Archive for the ‘Neuroinformatics’ Category

Advances in Neural Information Processing Systems (NIPS)

Sunday, April 7th, 2013

Advances in Neural Information Processing Systems (NIPS)

From the homepage:

The Neural Information Processing Systems (NIPS) Foundation is a non-profit corporation whose purpose is to foster the exchange of research on neural information processing systems in their biological, technological, mathematical, and theoretical aspects. Neural information processing is a field which benefits from a combined view of biological, physical, mathematical, and computational sciences.

Links to videos from NIPS 2012 meetings are featured on the homepage. The topics are as wide ranging as the foundation’s description.

A tweet from Chris Diehl, wondering what to do with “old hardbound NIPS proceedings (NIPS 11)” led me to: Advances in Neural Information Processing Systems (NIPS) [Online Papers], which has the papers from 1987 to 2012 by volume and a search interface to the same.

Quite a remarkable collection just from a casual skim of some of the volumes.

Unless you need to fill book shelf space, suggest you bookmark the NIPS Online Papers.

Neuroscience Information Framework (NIF)

Saturday, December 15th, 2012

Neuroscience Information Framework (NIF)

From the about page:

The Neuroscience Information Framework is a dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.

Example of a subject specific information resource that provides much deeper coverage than possible with Google, for example.

If you aren’t trying to index everything, you can out perform more general search solutions.

Streaming Analytics: with sparse distributed representations

Monday, May 28th, 2012

Streaming Analytics: with sparse distributed representations by Jeff Hawkins.

Abstract:

Sparse distributed representations appear to be the means by which brains encode information. They have several advantageous properties including the ability to encode semantic meaning. We have created a distributed memory system for learning sequences of sparse distribute representations. In addition we have created a means of encoding structured and unstructured data into sparse distributed representations. The resulting memory system learns in an on-line fashion making it suitable for high velocity data streams. We are currently applying it to commercially valuable data streams for prediction, classification, and anomaly detection In this talk I will describe this distributed memory system and illustrate how it can be used to build models and make predictions from data streams.

Slides: http://www.numenta.com/htm-overview/05-08-2012-Berkeley.pdf

Looking forward to learning more about “sparse distributed representation (SDR).”

Not certain about Jeff’s claim that matching across SDRs = semantic similarity.

Design of the SDR determines the meaning of each bit and consequently of matching.

Which feeds back into the encoders that produce the SDRs.

Other resources:

The core paper: Hierarchical Temporal Memory including HTM Cortical Learning Algorithms. Check the FAQ link if you need the paper in Chinese, Japanese, Korean, Portuguese, Russian, or Spanish. (unverified translations)

Grok – Frequently Asked Questions

A very good FAQ that goes a long way to explaining the capabilities and limitations (currently) of Grok. “Unstructured text” for example isn’t appropriate input into Grok.

Jeff Hawkins and Sandra Blakeslee co-authored On Intelligence in 2004. The FAQ describes the current work as an extension of “On Intelligence.”

BTW, if you think you have heard the name Jeff Hawkins before, you have. Inventor of the Palm Pilot among other things.

Structural Abstractions in Brains and Graphs

Wednesday, May 9th, 2012

Structural Abstractions in Brains and Graphs.

Marko Rodriguez compares the brain to a graph saying (in part):

A graph database is a software system that persists and represents data as a collection of vertices (i.e. nodes, dots) connected to one another by a collection of edges (i.e. links, lines). These databases are optimized for executing a type of process known as a graph traversal. At various levels of abstraction, both the structure and function of a graph yield a striking similarity to neural systems such as the human brain. It is posited that as graph systems scale to encompass more heterogenous data, a multi-level structural understanding can help facilitate the study of graphs and the engineering of graph systems. Finally, neuroscience may foster an appreciation and understanding of the various structural abstractions that exist within the graph.

It is a very suggestive post for thinking about graphs and I commend it to you for reading, close reading.

Picking the Connectome Data Lock

Tuesday, May 1st, 2012

Picking the Connectome Data Lock by Nicole Hemsoth

From the post:

Back in 2005, researchers at Indiana University and Lausanne University simultaneously (yet independently) spawned a concept and pet term that would become the hot topic in neuroscience for the next several years—connectomics.

The concept itself isn’t necessarily new, even thought the use of “connectomics” in popular science circles is relatively so.

….
[video omitted]

A hybrid between the study of genomics (the biological blueprint) and neural networks (the “connect”) this term quickly caught on, including with large organizations like the National Institutes of Health (NIH) and its Human Connectome Project.

For instance, the NIH is in the midst of a five-year effort (starting in 2009) to map the neural pathways that underlie human brain function. The purpose is to acquire and share data about the structural and functional connectivity of the human brain to advance imaging and analysis capabilities and make strides in understanding brain circuitry and associated disorders.

[images omitted]

And talk about data… just to reconstruct the neural and synaptic connections in a mouse retina and primary visual cortex involved a 12 TB data set (which incidentally is now available to all at the Open Connectome Project).

Mapping the connectome requires a complete mapping process of the neural systems on a neuron-by-neuron basis, a task that requires accounting for billions of neurons, at least for most larger, complex mammals. According to Open Connectome Project, the human cerebral cortex alone contains something in the neighborhood of 1010 neurons linked by 1014 synaptic connections.

That number is a bit difficult to digest without context, so how about this: the number of base-pairs in a human genome is 109.

I didn’t want anyone to feel I was neglecting the “big data” side of things, although 12 TB of data will only be “big data” for your home computer. ;-)

Moreover, Sebastian Seung, Professor of Computational Neuroscience at MIT and author of the book, Connectome, is quoted as speculating that memories may be represented in the patterns of connections between neurons. Which sounds familiar to anyone who has heard Steve Newcomb talk about the subjects that are implicit in associations.

I wonder if it is possible to represent a summation of the connectome, much in the same way that we accept lower resolution images for some purposes? So that the task isn’t a one-to-one representation of the connectome, which would be a connectome itself (a map equivalent to the territory itself is the territory, one of those philosophy things).

That’s a nice data structure/information theory problem that would not require dimming the lights in your neighborhood when your system boots up. At least until you wanted to run a simulation. ;-)

If you are interested in a game to make discoveries about the neural structure of the retina, see: http://www.eyewire.org/.

Data mining opens the door to predictive neuroscience (Google Hazing Rituals)

Tuesday, April 17th, 2012

Data mining opens the door to predictive neuroscience

From the post:

Ecole Polytechnique Fédérale de Lausanne (EPFL) researchers have discovered rules that relate the genes that a neuron switches on and off to the shape of that neuron, its electrical properties, and its location in the brain.

The discovery, using state-of-the-art computational tools, increases the likelihood that it will be possible to predict much of the fundamental structure and function of the brain without having to measure every aspect of it.

That in turn makes modeling the brain in silico — the goal of the proposed Human Brain Project — a more realistic, less Herculean, prospect.

The fulcrum of predictive analytics is finding the “basis” for prediction and within what measurement of error.

Curious how that would work in an employment situation?

Rather than Google’s intellectual hazing rituals, project a thirty-minute questionnaire on Google hires against their evaluations at six-month intervals. Give prospective hires the same questionnaire and then “up” or “down” decisions on hiring. Likely to be as accurate as the current rituals.

Announcing Google-hosted workshop videos from NIPS 2011

Wednesday, February 29th, 2012

Announcing Google-hosted workshop videos from NIPS 2011 by John Blitzer and Douglas Eck.

From the post:

At the 25th Neural Information Processing Systems (NIPS) conference in Granada, Spain last December, we engaged in dialogue with a diverse population of neuroscientists, cognitive scientists, statistical learning theorists, and machine learning researchers. More than twenty Googlers participated in an intensive single-track program of talks, nightly poster sessions and a workshop weekend in the Spanish Sierra Nevada mountains. Check out the NIPS 2011 blog post for full information on Google at NIPS.

In conjunction with our technical involvement and gold sponsorship of NIPS, we recorded the five workshops that Googlers helped to organize on various topics from big learning to music. We’re now pleased to provide access to these rich workshop experiences to the wider technical community.

Watch videos of Googler-led workshops on the YouTube Tech Talks Channel:

Not to mention several other videos you will find at the original post.

Suspect everyone will find something they will enjoy!

Comments on any of these that you find particularly useful?

A Well-Woven Study of Graphs, Brains, and Gremlins

Friday, February 24th, 2012

A Well-Woven Study of Graphs, Brains, and Gremlins by Marko Rodriguez.

From the post:

What do graphs and brains have in common? First, they both share a relatively similar structure: Vertices/neurons are connected to each other by edges/axons. Second, they both share a similar process: traversers/action potentials propagate to effect some computation that is a function of the topology of the structure. If there exists a mapping between two domains, then it is possible to apply the processes of one domain (the brain) to the structure of the other (the graph). The purpose of this post is to explore the application of neural algorithms to graph systems.

Entertaining and informative post by Marko Rodriguez comparing graphs, brains and the graph query language Gremlin.

I agree with Marko on the potential of graphs but am less certain than I read him to be on how well we understand the brain. Both the brain and graphs have many dark areas yet to be explored. As we shine new light on one place, more unknown places are just beyond the reach of our light.

Clojure and XNAT: Introduction

Saturday, February 4th, 2012

Clojure and XNAT: Introduction

Over the last two years, I’ve been using Clojure quite a bit for managing, testing, and exploratory development in XNAT. Clojure is a new member of the Lisp family of languages that runs in the Java Virtual Machine. Two features of Clojure that I’ve found particularly useful are seamless Java interoperability and good support for interactive development.

“Interactive development” is a term that may need some explanation: With many languages — Java, C, and C++ come to mind — you write your code, compile it, and then run your program to test. Most Lisps, including Clojure, have a different model: you start the environment, write some code, test a function, make changes, and rerun your test with the new code. Any state necessary for the test stays in memory, so each write/compile/test iteration is fast. Developing in Clojure feels a lot like running an interpreted environment like Matlab, Mathematica, or R, but Clojure is a general-purpose language that compiles to JVM bytecode, with performance comparable to plain old Java.

One problem that comes up again and again on the XNAT discussion group and in our local XNAT support is that received DICOM files land in the unassigned prearchive rather than the intended project. Usually when this happens, there’s a custom rule for project identification where the regular expression doesn’t quite match what’s in the DICOM headers. Regular expressions are a wonderfully concise way of representing text patterns, but this sentence is equally true if you replace “wonderfully concise” with “maddeningly cryptic.”

Interesting “introduction” that focuses on regular expressions.

If you don’t know XNAT (I didn’t):

XNAT is an open source imaging informatics platform, developed by the Neuroinformatics Research Group at Washington University. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. Thanks to its extensibility, XNAT can be used to support a wide range of imaging-based projects.

Important neuroinformatics project based at Washington University, which has a history of very successful public technology projects.

Never hurts to learn more about any informatics project, particularly one in the medical sciences. With an introduction to Clojure as well, what more could you want?