Papers for the week, 1/1 edition

Visual projection neurons in the Drosophila lobula link feature detection to distinct behavioral programs. Ming Wu, Aljoscha Nern, W. Ryan Williamson, Mai M Morimoto, Michael B Reiser, Gwyneth M Card, Gerald M Rubin.

The hippocampus as a predictive map. Kimberly Lauren Stachenfeld, Matthew M Botvinick, Samuel J Gershman.

Searching for Signatures of Brain Maturity: What Are We Searching For? Leah H. Somerville.

The misleading narrative of the canonical faculty productivity trajectory. Samuel F. Way, Allison C. Morgan, Aaron Clauset, Daniel B. Larremore.

Contribution of Head Shadow and Pinna Cues to Chronic Monaural Sound Localization. Marc M. Van Wanrooij and A. John Van Opstal.

The influence of pinnae‐based spectral cues on sound localization. Alan D. Musicant and Robert A. Butler.

Everyday bat vocalizations contain information about emitter, addressee, context, and behavior. Yosef Prat, Mor Taub & Yossi Yovel.

A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing.Haruo Hosoya, Aapo Hyvärinen.

cGAL, a temperature-robust GAL4–UAS system for Caenorhabditis elegans. Han Wang, Jonathan Liu, Shahla Gharib, Cynthia M Chai, Erich M Schwarz, Navin Pokala & Paul W Sternberg.

Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders. Min-Tzu Lo, David A Hinds, Joyce Y Tung, Carol Franz, Chun-Chieh Fan, Yunpeng Wang, Olav B Smeland, Andrew Schork, Dominic Holland, Karolina Kauppi, Nilotpal Sanyal, Valentina Escott-Price, Daniel J Smith, Michael O’Donovan, Hreinn Stefansson, Gyda Bjornsdottir, Thorgeir E Thorgeirsson, Kari Stefansson, Linda K McEvoy, Anders M Dale, Ole A Andreassen & Chi-Hua Chen.

 

Neurogastronomy, neuroenology, neuroneuroscience – does it actually tell us anything?

I should think that we are all pretty well aware of the trend to neuroify pretty much everything (neuroaesthetics, neuroeconomics, uh neuroecology). In a review of Gordon Shepherd’s book Neuroenology: How the Brain Creates the Taste of Wine, Steven Shapin spends some time ruminating on whether there is any actual use to all of this.

First, some comments on the ‘neuroenology’:

The distinctions between olfaction and gustation, and even between orthonasal and retronasal olfaction, are only a start. There are many more scientific facts to be understood about, for example, how wine moves around in the buccal cavity and then on to the pharynx and esophagus; how these muscle- and gravity-induced movements contribute to sensory experience; how swallowing is controlled by the sCPG (the swallowing central pattern generator); how swallowed wine leaves behind in the mouth and pharynx both a sticky “matrix” and “volatiles” which can be released when post-swallow respiration resumes; how the first expiration of breath after swallowing has the highest concentration of volatiles, which some tasters call “the aroma burst” and which they consider “the strongest contributor to the taste of wine”; how the nerves of the tongue and nasal epithelium are arrayed and what paths they take to the brain; how and where the various sensory modes are integrated into the experience of flavor; and how some aroma molecules come to elicit olfactory responses…

But: does it actually change how we perceive wine? Can it be used to broaden or deepen our appreciation for wine (or food in general)?

So does any of this newly acquired “objective” knowledge about sensory modes bear at all on the nature and quality of subjective experience? Yes, it may, and no anti-reductionist humanist should feel obliged to deny that. Nevertheless, some claims for the aesthetic significance of scientific knowledge seem dubious. For example, Shepherd writes about the importance of the mucus membranes in the mouth, assuring us that “being aware of the structure of the mucus membranes, their various receptors, and the sensations they produce will enrich the wine-tasting experience.” But other neuroscientific stories seem more plausibly experience-changing. Scientists’ accounts of the retronasal pathway, for example, have the capacity to alter the attention paid to different types of olfactory experience. Our senses engage with a field of potential experience: we can attend to some features of that field and not to others, making some sensible aspects part of our focal awareness, and backgrounding or bracketing others. Having a “private” conversation in a public room, we focus on our partner’s talk and not on the booming, buzzing “background” sound washing over us. Then we overhear someone mentioning our name and we realize that the background noise has been waiting to be turned into signal through a change in attentiveness…

Michael Baxandall’s marvelous accounts of what he called “the period eye” in Quattrocento painting told us how late medieval people looked at paintings — the eye attending to the areas of azure and gold in the Virgin’s clothing, guided there because of the known preciousness and expense of these pigments, just as the Quattrocento period eye attended to certain shapes because of the widely distributed mercantile skill in gauging the internal volumes of barrels from their visible surfaces. Knowing this, you can look at paintings in this way too. The French sociologist Antoine Hennion — also a wine lover — has proposed a “sociology of attention” in which features of the sensory field are framed, parsed, and differently stressed, and in which subjects momentarily make themselves passive with respect to the sensed object. (“Ah, yes, now I notice that.”) So the framing impulses that can change or enhance sense experience need not derive from sensory science, and in these cases they do not, but sensory framing may come from scientific accounts of the structures and processes of sense perception. Neuroenology relates several stories that do have the capacity to change — to reframe, to reconstitute — our sensory experience. It’s an authentic debt that some pleasures might owe to some scientific accounts…

Then there are neuroscientific accounts of what areas of the brain “light up” in functional magnetic resonance imaging (fMRI) when laboratory animals sniff different volatile substances. Neuroscientists also tell us that when you — but not, in this case, laboratory animals — are told that one of two wines you’re drinking costs more, even when the wines are in fact the same, a different area of the cortex lights up for the “expensive” wine, and does so more brightly. Yet both of these findings bear as much relationship to the experience of aroma as knowing the location of the fuel pump does to the experience of driving a car: the pump and the brain area relating to odor have got to be somewhere, but knowing where they are doesn’t add to, subtract from, or change the experiences of driving or drinking.

Finally, a note on neuromania:

[T]he Italian psychologists Paolo Legrenzi and Carlo Umiltà have called “neuromania.” This is the tendency to go beyond identifying the neural bases for beliefs and sensations to the claim that beliefs and sensations really are their neural bases. The first claim is unexceptionable: of course, sensations are the result of interactions between our neural structures and things in the world and elsewhere in our bodies. In this sense, neuroscience has begotten a set of pleonasms — using more words than necessary to convey a specific meaning — and these pleonasms have metastasized through contemporary culture. Insofar as our mental life is neurally based — and who now doubts that? – neuro-whatever might just be a potentially useful way of reminding us of this fact: “neuroaesthetics” is aesthetics; “neuroethics” is ethics; “neuromarketing” is marketing; “neuroeconomics” is economics — even if traditional practitioners of aesthetics, ethics, and the like have not routinely had much to say about which areas of the brain “light up” when we see a beautiful painting, do a good deed, or buy a new car, and provided that we appreciate that what “goes on in the brain” includes what people know, remember, feel, and feel to be worth their attention.

 

Yeah, but what has ML ever done for neuroscience?

This question has been going round the neurotwitters over the past day or so.

Let’s limit ourselves to ideas that came from machine learning that have had an influence on neural implementation in the brain. Physics doesn’t count!

  • Reinforcement learning is always my go-to though we have to remember the initial connection from neuroscience! In Sutton and Barto 1990, they explicitly note that “The TD model was originally developed as a neuron like unit for use in adaptive networks”. There is also the obvious connection the the Rescorla-Wagner model of Pavlovian conditioning. But the work to show dopamine as prediction error is too strong to ignore.
  • ICA is another great example. Tony Bell was specifically thinking about how neurons represent the world when he developed the Infomax-based ICA algorithm (according to a story from Terry Sejnowski). This obviously is the canonical example of V1 receptive field construction
    • Conversely, I personally would not count sparse coding. Although developed as another way of thinking about V1 receptive fields, it was not – to my knowledge – an outgrowth of an idea from ML.
  • Something about Deep Learning for hierarchical sensory representations, though I am not yet clear on what the principal is that we have learned. Progressive decorrelation through hierarchical representations has long been the canonical view of sensory and systems neuroscience. Just see the preceding paragraph! But can we say something has flowed back from ML/DL? From Yemins and DiCarlo (and others), can we say that maximizing the output layer is sufficient to get similar decorrelation as the nervous system?

And yet… what else? Bayes goes back to Helmholtz, in a way, and at least precedes “machine learning” as a field. Are there examples of the brain implementing…. an HMM? t-SNE? SVMs? Discriminant analysis (okay, maybe this is another example)?

My money is on ideas from Deep Learning filtering back into neuroscience – dropout and LSTMs and so on – but I am not convinced they have made a major impact yet.

“Firing,” by d. m. kingsford

pickatopic

I was roaming the streets of Denver during an ultra-long layover on Friday and ran into someone offering to write poems on the spot, on any topic. The topic: brains, neurons.

Merry Christmas, neuroscience community:

Firing by d.m. kingsford

Like a V-10,000,000
this thing, ordinary enough,
comprised of the same stuff
as everyone else’s,
making up a man of average intelligence,
kind, occasionally
(but his in-laws think he’s a
bastard)
and basically fulfilled.

this thing is firing
on all cylinders, heat beat,
renal systems in check,
temperature ok, and
at this moment,
the frontal lobe bearing down on
a crossword puzzle.

The same as Stephen Hawking.
Basically.

(Apologies for the loss of formatting.)

img_20161223_130803

Studying the brain at the mesoscale

It i snot entirely clear that we are going about studying the brain in the right way. Zachary Mainen, Michael Häusser and Alexandre Pouget have an alternative to our current focus on (relatively) small groups of researchers focusing on their own idiosyncratic questions:

We propose an alternative strategy: grass-roots collaborations involving researchers who may be distributed around the globe, but who are already working on the same problems. Such self-motivated groups could start small and expand gradually over time. But they would essentially be built from the ground up, with those involved encouraged to follow their own shared interests rather than responding to the strictures of funding sources or external directives…

Some sceptics point to the teething problems of existing brain initiatives as evidence that neuroscience lacks well-defined objectives, unlike high-energy physics, mathematics, astronomy or genetics. In our view, brain science, especially systems neuroscience (which tries to link the activity of sets of neurons to behaviour) does not want for bold, concrete goals. Yet large-scale initiatives have tended to set objectives that are too vague and not realistic, even on a ten-year timescale.

Here are the concrete steps they suggest in order to from a successful ‘mesoscale’ project:

  1. Focus on a single brain function.
  2. Combine experimentalists and theorists.
  3. Standardize tools and methods.
  4. Share data.
  5. Assign credit in new ways.

Obviously, I am comfortable living on the internet a little more than the average person. But with the tools that are starting to proliferate for collaborations – Slack, github, and Skype being the most frequently used right now – there is really very little reason for collaborations to extend beyond neighboring labs.

The real difficulties are two-fold. First, you must actually meet your collaborators at some point! Generating new ideas for a collaboration rarely happens without the kind of spontaneous discussions that arise when physically meeting people. When communities are physically spread out or do not meet in a single location, this can happen less than you would want. If nothing else, this proposal seems like a call for attending more conferences!

Second is the ad-hoc way data is collected. Calls for standardized datasets have been around about as long as there has been science to collaborate on and it does not seem like the problem is being solved any time soon. And even when datasets have been standardized, the questions that they had been used for may be too specific to be of much utility to even closely-related researchers. This is why I left the realm of pure theory and became an experimentalist as well. Theorists are rarely able to convince experimentalists to take the time out of their experiments to test some wild new theory.

But these mesoscale projects really are the future. They are a way for scientists to be more than the sum of their parts, and to be part of an exciting community that is larger than one or two labs! Perhaps a solid step in this direction would be to utilize the tools that are available to initiate conversations within the community. Twitter does this a little, but where are the foraging Slack chats? Or amygdala, PFC, or evidence-accumulation communities?

5 things I learned on Sunday at #sfn16

Just some irrelevant facts.

1. Toadfish can sing by vibrating their swim bladder, and can vocalize independent of breathing.

2. Scientists working in Drosophila are starting to see reafferent signals (signals representing motor commands such as walking or singing) in tons of places, from sensory neurons on downward. This is one of the areas where Drosophila neuroscientists are way ahead of mammalian neuroscientists.

3. The computations that visual neurons perform can fundamentally alter in conditions that seem like they should be similar, such as light levels (this is not just adaptation to statistics).

4. There are conditions in which retinal neurons can be synergistic and not redundant. This is a bit of a controversy in the field, with the common consensus that ganglion cells have ~10% redundancy. Apparently this is not always the case!

5. Drosophila (fruit flies) have a spatial short term memory that has been located in the central complex (actually, I am not clear exactly where the anatomical structure is located: it may be just outside of the central complex.)

#sfn16 starts tomorrow in San Diego

I know many of you will be there! I am giving a talk on Sunday morning at 8am. Since everyone will be fresh-faced and excited for the conference, I am sure it will not be a problem to be there that early, right? Right? The talk will be in room SDCC 30B on a new method to for unsupervised analysis of behavior which I am really, really excited about (we have gone beyond what the abstract says so ignore that).

Papers for the week, 10/30 edition

Recurrent Switching Linear Dynamical Systems. Scott W. Linderman, Andrew C. Miller, Ryan P. Adams, David M. Blei, Liam Paninski, Matthew J. Johnson. 2016.

The Serotonergic System Tracks the Outcomes of Actions to Mediate Short-Term Motor Learning. Takashi Kawashima, Maarten F. Zwart, Chao-Tsung Yang, Brett D. Mensh, Misha B. Ahrens. 2016.

A visual circuit uses complementary mechanisms to support transient and sustained pupil constriction. William Thomas Keenan, Alan C Rupp, Rachel A Ross, Preethi Somasundaram, Suja Hiriyanna, Zhijian Wu, Tudor C Badea, Phyllis R Robinson, Bradford B Lowell, Samer S Hattar. 2016.

Numerical analysis of homogeneous and inhomogeneous intermittent search strategies. Karsten Schwarz, Yannick Schröder, and Heiko Rieger. 2016.

Unexpected arousal modulates the influence of sensory noise on confidence. Micah Allen, Darya Frank, D Samuel Schwarzkopf, Francesca Fardo, Joel S Winston, Tobias U Hauser, Geraint Rees. 2016.

Vision Drives Accurate Approach Behavior during Prey Capture in Laboratory Mice.
Jennifer L. Hoy, Iryna Yavorska, Michael Wehr, Cristopher M. Niell. 2016.

Amygdala and Ventral Striatum Make Distinct Contributions to Reinforcement Learning. Vincent D. Costa,Olga Dal Monte, Daniel R. Lucas, Elisabeth A. Murray, Bruno B. Averbeck. 2016.

Potent optogenetic inhibition of behavior with anion channelrhodopsins.  Farhan Mohammad, James Stewart, Stanislav Ott, Katarina Chlebikova, Jia Yi Chua, Tong-Wey Koh, Joses Ho, Adam Claridge-Chang. 2016.

Interstellate Magazine: The Art of Neuroscience

interstellatemagazines

Caitlin Vander Weele has been curating a collection of stunning neuroscience images that really bring the brain to life (so to speak). Volume 1 is here and it is a beauty! You can also download the hi-res PDF if you’ve got a spare 210 MB lying around.

Some samples:
interstellateneurons2

interstellateneurons3

interstellateneurons1

Posted in Art

Coherent dots as art

norimichi_hirakawa_indivisible

One of the more influential experimental paradigms in sensory neuroscience is the coherent random dots task in which small dots flicker in and out of existence, with some small number of them moving either left or right, like flecks of snow on a windy winter day. An animal – a monkey, a mouse, a human – is forced to say in which direction these dots are moving, a task which gets harder as the number moving in a coherent direction gets smaller. You can see an example here (which is uploaded in quicktime for some reason). Versions of this task have been adapted to other sensations like audition.

I was in Seoul recently and visited the Seoul Museum of Art. Filled to the brim with amazing installations, one caught my eye. Much to the chagrin of my non-neuroscientist companions, I became entranced by a vivid representation of these seminal psychophysics studies. Norimichi Hirakawa, consciously or not, has manifested this ‘random noise’ into a form that is somehow accessible to a broad audience. Think of the possibilities inherent in that the next time that you run an experiment.

(I took some videos but could not find a good way to embed them as youtube and vimeo both attempt to lossily compress it – which is difficult when you are literally compressing noise.)