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

November 30, 2023

OpenWorm Annual Meeting 2023 (DevoWorm update)

It's that time again -- time for the OpenWorm Annual meeting. Below are the slides I presented on progress and the latest activities in the DevoWorm group. If anything looks interesting to you, and you would like to contribute, please let me know. Click on any slide to enlarge.












May 2, 2021

DevoLearn (Open-source) Maintenance and Evangelism

 2021 has been a busy year for the DevoLearn initiative. Not only has Mayukh Deb been busy maintaining and generating new versions of the DevoLearn pre-trained model, but I (Bradly Alicea) has been engaging in technology evangelism to advance awareness and involvement in the initiative.  The DevoLearn pre-trained model software (for C. elegans embryogenesis) is now at version 0.3.0, and has garnered 12 contributors making 165 commits (largely since January 2021). Our involvement in Google Summer of Code has bolstered many of these contributions. While our popularity is currently limited, we are trying to spread the word.

To that end, we have presented two versions of a promotional talk on using DevoLearn for facilitating Computational Developmental Biology research and education. The first presentation (DevoLearn: Engaging learners with Computational Developmental Biology) is a flash talk given to the OSF Education Un-conference on Open Scholarship Practices in Education Research, held in February. The second presentation was a longer (15-minute) presentation to the INCF Assembly (DevoLearn: a platform for open Developmental Data Science, Machine Learning, and Education), held in April.


As for developing the broader platform, Ujjwal Singh and I will be working this Summer to develop algorithms for colony morphogenesis and behavior in the Diatom genus Bacillaria. This will be added to the platform in a manner similar to the DevoLearn pre-trained model. In addition to the software development activities, Mayukh, myself, and Krishna Katyal have been the main contributors to the DevoWorm Onboarding Guide. Looking forward to an exciting future!


Update, 8/19:

All of this work has paid off! From the #devolearn Slack channel (OpenWorm Slack team).



December 18, 2020

Observer-dependent Models @ the Philosopher's Web Cafe

 


I gave a talk called "Observer-dependent Models" to the Philosopher's Web Cafe on December 11. I have made the slides available here, and the recording is here. Thanks to Jesse Parent (Orthogonal Lab Manager) and Charlotte Guo (series host) for hosting. It will be almost like being there (almost). 

The talk involved reviewing and redefining the role of observers in empirical and simulated systems. "Observer" refers mostly to computational agents (agent-based simulation and AI), although many of the ideas introduced here may apply to the analysis of empirical observations (experiments). Here is the abstract:

In many areas of science and philosophy, observers are seen as an integral part of understanding the natural world. Aside from a pedagogical role, observers are seen as less important in computational forms of inquiry. In this talk, I will reconsider a role for the observer in computational models as fully integrated with the agent. perhaps more fundamentally, causal outcomes and system dynamics are seen to be contingent on observers, while empirical observations themselves are dependent upon the actions of observers. As this is an article of faith in some interpretations of quantum mechanics, we extend this to algorithmic systems with a combinatorial solution space. The role for observers in computational and empirical investigations is established superficially using a number of concepts, including cybernetics, embodiment, and perceptual information processing. Then we will be introduced to more concrete examples of observer-oriented computational agents, such as observer-emitter systems and viewpoint networks. Finally, we will discuss how this approach goes beyond constructivism to consider multiple observers, multiple perspectives (relativism), and how they affect the interpretation of results.

There is a lot to follow up on from this talk, including a number of themes to explore within the topic of agent-based observers, with more to come in the new year. 



April 17, 2017

Breaking Out From the Tyranny of the PPT

Player 1 vs. Powerpoint (with a screenshot of the game Breakout). The image itself was made in PowerPoint, but I promise this post will not be recursive nonsense.


By now, you have probably chosen a side in the PowerPoint debate: namely, does it enhance or hinder scholarly communication? I will present both sides of this argument, but not argue to moderation. Rather, I will show that PowerPoint is good (or good to get rid of) only if you define your own style of presentation. In either case, you will need to "break out" of the box containing typical advice for creating PowerPoint presentations.


A number of people have argued (both rhetorically and in practice) that PowerPoint represents an enforced tyrrany on presented information. It forces big ideas into small compartments, defined by slide optimization and bullet points. What follows are a few examples of PowerPoint tyranny, or cases in which the default style of organization imposes constraints on communication and the exchange of ideas. 


A few years ago, Franck Frommer wrote a book on how PowerPoint makes us stupid [1]. Frommer's definition of stupid refers to impovrishing our ability to communicated logical flow, contextual detail, and the confusion of opinion and fact. Supprting this position is Peter Norvig's Gettysburg Address analysis, which suggests that the cognitive style of PowerPoint and its visual gimmickry often obscure rather than enhance the logical flow of a larger idea.


Example slide from the Gettysburg Address as a PowerPoint presentation.


Education might also benefit from breaking away from PowerPoint tradition. In fact, there is an argument to be made that the use of PowerPoint in education reduces course content to an overly-simplified, pre-packaged learning experience [2]. Dr. Chris Waters at Michigan State University has moved to eliminate PowerPoint lectures altogether in his undergraduate Microbiology course. He is instead adapting the existing presentations into a series of chalk talks which are more conducing to communicating scientific ideas. 


Perhaps the failures of PowerPoint are not about varied styles of communication across different domains of knowledge (scientific, business, legal), but more about the relevance of ideas and their overall structure. Relevance theory (Dan Sperber and Deidre Wilson) suggests that are biased according to what seems relevant [3]. Some of this is mediated by the cognition of attentional resources, but there is also an underappreciated role of cultural preferences and constraints. In the realm of science communication, the narrowly-defined relevance of typical PowerPoint design practice might encourage some aspects of scientific practice (science as memorization of facts, still images, simple graphs) at the expense of others (experimentation, data exploration, theory-building). 


The tyrrany of representational orthodoxy, PowerPoint style. On the other hand, this is actually pretty good in terms of available clip art. While perfectly suitable for business-oriented communication (e.g. team-building, simple storytelling), this may or may not be suitable for other domains of knowledge.


So how does one break out from the restrictions of PowerPoint? One way forward is shown by the artistic community's use of PowerPoint as an expressive medium. Like the latter-day explosion of animated .gif art on Tumblr [4], artists have been using PowerPoint to create animations and short videos. Interestingly, the limitations of PowerPoint for representing alternate forms of argumentation does not seem to limit artistic innovation [5]. Perhaps this has to do with the use of symbols rather than the ambiguity of linguistic syntax. 

A more argumentative-based way to approach PowerPoint is to adopt the Lessig Method of presentation [6], which presents ideas in only a few words in a large font. One example of this is Larry Lessig's "Free Culture" lecture, which connects a sequence of court cases and landmark ideas in sparse blocks of text. Whether this solves the ambiguity issue is not clear to me, but does provide a way to simplify without losing information.


The last several talks I have given include a final "Thanks for your Attention" Acknowledgements slide which features a graphic that has something to do with attention (visual illusion and/or obscure reference). This is one such example featuring Marshall McLuhan (e.g. breaking the message out of the medium).

UPDATED (4/23): Here is a presentation to the Association of Computational Heresy by Tom Wildenhain on how to construct a Turing Machine with PowerPoint. While it is a lot of fun, it does bring to mind some more creative uses of PowerPoint.


NOTES:
[1] Frommer, F. (2012). How PowerPoint Makes You Stupid: The Faulty Causality, Sloppy Logic, Decontextualized Data, and Seductive Showmanship That Have Taken Over Our Thinking. New Press, New York.

[2] Ralph, P. (2015). Why universities should get rid of PowerPoint and why they won’t. The Conversation, June 23.

[3] Sperber, D. and Wilson, D. (1995). Relevance: Communication and Cognition. Blackwell Publishers, Oxford, UK.

[4] Alicea, B. (2012). Moving the Still, courtesy of the .gifted. Synthetic Daisies blog, October 19.

[5] Greenberg, A. (2010). The Underground Art of PowerPoint. Forbes, May 11. Some examples of PowerPoint art (converted to YouTube videos) include:

a) "Infiltration" by Jeremiah Lee.

b) "Joiners" by blastoons.


[6] Reynolds, G. (2005). The "Lessig Method of Presentation". Presentation Zen blog, October 7.

February 21, 2017

New Orthogonal Laboratory Methods

Lately I have been incorporating two new tools into my research program's [1] infrastructure. One is a software tool with community support, and the other is a development of my own. 

The first addition is the Jupyter Notebook (sometimes called the iPython Notebook, as it is based on this platform). The Jupyter Notebook allows us to build repositories of methods, notes, code, and data analyses in an integrated manner. Jupyter Notebooks can be rendered in Github, making them freely accessible and distributable. For example, the DevoWorm project already has several notebooks hosted at Github. The long-term goal is to create notebooks for typical research activities, and using them for a host of purposes, from a Wiki-like instructional manual to supplemental materials for publications [2].

Jupyter Notebooks (example)

The other is a pipeline for project management with the goal of increasing participation and success in research. The idea is one that I have been bouncing around in my head based on my involvement with the OpenWorm Foundation community committee and personal experience. This could be a way to encourage more underrepresented and "high-risk" researchers to advance their work [3]. It is based on two exceedingly obvious principles: failure is not a breaking point for any research trajectory, and projects themselves should be defined in a bottom-up fashion (building on previous successes and experiences) [4]. Hopefully, this pipeline works well in implementation.

Building a Research Group Philosophy

UPDATE (2/22): I failed to include a snapshot of the Orthogonal Laboratory Slack team (currently with an n of 1). Slack is fast becoming a popular tool for laboratory management [5, 6], particularly those that are partially or fully virtual.



NOTES:
[1] I am in the process of turning Orthogonal Research into Orthogonal Laboratory. Currently it is a group of one (and a few collaborators). I am currently looking for an academic home, so putting the tools needed to scale up is worth the investment in time. More on this initiative later.

[2] Brown, C.T. (2017). Topics and concepts I'm excited about (Paper of the Future). Living in an Ivory Basement blog, January 9.

[3] the very notion of "high-risk research" is biased toward a fear of failure. Considering what is usually thrown into that bucket, "high-risk research" is a statement of cultural values more than an inherent risk. Removing the industrial, one-size-fits-all aspect of research might be a way to mitigate risk.

[4] sometimes you get lucky and get to define a project right out of the box. But in doing so, projects often end up exhibiting a hodgepodge quality that makes them seem unfocused.

[5] Perkel, J.M. (2017). How Scientists Use Slack. Nature, 541, 123-124.

[6] Washietl, S. (2016). 6 Ways to Streamline Communication in Your Research Group Using Slack. Paperpile blog, April 12.

October 22, 2015

Arriving at October 21, 2015...... and beyond

Last year I marked the date, and this year it became a "thing" (at east on the internet). So here are a few links to celebrate the famous date from the "Back to the Future" trilogy.

Billings, L.   Time Travel Simulation Resolves "Grandfather Paradox". Scientific American, September 2 (2015).

"What 'Back to the Future, Part II' Got Wrong (and right)", from the University of Illinois, Urbana-Champaign.


A welcome to the future, from Doc Brown himself:

COURTESY: Universal Studios.

And now..... a bit farther into the future...... The Economics of Star Trek, which is a really active area of internet scholarship:

Transcript of the recent New York ComicCon panel on Trekonomics.

Podcast on the "Economics of Star Trek", courtesy of FW: Thinking.

A few other takes on the Star Trek economy from Noahpinion, Joseph Dickerson, and Slate.

In the future, Spock is on the money. COURTESY: Rick Webb, The Economics of Star Trek: the proto-post scarcity economy.

December 11, 2014

May You (and your Lineage) Have a Long (Artificial) Life!

The nested pun is my way of announcing the arrival of ECAL 2015. Since I will be on the program committee for ECAL (European Conference for Artificial Life) 2015, I have been asked to publicize the call for papers, abstracts, and workshops. Here it is below — if interested, please consider submitting and attending.



* CALL   FOR   PAPERS *

ECAL 2015 - 13th EUROPEAN CONFERENCE ON ARTIFICIAL LIFE
“Embodiment, Interaction, Conservation”

The 13th European Conference on Artificial Life (ECAL 2015) will be held in York, United Kingdom, 20-24 July 2015, hosted by the York Centre for Complex Systems Analysis at the The University of York.


ECAL 2015 will showcase a wide range of topics in Artificial Life, bringing together world-leading researchers to discuss the latest advances in Artificial Life.  Artificial Life is an interdisciplinary field, and as such welcomes submissions from across the spectrum of scientific and humanities disciplines, that consider the main conference themes of “Embodiment, Interaction, Conservation”. 

THE ECAL programme committee invite you to submit full papers (8 pages) or abstracts (1 page) in the area of Artificial Life.  All submissions will undergo a detailed peer review process.  Full papers will be reviewed for relevance, scientific and/or engineering quality, sound methodology and use of appropriate analysis techniques. Abstracts will be reviewed for relevance and quality.


I M P O R T A N T   D A T E S   A N D   I N F O R M A T I O N

Submission papers:    Monday 2nd March, 2015
Notification of Acceptance: Friday 17th April, 2015
Paper CRC required:    Monday 18th May, 2015
Main Conference convenes: 20-24 July, 2015

Contact email for queries: ecal2015  groupyork.ac.uk


S U B M I S S I O N   F O R M A T

There are two options for submission: either full paper or abstract. Note that the format is exactly the same for both options. The only difference resides in the number of pages and type of contents:

* full papers have an 8-page maximum length and should report on new, unpublished work.

* abstracts are limited to a 1-page length and can report on previously published work, but offer a new perspective on that work. We encourage the use of LaTeX for the production of papers. 

Submission will be via the Easy Chair system.

Papers and abstracts will be selected for oral or poster presentation, with no distinction being made between full papers and abstracts.

* ORGANISING COMMITTEE *

General Chair: Prof. Susan Stepney
Technical Chair: Prof. Jon Timmis
Workshop Chair: Dr. Simon Hickinbotham
Special Sessions Chair: Dr. Leo Caves
Tutorial Chair: Dr. Fiona Polack
Local Chair: Dr. Paul Andrews
ISAL Summer School: Dr. Rene Doursat

September 10, 2013

The Value of Academic Work (brief exploration)

Here are two items cross-posted from Tumbld Thoughts. They are both relevant to innovation and the relative value of achievement. The first post (Need a Social Media strategy?) highlights the value of social media in the scheme of academic production. The second (On Value, Celebrity, and their Discontents) focuses on how value is both extracted from intellectual work and ascribed to its producers.

I. Need a Social Media strategy?


How do you use social media to promote your work? In academia, a term such as synergy is probably premature. However, C. Titus Brown, speaking at the BEACON Center congress, provided an overview (drawn mostly from personal experiences) of how social media can be used for promoting and advancing academic scholarship. 


The centerpiece of a social media strategy is the open-source archiving of your work. One popular option has been the arXiv preprint server. Growth in the number of new q-bio category submissions over the past ten years has exceeded 500%. There are other viable options for this as well. And this not only includes manuscripts, but computer code and datasets. Perhaps Aaron Schwartz will have the last laugh......

As a response to the issues raised in C. Titus' talk, the image below presents my personal (and perhaps idealized) pipeline for scholastic production, from hazy idea to finished product. 


II. On Value, Celebrity, and their Discontents


Here are two tangentially-related items about ideas and their relative value (with particular relevance to academia). The first article is about better ways to monetize innovation, and the second is about the value of ideas vs. the added value of celebrity.

I) Arbesman, S.   "Dark Intellectual Property": why we need a Kickstarter for patents. Social Dimension blog, July 25 (2013).
We need to democratize ways in which IP is discovered/ licensed. The focus of this article is on finding ways to shining light on the potential value in patents and other innovations that are often missed using current techniques. Some key points:

* we need to leverage the power of information technologies and social media to build IP marketplaces and connect innovators with investors.

* building a marketplace must go beyond property enclosure and include enabling better navigation of the patent system.

* we need to promote new ways of interacting with intellectual property (community vs. pure transactions).

* the use of auctions (e.g. bidding wars) will reduce the negative effects of patent troll behavior on IP markets.

* in general, the IP market is highly illiquid. This poses an ever-present problem for properly valuing innovations.


II) Hanson, R.   Beware Star Academia. Overcoming Bias blog, July 27 (2013).

This post focuses on the professionalization of many spheres of human creativity and innovation over the last century or so. Two examples include popular comedy and music, which have moved from freely-exchanged, well-known standards to "star" (e.g. personality-driven) performers and performances. Some key points:

* content and personality have become intertwined (example: Andy Warhol's art).

* academia may be exhibiting a similar trend. The structure of academia is a way to professionalize arguments and concepts of the world. 

* due to the nature of academic discourse and scientific inquiry, a consensus that subsumes individual arguments (e.g. theoretical syntheses) is required.

* to counter the "star power" trend, the focus should be more about ways intellectuals present arguments rather than arguments themselves.

* in cases where "star power" predominates (e.g. science popularizers), the standard of excellence should be rather people care about the overall impressiveness of an argument, or the actual argument being made?

Other (semi-relevant) articles I ran across while compiling this post:

Bilton, N.   Internet pirates will always win. New York Times, August 4 (2012).

Krugman, P.   Nate Silver, superstar. Conscience of a Liberal blog, August 5 (2013).

Jones, J.   Was celebrity really Warhol's legacy? Jonathan Jones On Art blog, May 13 (2009).

June 28, 2013

Human Augmentation Short Course -- Part II

I have been continuing to introduce an area of science and engineering called human augmentation to a broader audience using the "flash lecture" format discussed a few posts back. I have using my micro-blog Tumbld Thoughts as a test site for posting these lectures, and the social networking function of Tumblr (e.g. Tumblr radar) has garnered some sporadic direct interest (in the form of likes and re-posts). 

In this portion of the course (four lectures), we move beyond the basics and towards both more detailed phenomena related to augmentation and practical implementations of the technology.

I. Extending the Phenotype

In previous #human-augmentation posts, I briefly touched on the potential role of augmentation (e.g. wearing a prosthetic limb or see-though, head-mounted display) on physiological regulation. This may leave some readers puzzled, because often times these technologies do not directly interface with the nervous system. Nevertheless, once a technology provides a stand-in (or enhancer) of something the body does, it becomes incorporated into the body's physiology and representation of the world [1].

While technologies from rakes to nests have been found to represent an extended phenotype, an intelligent technology (one that includes an adaptive mitigation strategy) can actually serve to enhance or work in concert with an individual's ability for environmental adaptation [2]. Much like the diet and exercise regimen that helps a person lose weight, this ability exhibits great variation across individuals, which may be explained by pre-existing phenotypic or even genotypic differences.

The extent to which the technology participates in the physiological millieu depends of course on how much the augmentation assists in or takes over function. To understand this better, we can turn to the ergonomics definition of symbiosis, which defines "ergonomy" as the degree of coupling between human and mechanical device [3]. This ranges from tightly-coupled systems (implants that are seamlessly integrated into normal function) to ill-fitting systems (poorly-designed interfaces or computer mice).


II. Instrumented Motorcycle Helmet

Here is an example of performance augmentation in the form of an intelligent, see-through, and heads up display integrated into a motorcycle helmet. Brought to you by a start-up called LiveMap. The information presented in the field of view enables the wearer to improve their navigation ability and improve their riding experience. 

The first article (from Mashable - [4]) highlights the components of the helmet, which includes ambient information from multiple types of sensor (e.g. light sensor, microphone, GPS). This information is then fused and presented in a single location (in this case, the helmet) [5].


II. Wired Science Live Chat on Bionic Augmentation



Last week, I attended a live chat called "Our Cyborg Future", hosted by Wired Science. This was a live chat with two scientists in the field: John Rogers from UIUC and Michael McAlpine from Princeton [6]. These researchers work in a field called "bionics", where biological systems are augmented with electronics or other technology to either restore function or provide new sensory or performance capabilities.

The talk featured a number of visions for the future of bionic technologies and technologies for human augmentation. Fundamentally, the major challenge is to merge the language of electronics (e.g. electrons, phonons, and heat) with the language of biology (e.g. ions, proteins, and enzymes). While John Rogers is working towards electronically-augmented organs [7], Michael McAlpine is working towards using piezoelectric materials to harvest energy from biological motion and print 3-D structures such as tissue scaffolds. 

Three of the most interesting ideas [8] discussed during the talk:

* advances such as flexible [7] and bio-compatible electronics might be used to infuse a biological system with distributed electronics at the cellular and subcellular scale. This could include a range of components from silicon diodes to LEDs.

* the increases in brain-machine interface bandwidth due to flexible, laminated skin-like devices.

* the development of emerging technologies such as stretchable batteries, glucose fuel cells, implantable micro-heaters, and mechanical energy harvesting.


IV. The Role of Attention, Training, and critical Meta-Analysis

In a previous #human-augmentation post, I pointed to one experimental paradigm (environmental switching) that may serve as a natural (e.g. non-computational) filter for eliminating (e.g. mitigating) non-optimal performance due to environmental stresses or other challenges. This case is illustrative for two reasons: 

1) in cases where performance response curves are very complex and cannot be characterized by a simple mathematical function (e.g. a "U" shaped curve), a mitigation strategy involving physical chaos (rather than computational control) or other environmental manipulations may be more effective. In the first image (top), the potential dynamic effects of perturbation on attentional shifts during an episode of "Star Trek" is used as an example.

2) fully understanding the effects of mitigation may require more systematic experimental evaluation. One example of this involves the claim that long-term expertise with action video games improves cognitive abilities [9]. A meta-analysis of such studies [10] questions this assumption on several grounds, particularly with respect to the magnitude of improvement (e.g. effect size).

In this case of action video game expertise, two types of effect have been reported [10, 11]. The first involves relative expertise based on cross-sectional comparisons, which evaluate differences between gamers and non-gamers. The second involves acquired expertise (training in action video game play) as having numerous cognitive benefits.

The second type of effect is partially due to an effect called transfer of training (see image, lower left), in which skills acquired in one context can be transferred to another context. This effect also plays a role in human augmentation, and may exhibit a large degree of individual variation. However, there are three caveats raised in [10] that must be kept in mind not only for future action video game studies, but human augmentation studies as well:

* in studies that evaluate the effects of training, an adequate baseline for untrained performance must be used. 

* results should be generalizable to different settings and population (e.g. exhibit a high degree of experimental reproducibility).

* while there may be several improvements to performance/cognition attributable to prior training or experience with the activity in question, there may be many more outcomes that are unaffected by the treatment (action video games) or mitigation (human augmentation). 


NOTES:
[1] A few examples of this extension of the phenotype includes examples from humans (i), social insects (ii, iii), and animals (iv):

(i) Maravita, A. and Iriki, A.   Tools for the body (schema). Trends in Cognitive Science, 8(2), 79-86 (2004).

(ii) Turner, J.S.   The Extended Organism: The Physiology of Animal-Built Structures. Harvard University Press, Cambridge, MA (2002).

(iii) Turner, J.S.   Extended Phenotypes and Extended Organisms. Biology and Philosophy, 19, 327–352 (2004).

(iv) Schaedelin, F.C. and Taborsky, M.   Extended phenotypes as signals. Biological Reviews of the Cambridge Philosophical Society, 84(2), 293-313 (2009). 

[2] This ability, or adaptability, can be characterized using a parametric landscape as shown in a previous post.

[3] Licklider, J.C.R.   Man-Computer Symbiosis. IRE Transactions on Human Factors in Electronics, HFE-1, 4-11 (1960).

[4] Murphy, S.   A Motorcyclist's Dream: Google Glass in helmet form. Mashable, June 17 (2013).

[6] A transcript of the talk can be found here. Also see the McAlpine Research YouTube channel.

[7] For more on flexible robotics, please see this: Zheng, Y., He, Z., Gao, Y., and Liu, J.   Direct Desktop Printed-Circuits-on-Paper Flexible Electronics. Scientific Reports, 3, 1786 (2013).

[8] For more interesting ideas related to cyborgs and bio-inspired robotics, see these:

Rowe, A.   Top 10 Cyborg Videos. Wired Science, November 15 (2009)


[9] Green, C. and Bavelier, D.   Learning, Attentional Control, and Action Video Games. Current Biology, 22(6), R197-R206.

[10] Boot, W.R., Blakley, D.P., Simons, D.J.   Do action video games improve perception and cognition? Frontiers in Psychology, 2, 226 (2011).

[11] Simons, D.   Think video games make you smarter? Not so fast..... Daniel Simons blog, December 30 (2012).

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