatch between actual and expected visual input.


  • Knudsen EI, Fundamental Components of Attention. Annu. Rev. Neurosci. (2007) 30:57–78

    Notes: This review paper discussed a framework to understand attention and identifies four processes fundamental to attention: working memory, top-down control, competitive selection, and bottom-up filtering.

Referenced in On Intelligence

  • Mountcastle, Vernon B. An Organizing Principle for Cerebral Function: The Unit Model and the Distributed System, in Gerald M. Edelman and Vernon B. Mountcastle, eds., The Mindful Brain (Cambridge, Mass.: MIT Press, 1978).

  • Creutzfeldt, Otto D. Generality of the Functional Structure of the Neocortex, Naturwissenschaften, vol. 64 (1977): pp. 507-517.

  • Felleman, D. J., and D. C. Van Essen. Distributed Hierarchical Processing in the Primate Cerebral Cortex, Cerebral Cortex, vol. 1 (January/February 1991): pp. 1-47.

  • Sherman, S.M., and R.W. Guillery. The Role of the Thalamus in the Flow of Information to the Cortex, Philosophical Transactions of the Royal Society of London, vol. 357, no. 1428 (2002): pp. 1695-1708.

  • Rao, R. P., and D. H. Ballard. Predictive Coding in the Visual Cortex: A Functional Interpretation of Some Extra-Classical Receptive-field Effects, Nature Neuroscience, vol. 2, no. 1 (1999): pp. 79-87.

  • Guillery, R. W. Branching Thalamic Afferents Link Action and Perception, Journal of Neurophysiology, vol. 90 (2003): pp. 539-548.

  • Young, 170 M. P. The Organization of Neural Systems in the Primate Cerebral Cortex, Proceedings of the Royal Society: Biological Sciences, vol. 252 (1993): pp. 13-18.

    Notes: Papers mentioned in the back of Jeff’s book, “On Intelligence”


  • Bartlett Mel has written the most important papers on the local dendritic properties we use in the CLA. These are technical.

Free Courses (not specific to HTM/CLA)

  • Coursera: Computational Neuroscience by Rajesh P. N. Rao, Adrienne Fairhall (University of Washington)

    Notes: Excellent introduction to neuroscience from a computational point of view.

  • Coursera: Neural Networks for Machine Learning by Geoffrey Hinton (University of Toronto)

    Notes: Geoffrey Hinton is one of the leading experts on Deep Learning Networks.


I’m not sure how this should be different from the existing wiki page on Numenta’s github:

Good point. I think this wiki (and potentially others generally used by the community) will replace wikis we keep on Github. I believe the wikis are more valuable here close to the conversations, so maybe we should just collect all the missing bits from the Github wiki and shut it down (refer it to this one)?


@rhyolight Under the section “Other lists of HTM related papers”, you added the link, but it produces a 404 (of course, after having created the Mendeley account). Can you update this link? - report

HTM Theory Reading List (quick scan)

Generated: 8/9/2018 9:09:41 PM

100% scanned - 77/77 URLs checked, 74 OK, 3 failed

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@Bitking sent me the above post as a DM, but it is useful. I hope he doesn’t mind me sharing it. As anyone can see, there are a few broken links above. The old mailing list archive is missing. I’ll have to look into that, as I believe we’ve been paying for a read-only version of the mailing list HTML. The other links, I don’t know about.

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I copied the reading list page and updated it for my own use here
(Note that I deleted some entries)


Where can I find the paper that Mountcastle, Vernon B posted on the Mindful Brain 1978 which was referenced in On Intelligence? I’m very interested and I think what Prof. Mountcastle proposed in that paper the cortex runs a single basic algorithm in all areas is very important for the whole HTM theory.

The book is available for purchase here:

And this useful paper by Mountcastle is freely available here:
The columnar organization of the neocortex - Vernon B. Mountcastle - 1997

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See recent discussion in Crazy quilting in the cortex.

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the link is invalid. Could you please offer a new one?

There is this free and online Neuroscience (NS) book that I’ve been reading/referencing for a while now. For non NS people, I recommend it as it has a lot of great topics that are related to HTM especially the general concepts used from NS and including more computational aspects of the neuron. If you can run its simulation the better. Be careful though as it is an old book, so read at your own risk. The book is called Computational Cognitive Neuroscience.


Trying to download the pseudocode in the link behind the link you attached brings the following:

Home » Error 404: Page not found

Error! Problem, or Page Not Found

Sorry, the page you were looking for does not exist.

  • Either the page you were looking for is gone, or this website is currently having troubles.
  • Please Contact Us if you are having problems, and we will respond as soon as possible.
  • Visit the homepage for more information.

Is there a new location from which to download it?

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Fixed! Thanks!

Thank you very much, Matt!

The link works again and the files are very interesting and very well written.

Thanks and regards,


  • BrainConstellation
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