Integration dynamics and choice probabilities


Very informative post – “Integration dynamics and choice probabilities”

Originally posted on Pillow Lab Blog:

Recently in lab meeting, I presented

Sensory integration dynamics in a hierarchical network explains choice probabilities in cortical area MT

Klaus Wimmer, Albert Compte, Alex Roxin, Diogo Peixoto, Alfonso Renart & Jaime de la Rocha. Nature Communications, 2015

Wimmer et al. reanalyze and reinterpret a classic dataset of neural recordings from MT while monkeys perform a motion discrimination task. The classic result shows that the firing rates of neurons in MT are correlated with the monkey’s choice, even when the stimulus is the same. This covariation of neural activity and choice, termed choice probability, could indicate sensory variability causing behavioral variability or it could result from top-down signals that reflect the monkey’s choice. To investigate the source of choice probabilities, the authors use a two-stage, hierarchical network model of integrate and fire neurons tuned to mimic the dynamics of MT and LIP neurons and compare the model to what they find…

View original 436 more words


Depressing Quotes on Science Overflow – Reputation is the Gateway to Scientific Success

If you haven’t done so yet, go read this new E-life paper on scientific overflow, now. The authors interviewed “20 prominent principal investigators in the US, each with between 20 and 60 years of experience of basic biomedical research”, asking questions about how they view and deal with the exponential increase in scientific publications:

Our questions were grouped into four sections: (1) Have the scientists interviewed observed a decrease in the trustworthiness of science in their professional community and, if so, what are the main factors contributing to these perceptions? (2) How do the increasing concerns about the lack of robustness of scientific research affect trust in research? (3) What concerns do scientists have about science as a system? (4) What steps can be taken to ensure the trustworthiness of scientific research?

Some of the answers offer a strikingly sad view of the current state of the union:

On new open access journals, databases, etc:

There’s this proliferation of journals, a huge number of journals… and I tend not even to pay much attention to the work in some of these journals. (…) And you’re always asked to be an editor of some new journal. (…) I don’t pay much attention to them.

On the role of reputation in assessing scientific rigor and quality:

There are some people that I know to be really rigorous scientists whose work is consistently well done (…). If a paper came from a certain lab then I’m more likely to believe it than another paper that might have come from a different lab whose (…) head might be somebody that I know tends to cut corners, over-blows their conclusions, doesn’t do rigorous experiments, doesn’t appreciate the value of proper controls.

If I know that there’s a very well established laboratory with a great body of substantiated work behind it I think there is a human part of me that is inclined to expect that past quality will always be predicting future quality I think it’s a normal human thing. I try not to let that knee–jerk reaction be too strong though.

If I don’t know the authors then I will have to look more carefully at the data and (…) evaluate whether (…) I feel that the experiments were done the way I would have done them and whether there were some, if there are glaring omissions that then cast out the results (…) I mean [if] I don’t know anything I’ve never met the person or I don’t know their background, I don’t know where they trained (…) I’ve never had a discussion with them about science so I’ve never had an opportunity to gauge their level of rigour…

Another interviewee expressed scepticism about the rapid proliferation of new journals:

The journal that [a paper] is published in does make a difference to me, … I’m talking about (…) an open access journal that was started one year ago… along with five hundred other journals, (…) literally five hundred other journals, and that’s where it’s published, I have doubts about the quality of the peer review.

The cancer eating science is plain to see. If you don’t know the right people, your science is going to be viewed less favorably. If you don’t publish in the right journals, i’m not going to trust your science. It’s a massive self-feeding circle of power. The big rich labs will continue to get bigger and richer as their papers and grant applications will be treated preferentially. This massive mess of heuristic biases is turning academia into a straight up pyramid scheme. Of course, this is but a small sub-sample of the scientific community, but I can’t help but feel like these views represent a widespread opinion among the ‘old guard’ of science. Anecdotally these comments certainly mirror some of my own experiences. I’m curious to hear what others think.

The Bayesian Reproducibility Project


Fantastic post by Alexander Etz (@AlxEtz), which uses a Bayes Factor approach to summarise the results of the reproducibility project. Not only a great way to get a handle on those data but also a great introduction to Bayes Factors in general!

Originally posted on The Etz-Files:

The Reproducibility Project was finally published this week in Science, and an outpouring ofmedia articles followed. Headlines included “More Than 50% Psychology Studies Are Questionable: Study”, “Scientists Replicated 100 Psychology Studies, and Fewer Than Half Got the Same Results”, and “More than half of psychology papers are not reproducible”.

Are these categorical conclusions warranted? If you look at the paper, it makes very clear that the results do not definitively establish effects as true or false:

After this intensive effort to reproduce a sample of published psychological findings, how many of the effects have we established are true? Zero. And how many of the effects have we established are false? Zero. Is this a limitation of the project design? No. It is the reality of doing science, even if it is not appreciated in daily practice. (p. 7)

Very well said. The point of this project was not…

View original 3,933 more words


Short post – my science fiction vision of how science could work in the future

6922_072dSadly I missed the recent #isScienceBroken event at UCL, which from all reports was a smashing success. At the moment i’m just terribly focused on finishing up a series of intensive behavioral studies plus (as always) minimizing my free energy, so it just wasn’t possible to make it. Still, a few were interested to hear my take on things. I’m not one to try and commentate an event I wasn’t at, so instead i’ll just wax poetic for a moment about the kind of Science future i’d like to live in. Note that this has all basically been written down in my self-published article on the subject, but it might bear a re-hash as it’s fun to think about. As before, this is mostly adapted from Clay Shirky’s sci-fi vision of a totally autonomous and self-organizing science.

Science – OF THE FUTURE!

Our scene opens in the not-too distant future, say the year 2030. A gradual but steady trend towards self-publication has lead to the emergence of a new dominant research culture, wherein the vast majority of data first appear as self-archived digital manuscripts containing data, code, and descriptive-yet-conservative interpretations on centrally maintained, publicly supported research archives, prior to publication in traditional journals. These data would be subject to fully open pre-and post-publication peer review focused solely on the technical merit and clarity of the paper.

Having published your data in a totally standardized and transparent format, you would then go on write something more similar to what we currently formulate for high impact journals. Short, punchy, light on gory data details and heavy on fantastical interpretations. This would be your space to really sell what you think makes those data great – or to defend them against a firestorm of critical community comments. These would be submitted to journals like Nature and Science who would have the strictly editorial role of evaluating cohesiveness, general interest, novelty, etc. In some cases, those journals and similar entities (for example, autonomous high-reputation peer reviewing cliques) would actively solicit authors to submit such papers based on the buzz (good or bad) that their archived data had already generated. In principle multiple publishers could solicit submissions from the same buzzworthy data, effectively competing to have your paper in their journal. In this model, publishers must actively seek out the most interesting papers, fulfilling their current editorial role without jeopardizing crucial quality control mechanisms.

Is this crazy? Maybe. To be honest I see some version of this story as almost inevitable. The key bits and players may change, but I truly believe a ‘push-to-repo’ style science is an inevitable future. The key is to realize that even journals like Nature and Science play an important if lauded role, taking on editorial risk to highlight the sexiest (and least probable) findings. The real question is who will become the key players in shaping our new information economy. Will today’s major publishers die as Blockbuster did – too tied into their own profit schemes to mobilize – or will they be Netflix, adapting to the beat of progress?  By segregating the quality and impact functions of publication, we’ll ultimately arrive at a far more efficient and effective science. The question is how, and when.

note: feel free to point out in the comments examples of how this is already becoming the case (some are already doing this). 30 years is a really, really conservative estimate :) 


[VIDEO] Mind-wandering, meta-cognition, and the function of consciousness

Hey everyone! I recently did an interview for Neuro.TV covering some of my past and current research on mind-wandering, meta-cognition, and conscious awareness. The discussion is very long and covers quite a diversity of topics, so I thought i’d give a little overview here with links to specific times.

For the first 15 minutes, we focus on general research in meta-cognition, and topics like the functional and evolutionary signifigance of metacognition:

We then begin to move onto specific discussion about mind-wandering, around 16:00:

I like our discussion as we quickly get beyond the overly simplistic idea of ‘mind-wandering’ as just attentional failure, reviewing the many ways in which it can drive or support meta-cognitive awareness. We also of course briefly discuss the ‘default mode network’ and the (misleading) idea that there are ‘task positive’ and ‘task negative’ networks in the brain, around 19:00:

Lots of interesting discussion there, in which I try to roughly synthesize some of the overlap and ambiguity between mind-wandering, meta-cognition, and their neural correlates.

Around 36:00 we start discussing my experiment on mind-wandering variability and error awareness:

A great experience in all, and hopefully an interesting video for some! Be sure to support the kickstarter for the next season of Neuro.TV!

JF also has a detailed annotation on the brainfacts blog for the episode:

“0:07″ Introduction
“0:50″ What is cognition?
“4:45″ Metacognition and its relation to confidence.
“10:49″ What is the difference between cognition and metacognition?
“14:07″ Confidence in our memories; does it qualify as metacognition?
“18:34″ Technical challenges in studying mind-wandering scientifically and related brain areas.
“25:00″ Overlap between the brain regions involved in social interactions and those known as the default-mode network.
“29:17″ Why does cognition evolve?
“35:51″ Task-unrelated thoughts and errors in performance.
“50:53″ Tricks to focus on tasks while allowing some amount of mind-wandering.

Monitoring the mind: clues for a link between meta cognition and self generated thought


Jonny Smallwood, one of my PhD mentors, just posted an interesting overview of some of his recent work on mind-wandering and metacognition (including our Frontiers paper). Check it out!

Originally posted on The Mind Wanders:

It is a relatively common experience to lose track of what one is doing: We may stop following what someone is saying during conversation, enter a room and realise we have forgotten why we came in, or lose the thread of our own thoughts leaving us with a sense that we had reached a moment of insight that is now lost forever. One important influence on making sure that we can stay on target to achieve our goals is the capacity for meta-cognition, or the ability to accurately assess our own cognitive experience. Meta cognition is important because it allows us the opportunity to correct for errors if and when they occur. I have recently become interested in this capacity for accurately assessing the contents of thought and along with two different groups of collaborators have begun to explore its neural basis.

We were interested in whether meta-cognition is a…

View original 1,192 more words

Researchers begin posting article PDFs to twitter in #pdftribute to Aaron Swartz

Yesterday, as I was completing my morning coffee and internet ritual, @le_feufollet broke the sad news to me of Aaron Swartz’s death. Aaron was a leader online, a brilliant coder and developer, and sadly a casualty in the fight for freedom of information. He was essential in the development of two tools I use every day (RSS and Reddit), and though his guerilla attempt to upload all papers on JSTOR was perhaps unstrategic, it was certainly noble enough in cause. Before his death Aaron was facing nearly 35 years in prison for his role in the JSTOR debacle, an insane penalty for attempting to share information. We don’t know why Aaron chose to take his life, but when @la_feufollet and I tried to brainstorm a tribute to him, my first thought was a guerilla PDF uploading campaign in honor of his fight for open access. I’m not much of an organizer, so I posted in one of the many rising reddit threads and hoped for the best:


My posts on reddit are usually ignored, so I went about my business and assumed it was the last i’d hear of it. It was amazing to wake up this morning and see that redditors had responded strongly to the idea and that a flood of tweets tagged #pdftribute had appeared:


Eva Vivalt coined the #pdftribute hashtag, and helped bring anonymous onboard. Currently there are hundreds thousands of authors posting their PDFs. It’s amazing to see that the original promise of the internet – the spread of ideas- is thriving. Lately i’ve been feeling a bit pessimistic, worried that the net was becoming an overly gamed, astroturf-ridden meme-preserve for advertisers to groom to their financial needs. It’s great to see that the most exciting power of our newfound connectivity- driving ideas to spread freely and have impact without the restrictions of traditional hierarchical barriers- continues to thrive. I hope #pdftribute lives on in both force and spirit, and that we can all begin working toward a world in which all publicly funded research is available to anyone with net access.

UPDATE 13/1/13 4:00 EST:

For those of you who don’t feel comfortable violating your copyright, but want to join in #pdftribute, your best bet is to check the specifics of your publisher agreement. Most journals allow you to upload a pre-print manuscript to your personal website. Then you can go ahead and tweet the link to your website or the individual pre-print PDFs. Jonathan Eisen has a helpful list of 10 ways to post your papers on twitter here.

Otherwise, hide in the swarm today as a show of support for Aaron. By standing together we show that the future of research publishing is freedom of information. But tomorrow remember that we need to push through real copright reform. You can start by reading Aaron’s wonderful Guerilla Open Access Manifesto. If you are ready to commit to open access, you can sign the petition at There is also this We The People petition demanding legislation requiring journals to use an open-access publishing model Woops that petition has expired- start a new one!. As Matthew Green put it, lets push for an Aaron Swartz copyright reform act.


Some nice folks have put together a link scraper to collect PDFs tagged #pdftribute here:

Screen shot 2013-01-13 at 7.46.58 PM


If I may make a humble suggestion- it may be useful to follow a specific format for sharing your papers. This will make them easier to find later, and for journalists to compile some sharing stats. Here is my suggested example.

Screen shot 2013-01-13 at 2.12.23 PM


Eva Vivalt reports #pdftribute getting 500 tweets/hr, >2.5 million impressions!

Screen shot 2013-01-13 at 1.46.05 PM

Thesis… almost done!

Allo- just checking in to say I’m about 8 days away from submitting my thesis. Then i’m off to Italy for some much needed R&R followed by SFN2012 in New Orleans. I’ll be blogging regularly again this fall once I’ve had a chance to recoup. Lots of fun new stuff coming including a new direction for my research, new projects, ideas, and all that comes with finally finishing a PhD.