Showing posts with label lectures-YouTube. Show all posts
Showing posts with label lectures-YouTube. Show all posts

July 31, 2020

Hybrid Models and Representations, latest developments

Our research group Representational Brains and Phenotypes has recently been doing a lot of work in the area of embodied nervous systems simulation. Our go-to model over the past year and a half [1] has been the Braitenberg Vehicle (BV), which makes explicit the relationships between interactions with the environment, a neuronal network, and behavior. In the recently open-sourced Meta-Brain Models initiative, we are looking beyond the highly-limited representational framework of the BV by creating hybrid models that combine Vehicles with a representation-rich model (one that specifies symbolic and semantic properties).  

Representational Brains and Phenotypes website. Click to enlarge.

A few weeks ago, members of our research group presented on this topic at the DevoNN (virtual) workshop. Our paper and presentation "Developmental Embodied Agents as Meta-brain Models" introduced the Meta-brain concept to a wider audience, which in this case coupled a developmental Braitenberg Vehicles (dBV) and Contextual Geometric Sturctures (CGS) [2,3]. dBV and CGS are coupled as layers that interact in ways that resemble central nervous systems [4]. Other model combinations are possible, but must conform to the representation-free/representation-rich layering.

 
DevoNN logo and the layered representations approach. Click to enlarge.

This has the potential to leverage not only embodied aspects of intelligent behavior, but its symbolic aspects of as well. There are also opportunities to expand our layered representations in the direction of growth, form, and analogues of biological plasticity [5]. DevoNN was part of Artificial Life 2020, which was in itself a great virtual conference experience. Everything from digital evolution to robotics, and from computational social science to adaptive systems. 


While our extended abstract is not in the Proceedings, I was also able to given a lightning talk on the OpenWorm approach to virtual organisms. 

OpenWorm lightning talk. Click to enlarge.


NOTES:
[1] Check out our Saturday Morning NeuroSim research meetings on YouTube. Contact the Orthogonal Research and Education Lab if you would like to join in!

[2] Dvoretskii, S., Gong, Z., Gupta, A., Parent, J., and Alicea, B. Braitenberg Vehicles as Developmental Neurosimulation. arXiv, 2003.07689. doi:10.13140/RG.2.2.31149.23526.

[3] Alicea, B. Contextual Geometric Structures: modeling the fundamental components of cultural behavior. Proceedings of Artificial Life, 13, 147-154.

[4] examples include the relationship between the Thalamus and Neocortex of Mammals. For functional and evolutionary context, see: Karten H.J. (2015). Vertebrate brains and evolutionary connectomics: on the origins of the mammalian "neocortex". Philosophical Transactions of the Royal Society B, 370, 20150060

[5] this recent paper is the subject of a presentation at the Dynamics Days Digital conference, but is providing some inspiration for further development towards AI innateness: Alicea, B. (2020). Developmental Incongruity as a Dynamical Representation of Heterochrony. ResearchGate, doi:10. 13140/RG.2.2.17401.08807/1

March 11, 2020

Silver Linings of COVID-19

PLoS headquarters when most of its staff is working remotely (click to enlarge).

A Brady Bunch pun on remote work from our friends at Numenta (click to enlarge).

This potentially tasteless title brings to mind the positive elements of canceling classes, academic conferences, and workplace meetings: the ability to do these activities virtually. Among my current projects, I am involved in a number of working groups that are entirely virtual. These group utilize Zoom and Google Meet to give talks and hold meetings, with Github, Google Docs, and a host of other tools to manage contributions and research products (papers, talks, social media posts). This might be called the "Zoom/Slack" paradigm. Below is a Twitter thread from a Sloan Foundation program officer that asks for thoughts on alternatives to this standard.


In 2014, I posted on a concept called a theory hackathon, which was held as a hybrid physical and virtual event. The idea is to define and work on problems that are best solved in teams where not all members can meet live. But online meetings are evolving beyond awkward encounters and technical glitches. Often, live physical meetings are meant to cement social ties. Indeed, below is an informal survey that asks this very question.


In general, live physical conferences seem to be useful for social connection. Revisiting the tweet from Josh Greenberg, perhaps what is needed aside from virtual meeting spaces and file exchange/ chat functionality is a frictionless social platform. This could be conventional social media, or more likely a virtual reality platform integrated with live video/version controlled file exchange/chat capabilities.

Virtual meetings and virtual work are not without their own rhythm and customs. Aside from the potential for social disconnection, it also poses a challenge for personal habituation and ultimately productivity. Below is a link to a Twitter thread that gives tips for meeting virtually for people who are unaccustomed to doing so.

Online meeting tips from Mozilla Open Leaders (click to enlarge).

Carpentries-style tips for synchronous online meetings (click to enlarge).

There are also tips for working from home more generally. As with virtual meetings, capacity to work remotely has been accelerated in the age of social media [1]. The link below gives tips about working from home as an adjustment from working in a large office or public place. Generally, virtual work does require a change in expectations, from dealing with technical glitches to dealing with gaps in social presence [2].

Tips on adjusting to working at home (click to enlarge).

Well-being while working from home (download) (click to enlarge).

Draft workbook on how to host an online conference (click to enlarge).

Online conference are more than simply scaling up virtual meetings. There is a method to conducting and organizing online conferences [3], and there are a number of options regarding the medium. Returning to the issue of greater social connectivity in virtual meeting, one solution is to hold the conference in a virtual world such as Second Life. In this type of meeting, you are able to meet other people as avatars, and even interact with the venue itself. Below are two examples of my experiences with Second Life academic events in the past, one being a continuing lecture series called Embryo Physics, and the other a conference called Simulation and Second Life.


Tour of the Embryo Physics Course @ Silver Bog, Second Life (click to enlarge).


My avatar at the Simulation and Second Life conference, 2007 (click to enlarge).

As a bonus, there is a new agent-based model of COVID-19 transmission created by Paul Smaldino and implemented in NetLogo. This model demonstrates the efficacy of social distancing (hence the resurgent interest in working virtually).

Discussion of COVID-19 transmission model as a Twitter thread (click to enlarge).

Be sure to also check out the Living Computation Foundation's "Pandemic in a Box"! Click to enlarge.


NOTES:
[1] Williams, A. (2017). How the Rise of Social Media Fostered a Culture of Remote Working. Social Media Week, April 14.

[2] Oh, C.S., Bailenson, J.N., and Welch, G.F. (2018). A Systematic Review of Social Presence: Definition, Antecedents, and Implications. Frontiers in Robotics and AI, doi:10.3389/frobt.2018. 00114.

[3] Reshef, O., Aharonovich, I., Armani, A., Gigan, S., Grange, R., Kats, M.A., Sapienza, R. (2020). How to organize an online conference. arXiv, 2003.03219.

October 30, 2019

Pre-trained Models for Developmental Biology

Authors: Bradly Alicea, Richard Gordon, Abraham Kohrmann, Jesse Parent, Vinay Varma
This content is cross-posted to The Node Developmental Biology blog. 


Our virtual discussion group (DevoWormML) has been exploring a number of topics related to the use of pre-trained models in machine learning (specifically deep learning). Pre-trained models such as GPT-2 [1], pix2pix [2], and OpenPose [3] are used for analyzing many specialized types of data (linguistics, image to image translation, and human body features, respectively) and have a number of potential uses for the analysis of biological data in particular. It may be challenging to find large, rich, and specific datasets for training a more general model. This is often the case in the fields of Bioinformatics or Medical Image analysis. Data acquisition in such fields is often restricted due to the following factors:

* privacy restrictions inhibit public access to personal information, and may impose limits on data use.

* a lack of labels and effective metadata for  describing cases, variables, and context.

* missing data points, which require a strategy to normalize and can make the input data useless.

We can use these pre-trained models to extract a general description of classes and features without requiring a prohibitive amount of training data. We estimate that the amount of required training data may be reduced by an order of magnitude. To get this advantage, pre-trained models must be suitable to the type of input data. There are a number of models specialized for language processing and general use, but options are fewer within the unique feature space of developmental biology, in particular. In this post, we will propose that developmental biology requires a specialized pre-trained model. 


This vision for a developmental biology-specific pre-trained model would be specialized for image data. Whereas molecular data might be better served with existing models specialized for linguistic- and physics-based models, we seek to address several features of developmental biology that might be underfit using current models:

* cell division and differentiation events.

* features demonstrating the relationship between growth and motion.

* mapping between spatial and temporal context.

Successful application of pre-trained models is contingent to our research problem. Most existing pre-trained models operate on two-dimensional data, while data types such as medical images are three-dimensional. A study by Raghu et.al [4] suggests techniques specified by pre-trained models (such as transfer learning by the ImageNet model) applied to a data set of medical images provides little benefit to performance. In this case, performance can be improved using  data augmentation techniques. Data Augmentation, such as  adding versions of the images that have undergone transformations such as magnification, translation, rotation, or shearing, can be used to add variability of our data and improve the generalizability of a given model.


One aspect of pre-trained models we would like to keep in mind is that models are not perfect representations of  the phenomenology we want to study. Models can be useful, but are often not completely accurate. A model of the embryo, for example, might be based on the mean behavior of the phenomenology. Transitional states [5], far-from-equilibrium behaviors [6], and rare events are not well-suited to such a model. By contrast, a generative model that considers many of these features might generally underfit the mean behavior. We will revisit this distinction in the context of “blobs” and “symbols”, but for now, it appears that models are expected to be both imperfect and incomplete.

The inherent imperfection of models is both good and bad news for our pursuit. On the one hand, specialized models cannot be too specific, lest they overfit some aspects of development but not others. Conversely, highly generalized models assume that there are universal features that transcend all types of systems, from physical to social, and from artificial to natural. One example of this is found in complex network models, widely used to represent everything from proteomes to brains to societies. In their general form, complex network models are not customized for specific problems, relying instead on the node and edge formalism to represent interactions between discrete units. But this also requires that the biological system be represented in a specific way to enforce the general rules of the model. For example, a neural network’s focus on connectivity requires representations of a nervous system to be simplified down to nodes and arcs. As opposed to universality, particularism is an approach that favors the particular features of a given system, and does not require an ill-suited representation of the data. Going back to the complex networks example, there are specialized models such as multi-level networks and hybrid models (dynamical systems and complex networks) that solves the problem of universal assumptions.

Another aspect of pre-trained models is in balancing the amount of training data needed to produce an improvement in performance. How much training data can we save by applying a pre-trained model to our data set? We can reformulate this question more specifically to match our specific phenomenon and research interests. To put this in concrete terms, let us consider a hypothetical set of biological images. These images can represent discrete points in developmental time, or a range of biological diversity. Now let us suppose a developmental phenotype for which we want to extract multiple features. What features might be of interest, and are those features immediately obvious? 

In the DevoWorm group (where we mostly deal with embryogenetic data), we have approached this in two ways. The first is to model the embryo as a mass of cells, so that the major features of interest are the shape, size, and position of cells in an expanding and shifting whole. Last summer, we worked on applying deep learning to

* Caenorhabditis elegans embryogenesis. Github: https://github.com/devoworm/GSOC-2019.

* colonies of the diatom Bacillaria paradoxa. Github: https://github.com/devoworm/Digital-Bacillaria.

While these models were effective for discovering discrete structural units (cells, filaments), they were not as effective at directly modeling movement, currents, or transformational processes. The second way we have approached this is to model the process of cell division and differentiation as a spatial and discrete temporal process. This includes the application of representational models such as game theory [7] and cellular automata [8]. This allows us to identify more subtle features that are not directly observable in the phenotype, but are less useful for predicting specific events or defining a distinct feature space. 

Our model must be capable of modeling multiple structural features concurrently, but also sensitive to scenarios where single sets of attributes might yield more information. Ideally, we desire a training dataset that perfectly balances “biologically-typical” motion and transformations with clearly masked shapes representing cells and other phenotypic structures. Generally speaking, the greater degree of natural variation in the training dataset, the more robust the pre-trained model will turn out to be. More robust models will generally be easier to use during the testing phase, and result in a reduction in the need for subsequent training. 


Finally, specialized pre-trained models bring up the issue of how to balance rival strategies for analyzing complex processes and data features. Conventional artificial intelligence techniques have relied on a representation which relies on the manipulation of symbols or a symbolic layer that results from the transformation of raw data to a mental framework. By contrast, modern machine learning methods rely on data to build a series of relationships that inform a classificatory system. While a combination of these two strategies might seem obvious, it is by no means a simple matter of implementation [9]. The notion of “blobs” (data) versus “symbols” (representations) draws on the current debate related to data-intensive representations versus formal (innate) representations [10-12], which demonstrates the timeliness of our efforts. Balancing these competing strategies in a pre-trained model allows us to more easily bring expert knowledge or complementary data (e.g. gene expression data in an analysis of embryonic phenotypes) to bear.

We will be exploring the details of pre-trained models in future discussions and meetings of the DevoWormML group. Please feel free to join us on Wednesdays at 1pm UTC at https://tiny.cc/DevoWorm or find us on Github (https://github.com/devoworm/DW-ML) if you are interested in discussing this further. You can also view our previous discussions on the DevoWorm YouTube channel, DevoWormML playlist (https://bit.ly/2Ni7Fs2).

References:
[1] Radford, A., Wu, J., Child, R., Luan, D., Amodei, D., and Sutskever, I. (2019). Language Models are Unsupervised Multitask Learners. OpenAI, https://d4mucfpksywv.cloudfront.net/better-language-models/language_models_are_unsupervised_multitask_learners.pdf.

[2] Isola, P., Zhu, J-Y., Zhou, T., Efros, A.A. (2017). Image-to-Image Translation with Conditional Adversarial Nets. Proceedings of Conference on Computer Vision and Pattern Recognition (CVPR).

[3] Cao, Z., Hidalgo, G., Simon, T., Wei, S-E., and Sheikh, Y. (2018). OpenPose: Realtime Multi-Person 2D Pose Estimation using Part Affinity Fields. arXiv, 1812.08008.

[4] Raghu, M., Zhang, C., Kleinberg, J.M., and Bengio, S. (2019). Transfusion: Understanding Transfer Learning for Medical Imaging. arXiv, 1902.07208.

[5] Antolovic, V., Lenn, T., Miermont, A., Chubb, J.R. (2019). Transition state dynamics during a stochastic fate choice. Development, 146, dev173740. doi:10.1242/dev.173740.

[6] Goldenfeld, N. and Woese, C. (2011). Life is Physics: Evolution as a Collective Phenomenon Far From Equilibrium. Annual Review of Condensed Matter Physics, 2, 375-399. doi:10.1146/annurev-conmatphys-062910-140509.

[7] Stone, R., Portegys, T., Mikhailovsky, G., and Alicea, B. (2018). Origins of the Embryo: Self-organization through cybernetic regulation. Biosystems, 173, 73-82. doi:10.1016/j.biosystems.2018.08.005.

[8] Portegys, T., Pascualy, G., Gordon, R., McGrew, S., and Alicea, B. (2016). Morphozoic: cellular automata with nested neighborhoods as a metamorphic representation of morphogenesis. In “Multi-Agent Based Simulations Applied to Biological and Environmental Systems“. Chapter 3 in "Multi-Agent-Based Simulations Applied to Biological and Environmental Systems", IGI Global.

[9] Garnelo, M. and Shanahan, M. (2019). Reconciling deep learning with symbolic artificial intelligence: representing objects and relations. Current Opinion in Behavioral Sciences, 29, 17–23.

[10] Zador, A.M. (2019). A critique of pure learning and what artificial neural networks can learn from animal brains. Nature Communications, 10, 3770.

[11] Brooks, R.A. (1991). Intelligence without representation. Artificial Intelligence, 47, 139–159.

[12] Marcus, G. (2018). Innateness, AlphaZero, and Artificial Intelligence. arXiv, 1801.05667.

Resources:
* Model Zoo: pre-trained models for various platforms: https://modelzoo.co/

* DevoZoo: developmental data for model training and analysis: https://devoworm.github.io/


* Popular papers on medical image segmentation along with code:  https://paperswithcode.com/area/medical/medical-image-segmentation




August 27, 2018

Final Google Summer of Code presentations are live!

The final presentation for Google Summer of Code students in the Representational Brains and Phenotypes (Sam and Jim) and DevoWorm (Arnab) groups are now available! The summer went quite well: skills were taught, lessons were imparted, and computing projects were advanced. Here are the links to each project submission and summary video.


Sam's final talk (YouTube) and project repository (Github).


Arnab's final talk (YouTube) and project repository (Github).


Cheng-Hsun (Jim)'s final talk (YouTube) and project repo (Github).

Sam and Jim worked to advance the Contextual Geometric Structures framework (link 1, link 2) using different approaches. Both projects involved a mix of evolutionary algorithms, computational linguistics, hybrid modeling, and representational AI. The Google n-gram database was used to provide a source of training data.

Arnab worked on an XML framework for organizing embryo data at the cellular level. This not only provides the DevoWorm group with a link to more specific XML and simulation frameworks, but also moves us towards network-based representational models of the embryo.

September 11, 2017

This Concludes This Version of Google Summer of Code


I am happy to announce that the DevoWorm group's first Google Summer of Code student has successfully completed his project! Congrats to Siddharth Yadav from IIT-New Delhi, who completed his project "Image Processing with ImageJ (segmentation of high-resolution images)".

Our intrepid student intern

His project completion video is located on the DevoWorm YouTube channel. This serves as a counterpart to his "Hello World" video at the beginning of the project. The official project repo is located here. Not only did Siddharth contribute to the data science efforts of DevoWorm but also contributed to the OpenWorm Foundation's public relations committee.

Screenshot from project completion video

As you will see from the video, a successful project proceeds by organizing work around a timeline, and then modifying that timeline as roeadblocks and practical considerations are taken into account. This approach resulted in a tool that can be used by a diverse research community immediately for data extraction, or build upon in the form of future projects. 

In terms of general advice for future students, communicate potential problems early and often. If you get hung up on a problem, put it aside for awhile and work on another part of the project. As a mentor, I encourage students to follow up on methods and areas of research that is most successful in their hands [1]. In this way, students can find and build upon their strengths, while also achieving some level of immediate success. 


NOTES:
[1] This seems like a good place to plug the Orthogonal Research Lab's Open Career Development project. In particular, check out our laboratory contribution philosophy.

June 5, 2017

"Hello World", project version

The DevoWorm group has two new students that will be working over this summer on topics in computational embryogenesis. To begin their projects, I have asked each student to prepare a short presentation based on their original proposal, which serves as a variant of the traditional "Hello World" program. We will then compare this talk with one they will give at the end of the summer to evaluate their learning and accomplishment trajectory.

One student (Siddharth Yadav, who is a current Google Summer of Code student) is interested in pursuing work in computer vision, machine learning, and data science, while the other (Josh Desmond, a Google Summer of Code applicant) is interested in pursuing work in computational biology and modeling/simulation. You may view their presentations (about 20 minutes each) below, and follow along with their progress at the DevoWorm Github repository [1].

Siddharth Yadav's project talk  YouTube

Josh Desmond's project talk  YouTube

NOTES:
[1] Siddharth's project repo (GSoC 2017) and Josh's project repo (CC3D-local).

December 1, 2016

Searching for Food and Better Data Science at the Same Time

Two presentations to announce, both of which are happening live on 12/2. The first is the latest OpenWorm Journal Club, happening via YouTube live stream. The title is "The Search For Food", and is a survey of a recently-published paper on food search behaviors in C. elegans [1].


While the live-stream will be available in near-term perpetuity [2] on YouTube, the talk will begin at 12:45 EST [3]. The abstract is here:
Random search is a behavioral strategy used by organisms from bacteria to humans to locate food that is randomly distributed and undetectable at a distance. We investigated this behavior in the nematode Caenorhabditis elegans, an organism with a small, well-described nervous system. Here we formulate a mathematical model of random search abstracted from the C. elegans connectome and fit to a large-scale kinematic analysis of C. elegans behavior at submicron resolution. The model predicts behavioral effects of neuronal ablations and genetic perturbations, as well as unexpected aspects of wild type behavior. The predictive success of the model indicates that random search in C. elegans can be understood in terms of a neuronal flip-flop circuit involving reciprocal inhibition between two populations of stochastic neurons. Our findings establish a unified theoretical framework for understanding C. elegans locomotion and a testable neuronal model of random search that can be applied to other organisms.
The other presentation is one that I will give at the Champaign-Urbana Data Science Users' Group. This will be a bit more informal (20 minutes long), and part of the monthly meeting. The meeting will be live (12 noon CST) at the Enterprise Works building in the University Research Park. The archived slides are located here. The title is "Open Data Science and Theory", and the abstract is here:
Over the past few years, I have been working to develop a way to use secondary data and Open Science practices and standards for the purpose of establishing new systems-level discoveries as well as confirming theoretical propositions. While much of this work has been done in the field of comparative biology, many of the things I will be highlighting will apply to other disciplines. Of particular interest is in how the merger of data science and Open Science principles will facilitate interdisciplinary science.

NOTES:
[1] Subtitle: To boldly go where no worm has gone before. Yup, Star Trek pun. Full reference: Roberts, W. et.al   A stochastic neuronal model predicts random search behaviors at multiple spatial scales in C. elegans. eLife, 2016; 5: e12572.

[2] for as long as YouTube exists.

[3] Click here for UTC conversion.

August 1, 2013

Universal Patterns and Origins of Innovation

Here are two recent posts on innovation originally featured on my micro-blog, Tumbld Thoughts. Each post reviews a comtemporary book on the patterns inherent in the innovation process. The first (I) features several different archetypes, while the second (II) features the kinds of environments that are key for maximizing innovation.

I. Universal Patterns of Innovation


Interesting book I ran across recently on the universal "patterns" that seem to underlie innovation and invention [1]. While the book is about much more than this, one core theme is the practice of discovery and what we might learn from looking at the practices of different inventors. 


One way to take advantage of these patterns is to learn the rules of innovation. These rules are defined as the underlying talent, knowledge, and allocation of resources neccessary for innovation. Another lesson learned is to recognize there are at least three principles (better understood as personal styles) that define great inventions. These are:

1. Serendipity, or being able to exploit chance discoveries. William Shockley's work with semiconductors (leading to the transistor) best exemplifies this principle.

2. Proof-of-principle, or the 99% perspiration, 1% inspiration approach. Thomas Edison's work on the incandescent lightbulb best exemplifies this principle.

3. Inspired Exertion, or the greater than 1% inspiration approach. Jeff Hawkins' work in developing the Palm mobile computer best exemplifies this principle.

The third lesson that leads us to innovation is to study the designs of great innovators. See these Synthetic Daisies post from 2009 and 2011 on my own (evolving) thoughts on this topic.


II. The Origins of Innovation


Here is a link to a sped-up whiteboard animation video featuring content from Steven Johnson's book "Where Good Ideas Come From: the natural history of innovation" [3]. His main thesis is that innovation tends to occur in connected spaces such as cities, reefs, and webs [4]. As mentioned at the end of the video: "chance favors the connected mind".



Innovation also occurs as a process. One of these processes is called the slow hunch. The example Johnson gives for this is Tim Berners Lee and invention of the internet. At first, the proto-internet was conceived as a way to organize personal data. The next stage involved extending the connectivity aspect to interpersonal tangles. Finally, a version of the internet we all recognize came to fruition as a dynamic set of interconnected documents and links. This process of successive iteration took years to achieve.


NOTES:

[1] Alesso, H.P., Smith, C., and Burke, J.   Connections: Patterns of Discovery. Wiley/IEEE Press (2008).

[2]  Alicea, B.   Innovation Class/Book. Synthetic Daisies blog, June 30 (2009) AND Alicea, B.   In praise of repetition? Synthetic Daisies blog, April 11 (2011).

[3] Also see his TED talk on the book. For more sped-up whiteboard animations on innovation and the process of invention, please see: Alicea, B.   New Directions in Making Innovation Pay. Synthetic Daisies blog, June 1 (2013).

[4] The city is a literal city (particularly the mixing that occurs on city streets), the reef is a space that metaphorically resembles a coral reef (diverse individuals visit to feed and mingle), and the web is a network (made explicit in the internet).

March 3, 2013

On worms, cities, brains, and behavior

These features are being cross-posted from my micro-blog, Tumbld Thoughts.



Here is a link to an excellent review in the blog Neuroanthropology [1] on recent work by Cornelia Bargmann [2] using C. elegans [3] as a model for uncovering the "building blocks" of sensorimotor behavior -- and its relationship with experience [4]. This work advances the idea that neuropeptides (e.g. oxytocin and vasopressin) organize behavioral complexity in a manner similar to how Hox genes organize phenotypic development [5].


This is a brand new paper (as of 2/28/2013) from the Nicolelis Lab at Duke on brain-to-brain interfaces (BTBI). BTBIs [6] are similar to BCI/BMI technology [7], but instead of neural signals driving a computer interface or machine, they are used to stimulate the brain of a conspecific (in this case, another rat on another continent [8], as shown in above image and described in the paper).


Finally, here is an image and linkfest related to the pre-release hype surrounding SimCity5. Unique features of the updated release include the use of tilt-shift photography and the Glassbox game engine. The Sims (humanoid agents) are also a bit more human-like.

So to provide context, here are four Wired Science blog posts by Sam Arbesman. The first post [9] is the connection between LEGO and SimCity as modeling tools (e.g. modeling cities at small scales). The second and third posts [10, 11] involve understanding the scale of cities in the context of their importance and how Kolmogorov complexity [12] can characterize this scalar relationship.

The fourth post describes a paper by Mark Changizi [13] in which the number and frequency of distinct types of LEGO piece contribute to the overall complexity of objects being built [14]. These mathematical principles (known as scaling laws) can be applied to understanding both the top-down design and bottom-up emergent complexity of cities.

NOTES:

[1] Lende, D.   Cornelia Bargmann and the Building Blocks of Behavior. Neuroanthropology blog. February 20 (2013).


Also see an article from 2012, in which she weighs in on the idea of building a connectome: Bargmann, C.I.   Beyond the connectome: how neuromodulators shape neural circuits. Bioessays, 34(6), 458-465 (2012). 

[3] C.elegans has a complexity of just 959 cells (the brain has 302 cells). This makes this nematode a potentially tractable model for whole-organism understanding and emulation of simple behaviors (but see article [2] for difficulties in achieving this). 

See the following review article for more information: Ankeny, R.A.   The natural history of Caenorhabditis elegans research. Nature Reviews Genetics, 2(6), 474-479 (2001).

[4] Hall, S.S.   As the worm turns. Nature News. February 20 (2013).

[5] For more information on how neuropeptides may organize social and other behaviors, please see the following review in which neuropeptides are called the "dark matter" of social neuroscience: Insel, T.R.   The Challenge of Translation in Social Neuroscience: a review of oxytocin, vasopressin, and affiliative behavior. Neuron, 65(6), 768–779 (2010).

[6] Paper: Vieira, M-P., Lebedev, M., Kunicki, C., Wang, J., and Nicolelis, M.A.L.   A brain-to-brain interface for real-time sharing of sensorimotor information. Scientific Reports, 3, 1319 (2013).

In addition, here is a video of the experiment and an article in The Scientist.


[8] Rat-to-rat communication (North America to South America and back), referred to in the paper as a "rat dyad". Map courtesy Google Earth.

[9] Arbesman, S.   LEGO Meets SimCity. Wired Science, February 20 (2013).

[10] Arbesman, S.   The Scale and Context of Cities. Wired Science, March 12 (2012).

[11] Arbesman, S.   The Complexity of Cities and SimCity. Wired Science, June 14 (2012).

[12] Hutter, M.   Algorithmic Complexity. Scholarpedia, 3(1), 2573 (2008).

[13] Changizi, M.A., McDannald, M.A., and Widders, D.   Scaling of differentiation in networks: nervous systems, organisms, ant colonies, ecosystems, businesses, universities, cities, electronic circuits, and Legos. Journal of Theoretical Biology, 218(2), 215-237 (2002).

[14] Arbesman, S.   The Mathematics of Lego. Wired Science, January 6 (2012).

February 1, 2013

Projective Models: a new explanatory paradigm


Predictive models are well-known, and have been deployed in a number of high-profile technologies. From IBM’s Watson [1] to the development of autonomous aircraft [2], predictive models use a statistical basis for making inferences about future events. Theoretical models of the brain suggest that the brain is a prediction machine, inferring the world from past events [3]. Yet how intelligent can a statistical model be, especially with regard to complex events?  What is needed (and what already exists in the world of futurism) is something called a projective model. Projective models are predictions about the future, but not solely based on past events. Unlike predictive models, projective models are largely based on mental models. They might also be called "blue sky" models [4]. However, they share attributes that might help scientists and futurists build better models of future events.

The success of projective models depends on a tension between uniformity and empirically-driven outliers. Every January 1, lists of predictions for the upcoming year are unveiled. There are elements of uniformity in that historical trends are continued. However, improper predictions of economic collapse and failure to predict deaths and accidents demonstrate the difficulties of properly incorporating outliers. While outlier incorporation is a feature of predictive models, they are a particularly important component of projective models, and a critical component of getting projective statements correct.

I lived in this year. I'm not sure this came to fruition.

But, this could be the way the world works in the 25th century.

In order to make a coherent statement about the future, projective models (as well as predictive models) must assume that trends represent some kind of norm. In projective models, normative parameters are not based on averaging, but on popular heuristics for making a projection. The three most common of these are: 1) assume things stay the same, 2) catastrophe (or comeuppance) is coming soon, and 3) things will decrease/increase linearly. Much like curve-fitting exercises that are part of predictive modeling, projective model heuristics make assumptions about the behavior of the system in question. Likewise, the existence of inherently unpredictable events (such as black swans – [5]) affects projective and predictive models alike.

Three different scenarios for projective models: TOP: things stay the same, MIDDLE: constant increase or decrease over time, BOTTOM: big events change everything.

So the first phenomenon that drives reality away from predictions involve data-driven trends from past that do not necessarily lead to trends in the future. We cannot truly know what the future holds, and so must use extrapolation to make such statements. In the case of economic or other model-based projections (generated using traditional predictive model methodologies), improper assumptions can lead to deceptive results [6]. Sometimes, these extrapolations are interpreted as innumeracy [7]. But since they are imprecise statements, they can sometimes be correct. But what else contributes to incorrect projections?

The other phenomenon that drives reality away from predictions is phase change behavior. Currently, there is a debate as to whether or not the era of economic growth is over in the developed nations. This involves more than just getting the statistical trend correct. It involves getting the transition from one historical phase (growth interspersed with periods of decline) to another phase (dominant periods of flat growth).

Futurism demonstrates the relatively high failure rate of projective models. A recent Paul Krugman blog article [8.1] mentions Herman Kahn's list of predictions for the Year 2000, circa 1967 [9]. Many of these predictions are incorect, but approximately 26% were fulfilled in one way or another. The reasons for this somewhat low success rate and the nature of fulfilling a prediction have led me to come up with three criteria for judging whether or not a prediction is likely to be wrong, fulfilled, or partially fulfilled on a short or moderate historical timescale [10].

What makes a technological prediction fundamentally incorrect?

I will now introduce three reasons why I think future technological projections are often incorrect. These involve historical and physical factors that are often at odds with human intuition and the conception of a mental model:

1) No technological or historical precedent at the time of prediction. If there is no precedent for world peace, why would you predict it to be so fifty years in the future? The amount of development needed not only to make something a reality but to produce it in a replicable fashion (or at the appropriate economy of scale) will roughly determine the amount of time needed to realize the prediction. A related issue involves historical contingency (sometimes also referred to as "lock-in"). It is often easy to predict gains in an existing technological framework [11]. It is much harder to imagine an entirely new paradigm. The movie "Back to the Future, Part II" features an example of this. The movie, partially set in 2015, not only featured flying cars, but a fax machine in every room of the house.

The subject of [8.1, 8.2] is the self-driving car, which was envisioned in the 1990 version of "Total Recall". Now, of course, the self-driving car is becoming a reality. But consider that many of the component technologies that enable the self-driving car (e.g. linear filter, computer vision, GPS) have been around for a few decades. And related varieties of autonomous robot are in the process of changing the economic and social landscape [8.3]. It is incremental developments along that trajectory that have enabled the self-driving car rather than de novo innovation. This is not to say that de novo innovations do not occur or have an effect on the future. Indeed they do, as the rise is innovations surrounding the internet (e.g. social media, online shopping) demonstrate. However, even here, such innovations are dependent on a trajectory of technological advancement and cultural imagination [12].

2) Prediction requires a relatively high energetic threshold (e.g. flying cars). Why don't we have flying cars yet? Or better yet, why are big predators so rare [13]? The answer, or course, involves the energetic requirements involved. If the energetic requirements for a technology are very high (e.g. warp drive), the less likely they will be conceived or developed without an accompanying source of energy. This has, of course, has been the limiting factor for the development of long-range electric cars. How can ecological and predictive models help us understand why projective models can often fail?

In [13], it is argued that ecological constraints (namely, the big predators' energetic footprint) prevent large animals from becoming too numerous. And so it is with the development of technologies that require a high energy density [14]. As much as I think Moore’s Law analogies are severely overused, one is actually appropriate here. According to Moore’s Law, innovations have been able to make the size of transistors decrease by half linearly over time. However, this trend is now being threatened by a fundamental size limitation. Similarly, there exist fundamental energetic limitations to many technologies, and make advances that require high energy requirement improbable.

How big is too big? Can things be scaled up infinitely? Or are there clear energetic limits to realizing certain technologies?

3) Prediction is on a highly complex system (e.g. diagnosis of disease, cyborgs). In general, technologists are either dismissive of complexity or treat it as a quasi-religious mystery. We know from recent unpleasantness in financial markets that complexity can wreak havoc on predictive models. The effects of complexity on projective models are even more problematic. Sometimes, the system that is supposed to be conquered or created to generate the prediction is much more complex than previously assumed.

One example of this comes from the promises made after the initial draft of the human genome was introduced in 2001 [15]. The sequencing work was done faster than expected, and it was assumed that sequence data could provide the necessary information for a curing most diseases in a short period of time. The tenth anniversary was marked with a NYT article [16] contemplating why a lot of the early predictions either never came to fruition or are slow in coming true. What was not taken into account in these early predictions was the sheer complexity of human physiology and its role in disease.

I woke up and discovered complexity! Examples from social (top) and physical (bottom) systems.

4) The Nostradamus Effect: when projective models go bad? The Nostradamus effect can be defined as a prediction that consists of vague, verbal statement can be easily fit to the empirical world. The Nostradamus effect is essentially the opposite of the traditional scientific method. Generally, scientific inquiry proceeds from empirical observations, which result in a theory. The Nostradamus effect uses vague hypotheses that are then matched to future events.

I remember when I was about 10 years old, I was impressed by Nostradamus' predictions, which I was introduced to by a TV presentation by Orson Wells [17]. This inspired a trip to the local library, where I checked out an abridged version of Nostradamus. What I found was underwhelming: his predictions consist of vague axioms which can be applied to any number of scenarios. In the world of predictive models, such a model would be both noisy and prone to false positives.

"Measuring" the future -- a losing battle? Will being more precise in our projections help or hurt their accuracy?


One way to improve the accuracy of projective models is to work towards a semantically-oriented model based on a hybrid Markovian-Bayesian architecture. This would allow us to approximate the current state of the technological innovation as a series of states, but also takes into account conditional information, which accounts for unexpected events. Of course, we would also have to include a number of variables accounting for technological shifts (sudden and gradual), and their underlying causes. Even this would probably not be sufficient for dealing with unpredictable events, and so would also require a stochastic or chaotic component to generate scenarios consistent with the current limitations of future projections.

Even the most elaborate and efficient of models would most likely only make us marginally better than Nostradamus at projecting future trends. Therefore, a way to merge predictive and projective models in a way that would benefit each would be to acquire long historical (or time-series) datasets in the same way we currently acquire (and hype) "big" data [18]. Such an approach will give us both a quantitative and qualitative appreciation of technological evolution that is sometimes missing from many futurist-type predictions.


NOTES:
[1] “The AI Behind Watson”. AAAI technical paper.

[2] Economist article ("This is Your Ground Pilot Speaking") on autonomous aircraft.

[3] Dayan, P. and Abbott, L.F.  Theoretical Neuroscience. MIT Press (1998). AND Hawkins, J. and Blakeslee, S. On Intelligence. Times Books, New York (2003).

[4] For examples of future projections and how they play out in history, see the following features:

1) IEEE Spectrum. Feature: Life in 2030. Podcasts and Videos.

2) Armstrong, S.  Assessing Kurzweil: the results. Less Wrong blog. January 16. (2013)

3) What 2012 Stuff Will Seem Crazy in 2060? The David Pakman Show, YouTube. January 4 (2013).

[5] Taleb, N.N.  The Black Swan: the impact of the highly improbable. Random House, New York (2010).

Visions of the future that involve utopian or dystopian settings are often based on over-interpreting the effects of these large-scale shifts. Especially in terms of the proposed "comeuppance" scenario, a common science fiction trope involves a dystopian outcome from the extreme development of technology (e.g. "1984", "Animal Farm").

[6] See these Wikipedia pages on Statistical Assumptions and Economic Forecasting. And then read these blog posts on economic projections and weather forecasts:

1) Krugman, P.  The Mostly Solved Deficit Problem. Conscience of a Liberal blog. January 10 (2013).

2) Krugman, P.  Future Inequality, according to the CBO. Conscience of a Liberal blog. December 27 (2012).

3) Robson, D.  How good are the Weather Channel's predictions? Short Sharp Science blog. February 6 (2009).

[7] Seife, C.  Proofiness: the dark arts of mathematical deception. Viking Press, New York (2010).

[8] A series of blog posts on the potential of autonomous intelligence and it's effects on the economy and our society in general. This topic is becoming a popular one -- the following are merely a starting point:

1) Krugman, P.  Look Ma, No (Human) Hands. The Conscience of a Liberal blog, January 25 (2013).

2) Thrun, S.  What we're driving at. Official Google blog. October 9 (2010)

3) Kaminska, I.  The Tech Debate Blasts Off. Towards a Leisure Society blog. December 28 (2012).

[9] re-visited and rated courtesy of Leonard Richardson's Crummy blog. Also see his piece on "The Future: a retrospective" (reflections on the the book "Future Stuff").

[10] My definition of short to moderate historical timescales are on the order of 20 to 200 years. This time window can vary based on both context and the current point in time relative to critical sociohistorical events, cultural change, technological revolutions, etc.

[11] Or perhaps not. A good historical yardstick for this is the book "Future Shock" by Alvin Toffler (first published in 1970). Upon reading it in 2013, is it utopian, dystopian, or accurate (or elements of all three)?
Also, here is a link to a documentary on Future Shock narrated by Orson Wells (from 1972).


[12] For more information, please see the following lecture by David Graeber entitled "On Bureaucratic Technologies and the Future as Dream-Time", which discusses the role of existing bureaucracies (social structures) and cultural imagination in technological innovation.

[13] This paraphrases a title of a book by Paul Colinvaux: "Why are Big Fierce Animals Rare?", Princeton University Press, 1979.

[14] A related problem is the improvement of existing technologies, such as more sustainable energy sources for jet aircraft and rockets. Please see this ASME Knowledgebase entry for more information.

[15] International Human Genome Sequencing Consortium  Initial sequencing and analysis of the human genome. Nature, 409, 860-921 (2001) AND Venter, C. et.al  The sequence of the human genome. Science, 291(5507), 1304-1351 (2001).

[16] A series of New York Times articles associated with the 10th anniversary of the draft full human genome sequence:

1) Pollack, A.  Awaiting the Payoff. NYT, June 14  (2010).

2) Wade, N.  A Decade Later, Genetic Map Yields Few New Cures. NYT, June 12  (2010).

3) Editoral: The Genome, 10 Years Later. NYT, June 20  (2010).

[17] "Nostradamous: the man who saw tomorrow". Narrated by Orson Wells (circa 1981). Watch on Vimeo.

[18] Arbesman, S.  Stop Hyping Big Data and Start Paying Attention to ‘Long Data’. Social Dimension blog, January 29.

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