Paper:
A probabilistic population code based on neural samples
Sensory processing is often characterized as implementing probabilistic inference: networks of neurons compute posterior beliefs over unobserved causes given the sensory inputs. How these beliefs are computed and represented by neural responses is much-debated (Fiser et al. 2010 . Here, we show that these alternatives -contrary to common assumptions -are not mutually exclusive and that the very same system can be compatible with all of them. As a central analytical result, we show that modeling neural responses in area V1 as samples from a posterior distribution over latents in a linear Gaussian model of the image implies that those neural responses form a linear Probabilistic Population Code (PPC, Ma et al. 2006). In particular, the posterior distribution over some experimenter-defined variable like "orientation" is part of the exponential family with sufficient statistics that are linear in the neural sampling-based firing rates.

Review:
REPLY TO THE AUTHORS' FEEDBACK ============================== Thank for very much for the response and the very concrete description of changes. I can picture how the updated manuscript looks. With the presentation issues out of the way, I raised my score to 9 points, i.e., a strong vote for acceptance.  Just for completeness, allow me to clarify the "Strictly speaking the statement is correct” (L163ff). In the idealized experiment considered in Fig 3, there are two sources of stochasticity: The neural samples x|I and the images I|T(s). For the main result ( eqs (6)-(8) ), the images I have been marginalized out. Thus, I understand the discussion around L163ff such that the network can describe the _average_image_T(s)_ well in case of a complete model A. The term "image" alone (without an attribute such as "average") is defined as the noisy realization I, according to line 76. Therefore, the sentence "Ax̄ will exactly reconstruct the input image" [...the limit can only refer to the x-samples.] describes the network's ability to capture also the noise-realization in I. For a complete model A, this is indeed the case. So, strictly speaking the statement is correct. But the discussion, as I understand it, refers to the average image, or prototype, T(s).  Anyhow, "Congratulations!" to a great piece of science. In light of the topic's relevance, I recommend this paper for a talk.  SUMMARY =======  The authors investigate the relation between sample-based codes and probabilistic populations codes (PPCs), two prevalent -- and often competing -- theoretical interpretations of neural activity for representing Bayesian computations in brain circuits. As the main result, the authors reconcile the two interpretations by showing analytically and in computer simulations how a sample-based code can yield a PPC code in the limit of many samples. For this, the authors set out with two independent, widely accepted modeling assumptions: (1) A linear Gaussian generative model of the input with neural sampling activations as latent variables. (2) An almost unrestricted Gaussian generative model of the input conditioned on a relevant stimulus parameter. Marginalizing over inputs followed by some mathematical massaging leads to the main result: a PPC form for p( stimulus parameter | neural activations ). The paper then discusses some often debated topics (multimodality, nuisance variables, linear vs log-probabilities) from the unified standpoint of their model.   QUALITY: 6  ==========  + The introduction is very thoughtfully written: precisely carving out the assumptions and differences of the two compared interpretations. + This is one of the few papers on this topic that do not intend to bolster up one interpretation over the other. - It would be interesting to see if the derivation holds for more general (exponential family) generative models beyond linear Gaussian.  + I think that the derivation is correct, once the reader... - corrected the many small mistakes in the equations, - skipped over copy&paste ruins (entire lines could be removed), - ignored unused and false assumptions, - guessed the definition of multiple undefined important quantities.  These issues impact both quality and clarity of the manuscript. Please see below for details.   CLARITY: 3 ==========  The presentation of the central derivation in sections 2 and 3 leaves (politely speaking) the impression of a very hasty writing process. Besides the above-mentioned errors, there is no high-level outline of the argumentation. Figure 1 could help explaining this, but the figure is never referred to in the main text. And the argumentation would be so simple:  [A] From eq. (2) and assuming conditionally independent samples (x^i ⊥ x^j | I) follows eq (4). [B] From eq. (4) and the stimulus model ( what should be eq. (3); currently unnumbered ) follows eq. (5) in the limit of many samples. [C] Eq (5) can be cast into the canonical PPC form eq (6) - (8) by identifying r with x^[1:t].  The last step, identifying r with x^[1:t], is completely omitted in the manuscript, but crucial since this connects the quantities of the two interpretations.  Overall, the clarity of presentation is the major weakness of the manuscript. Should the manuscript be rejected for this reason (which is not unlikely), I would like to encourage the authors to get the maths correct and resubmit to a leading computational neuroscience journal (e.g., PLoS CompBiol or PNAS).   ORIGINALITY: 8 ==============  The investigated question is around already for several years. The paper is original in that someone finally worked out the details of the maths of both representations. This is a very important contribution which requires a fine understanding of both theories. A big "Thanks" to the authors for this!  Yet, I think that two relevant papers are missing:  - Savin, C., Deneve, S. Spatio-temporal representations of uncertainty in spiking neural networks, Advances in Neural Information Processing Systems 27, 2014.   This paper relaxes the assumption of a one-to-one correspondence between neurons and latent variables for sampling.  - Bill J, Buesing L, Habenschuss S, Nessler B, Maass W, et al. (2015) Distributed Bayesian Computation and Self-Organized Learning in Sheets of Spiking Neurons with Local Lateral Inhibition. PLOS ONE   In the discussion section, a similar relation between sampling and PPCs is outlined, for the case of a generative mixture model instead of the linear Gaussian model considered here.   SIGNIFICANCE: 10 ================  Sampling vs PPC representations is a hotly debated topic for years, staging the main track talks of the most important computational neuroscience conferences. Reconciling the two views is highly relevant for anyone who studies neural representations of uncertainty.   CONCLUSION ==========  This is one of the papers, I feel thankful that it has finally been written (and researched, of course). Unfortunately, the paper suffers from an unjustifiable amount of typos and errors in the maths. If accepted to NIPS, I would suggest a talk rather than a poster. Overall, I tend to recommend acceptance, but I could perfectly understand if the quality of presentation does not merit acceptance at NIPS.  Due to the very mixed impression, I assigned a separate score to each of the four reviewing criteria. The geometric mean leads to the suggested overall score 6/10.    SPECIFIC COMMENTS =================  - L163ff: Strictly speaking the statement is correct: A complete basis A permits to perfectly model the noise in I \sim N(T(s), noise). But I think this is not what the authors mean in the following: The example addresses how well Ax approximates the template T(s) without a noise sample. If so, the discussion should be corrected.   Errors in the derivation / equations ------------------------------------  Since I walked through the derivation anyway, I also include some suggestions.  - Eq (1): The base measure is missing: ... + f(s); alternatively write p(s|r) \propto exp(...) to match eq (6) of the main result. - L66: Missing def. of PF_i; required e.g. in line 137 - L90: p(s|x) not r - L90 and general: The entire identification of r  multiple samples x^[1:t] is missing, but crucial for the paper. - Eq after L92: This should be eq (3). These are the "forward physics" from stimulus generation to spikes in the retina. The name p_exp(I|s) is used later in L109ff, so it should be assigned here. - Eq (3): Copy of the previous eq with wrong subscript. Could be deleted, right? - Eq after L106: Missing def of \bar x = 1/t \sum x^i (important: the mean is not weighted by p(x^i) ) - Eq after L107: p_exp(x|s) is not defined and also not needed: delete equation w/o replacement - L108 and L109: The equality assumption is undefined and not needed. Both lines can be deleted. The next eq is valid immediately (and would deserve a number). - L117 and eq 6: At some point r (from eq 1) and x^[1:t] must be identified with another. Here could be a good point. Section 4 could then refer to this in the discussion of binary x^i and longer spike counts r.   Minor Points ------------  - Figure 1 is not referred to in the text. - L92: clarify "periphery" (e.g. retinal ganglion cells). This is an essential step, bringing the "pixel image" into the brain, and would deserve an extra sentence. - L113: The Gaussian converges to a dirac-delta. Then the integration leads to the desired statement.   Typos -----  - Figure 1, binary samples, y_ticks: x_n (not N) - Caption Fig 1: e.g.,~ - L48: in _a_ pro... - L66: PF_n (not 2) - L71: ~and~ - L77: x^(i) not t  [general suggestion: use different running indices for time and neurons; currently both are i] - Almost all the identity matrices render as "[]" (at least in my pdf viewer). Only in the eq after L92, it is displayed correctly. - Footnote 1: section_,_ valid for infinitely _many_ samples_,_ ... - L106: Dr - Caption Fig 2: asymptotic - L121: section 3 (?, not 4) - L126: neuron~s~ - Figure 3C: ylabels don't match notation in 3B (x and x'), but are illustrations of these points - L165: ~for~ - L200: invariant - L220: _is_ - L229: _easy_ or _simple_ - L230: correspond _to_ - L232: ~a~ - L242: ~the~