NeurIPS 2020

Experimental design for MRI by greedy policy search

Review 1

Summary and Contributions: This paper proposes a policy gradient approach active sampling for deep-learning accelerated MRI.

Strengths: I like the approach this paper takes. Applying policy gradient methods to sample selection makes a lot of sense, and they show an interesting and possibly unexpected result. The paper uses standard baselines and shows clear experimental results. When the simplifying assumption of a fixed pertained model is made, I feel there are some relations to other problems that could be considered or mentioned. For example, the feature selection problem in machine learning is very similar and has been heavily studied. The are various "subset selection" problems that are related. Although, there is not much mention of these related problems in other papers on active acquisition.

Weaknesses: The use of a single unet model is reasonable given it's not the main focus of the paper, however it would be nice to see a model closer to the state-of-the-art used instead. The reconstructions from the single unet are very far behind the SOTA. Using a fixed pretreated model is obviously not ideal, however training a model concurrently with an adaptive sampling pattern is probably impractical. It would be nice to also include equispaced masks as a baseline in the experiments, they generally out-perform random significantly, as noted in [37]. Offset equispaced masking is often even more effective (

Correctness: Looks correct.

Clarity: The paper is relatively clear, although the discussion of policy gradient may be a little verbose given how standard the technique has become

Relation to Prior Work: Discussion and citation of related work is very comprehensive.

Reproducibility: Yes

Additional Feedback: There is a arxiv preprint which appears to be concurrent work to this, which uses RL for the same problem: Following NeurIPS policies, this is not considered existing work for the purposes of novelty, although it would be good to cite it in the camera ready. UPDATE: I think this paper is relevant to NeurIPS, and I have discussed this with the other reviewers.

Review 2

Summary and Contributions: This paper presents a reinforcement learning (RL) approach for adaptive MRI experimental design, whereby the choice of frequency to scan is conditioned on current partial reconstructions, on a per-image basis. The paper formulates this problem as a Markov Decision Process (MDP), and derives a policy gradient algorithm for solving it. The experiments study the benefits of adaptive policies by comparing them with a non-adaptive one-step oracle, with the results suggesting that the proposed approach is beneficial. The results also compare favorably to those of a recent adaptive approach.

Strengths: * This paper makes a valuable contribution to the literature on MRI reconstruction and acceleration. In particular, deep learning (DL) reconstruction approaches for MRI have seen success in recent years (illustrated by results of the NeurIPS 2019 fastMRI challenge), but the study of deep adaptive MRI acquisition methods is still in its infancy. Such adaptive policies have implications to improve personalized healthcare and reduce patient discomfort. However, to date there are only few pieces of work tackling this topic in the DL literature, and to the best of my knowledge, no published work doing it from an RL perspective. As such, this paper contribution is both significant and novel. It is also of relevance to the NeurIPS community, evidenced by the fastMRI NeurIPS challenge mentioned above (using the same dataset as this paper), and an upcoming version for 2020 using brain data. * The proposed reinforcement learning method is sensible and the empirical results validate its potential. The experimental section is reasonably compelling, as they compare favorably with one of the only two recent DL-based adaptive MRI acquisition methods that I'm aware of. Furthermore, comparison with a greedy non-adaptive oracle helps bring forward the point that adaptive policies are useful and worth exploring in more depth (even beyond their proposed method). Additionally, their results suggesting that greedy policies outperform non-greedy policies is interesting, and I appreciate the experimental analysis done to investigate this point further.

Weaknesses: * In the related work section, the comparison between the present approach and the two most similar approaches [18, 44] is lackluster. In the case of [44] this is particularly important, since there was no empirical comparison to that work. There is also no explanation as to why such a comparison was not done. * The experimental results are done on only one MRI dataset, and images are cropped to a small size (128x128) for computational reasons (raw k-space data in fastMRI dataset is of size 368x640). Therefore, the experiments are done on a highly simplified setting, and it is hard to infer how well these results would scale to a more practical setting. * The differences between the AlphaZero approach and the proposed method are statistically significant but the effect is small, particularly considering the gap with respect to the adaptive greedy method. * The analysis of greedy vs. non-greedy is interesting, but the conclusions that can be drawn from it are still limited. It would have been valuable to study whether properties of the data favor the use of greedy policies. It is possible that the higher variance of the non-greedy method offers only a partial explanation for this result.

Correctness: There are some subtleties hidden in the MDP formulation. I'd argue that the problem, as formulated, is non-Markovian, since the reward function depends on the ground truth image, which cannot be accessed from state information alone. Formally, the function r(s, s') could return more than one value for a given s, s' pair, in the case where two or more ground truth images were consistent with the observations in s'. The text also mentions that " action a can lead to various next states s' and rewards", but then this point seems to be ignored in the policy gradient formulation, which, as far as I can tell, implicitly assumes that the transition function p(s'|s,a) is deterministic. That being said, I think these are technical details that would not ultimately affect much in the algorithmic implementation, but they do detract from the presentation in the paper and should be corrected.

Clarity: The paper is for the most part well written, although some aspects can be improved: - According to the text preceding it, Eq. (2) is supposed to define the policy as the one that maximizes quality after M steps, yet the equation uses lowercase m. This is confusing since the first paragraph in Section 3.2. specifically defines m \leq M, where M is the budget. Is the "m" in Eq. (2) a typo? If not, is there missing an additional maximization over all possible values of m from 1 to M? If the equation is correct, then this point can probably be explained more clearly. - Is there a \gamma missing from Eq. (5)? If not, then there is some explanation missing as to why this is not necessary for the non-greedy policy gradient formulation.

Relation to Prior Work: I'm not an expert in the vast MRI acquisition literature, but the discussion of related work appears thorough, including positioning of this work with respect to pre-DL work on mask design with compressed sensing using both non-adaptive and adaptive methods. The discussion also includes several non-adaptive DL-based acquisition methods, and also a discussion of the closest approaches to the paper in the DL literature [18, 44]. However, as mentioned above, the differences of the proposed method and [18, 44] should be discussed in more detail.

Reproducibility: Yes

Additional Feedback: - Is the use of a random policy just a by product of a policy gradient formulation? Is there a reason why a deterministic policy wouldn't be better? (Note that there are also deterministic policy gradient methods available, such as DDPG). - Which specific dataset from the fastMRI data was used? Was it DICOM knee data or was it raw k-space data? This is important, since, as mentioned above, raw k-space data is significantly larger than 128x128. If you are using raw data, can you discuss how your method scales to larger sizes images? ===== POST-REBUTTAL ====== Thanks to the authors for their careful rebuttal. I will keep the score provided in my review, recommending acceptance, and, in general, I'm very positive about this submission and I hope to see it published at NeurIPS. Nevertheless, I agree with other reviewers about the claims regarding greedy vs. non-greedy being insufficiently supported. For example, the statement "In this paper, we show that greedy methods outperform non-greedy methods on the MRI subsampling problem." is overly strong, considering that only one dataset and one solution method was used. Furthermore, the experiment regarding SNR merely shows a correlation between high gradient noise and underperformance in non-greedy methods, not necessarily a causal relation. Overall, I agree with the authors' rebuttal comment in lines 5-7 about what their primary claims are, but I do not think the paper is written in accordance with what they said in this rebuttal. The writing in introduction and conclusion are written with more definite statements than implied by the stated claim that "variance provides at least a **partial** explanation for the greedy/non-greedy performance gap". I suggest that the authors tone down the greedy vs. non-greedy discussion, and place greater emphasis on the more general policy gradient solution methodology as the main contribution of this work.

Review 3

Summary and Contributions: The paper proposes a novel approach for optimizing sampling in accelerated magnetic resonance imaging (MRI). They propose to leverage deep policy gradient methods, and show improvement over competitive baselines. In addition, they conjecture that the counter-intuitive result that greedy policy gradient approaches outperform non-greedy one originates from the presence of noise in the non-greedy objective's gradients. They empirically verify their claim by studying the signal-to-noise-ratio of the gradients of their greedy and non-greedy methods.

Strengths: The problem of optimizing sampling for MRI has become vastly investigated in the last years, and several exciting applications of experiment designs or reinforcement learning could find an application to MRI, which is very valuable to demonstrate their value in medical applications. It is also surprising that very few works have tried to apply RL methodologies to MRI sampling optimization, so this work could also serve as a proof-of-concept. The proposed approach of leveraging policy gradient methods is a natural approach to tackle the problem of sequentially optimizing sampling pattern with a discrete distribution of locations to be acquired. The results show small, yet consistent improvements over the baselines - including competitive ones - on different horizons, and the analysis of the noise in the gradients helps confirm the hypothesis of the authors.

Weaknesses: The main claim of the paper is the hypothesis that the noise in the non-greedy objective's paper is the reason why the greedy method can outperform it. However, I think that the empirical methodology is not strong enough to back this claim up, as the experiments are carried out on a single dataset, using a single network architecture and reported with a single performance metric. I think that the hypothesis would be much more clearly substantiated if the noise in the gradients were shown to be a consistent trend in various setting; I am afraid that, in the current state, the conclusion could be an anecdotical performance of the given setting. In addition, if I'm correct, RL models are prone to unstable training and are generally hard to train well. How can you confidently ensure that this behaviour isn't due to the RL policy not being trained for long enough? I also think that the experimental validation could be deeper. In particular, I think that the results with $\gamma \in (0,1)$ should be considered. It would be interesting to see whether a more greedy-like setup (gamma closer to 0) consistently shows less noise in the gradient than a non-greedy-like (gamma closer to 1) one, and this would strengthen the author's claim. Such questions should, in my opinion, be addressed in the paper. ----- AFTER REBUTTAL: I want to first thank the authors for their reply. After reading the reply and further discussing the paper with the reviewers, I will raise my score to weak accept. The other reviewers convinced me to reconsider the proof-of-concept of RL-based solutions for MRI optimization as a strong enough contribution on its own. Also, outperforming the MCTS-based approach is a strong result. I believe that the larger scale experiments and the exploration of gamma in [0,1] will make the paper stronger overall. However, I am still convinced that in its current form, the paper puts forth claims that are too strong regarding the noise in the gradient being the reason of the superior performance of greedy methods. I strongly encourage the authors to reword their statement (see for instance the abstract) to emphasize that what they provide is a possible, partial explanation of the phenomenon. I would expect the hypothesis to be validated on another dataset at the very least before claiming to have "experimentally verif[ied] that this noise leaves the non-greedy models unable to adapt their policies".

Correctness: As mentioned above, my biggest fear is that the result wouldn't hold as clearly in other settings.

Clarity: The paper is mostly well written, and the MRI-specific jargon is well defined and clear to understand. I have a couple of suggestions that could maybe improve the clarity of the presentation. - In the theoretical part, I think that some notation might be confusing for the reader. s and a are used to denote state and actions respectively, but S and A denote a subsampling operator and the reconstructed data, whereas in standard the likes of Sutton's RL book, this usually denotes the random variable to state and actions. Maybe using something else could disambiguate this? - In my opinion, equation 2 does not really capture the idea that you want your policy to give you the best prediction at each step to overall reach the best possible performance when you exhaust the sampling budget. - It is not totally clear how the oracle baseline works. It is said to be non-adaptive, but I don't understand how it is obtain? Do you greedily compute on the test set the location which will improve most your SSIM - From an experimental perspective, I think that appendix A does a really nice job at providing most needed information to reproduce the results. However, I would consider adding more details on the training itself. First, I think that you could provide slightly more details about the parameters that you used (e.g. parameters of Adam, restatement of the objective functions, ...). Secondly, I think that adding a section on the training of the RL models themselves would help: I know that it's common practice to use replay memories (maybe it's not applicable there) and things like that to make the training of the model more stable. An pseudo-code like description of the detailed training procedure would certainly be useful.

Relation to Prior Work: The discussion is overall clear. I noticed two small points that might be imprecise in related literature: - [30] is cited in the introduction and in section 2, but it seems that from the description around line 94, that the model uses a single network for conditional generation and prediction of the next move, which is not what is stated around line 42. - I think that [10, 11, 29] aim mainly at providing a greedy, non-adaptive sampling mask from scratch, and the main benefit that they bring is that they do not depend on a heuristic distribution, but rather build their estimate only through the training data. I also wonder why the authors did not connect the work more explicitly to the REINFORCE [1] approach and did not acknowledge the host of research carried out in trying to reduce the noise in the gradient variance. See for instance [2] and references therein. [1] Williams, Ronald J. "Simple statistical gradient-following algorithms for connectionist reinforcement learning." *Machine learning* 8.3-4 (1992): 229-256. [2] Kool, Wouter, Herke van Hoof, and Max Welling. "Estimating gradients for discrete random variables by sampling without replacement." *arXiv preprint arXiv:2002.06043* (2020).

Reproducibility: No

Additional Feedback: Remarks. I find it strange that this paper, which is about MRI sampling optimization, does not show any reconstructed image. I think that a visual assessment of the different methods could be useful. Questions. - Could you elaborate on why did you chose to use SSIM over PSNR? - In Table 2, do you have an idea why is the SNR largest for greedy at epoch 20? - As the paper is built around the noise in the different approaches, couldn't experimenting with different baselines in (5) and (6) actually help reduce the variance in the gradients? Possible Mistakes. - In equation (2), shouldn't m+1 be replaced with M? l. 136 speaks of improved quality after M steps. - l. 280, shouldn't the denominator be 1/(B-1) and not 1/B(B-1)? Notation. - r(A_{t'}, A_{t'+1}) does not explicitly show the dependence on x, maybe putting it as a subscript could make the dependence clearer?