Peer Review History
| Original SubmissionMarch 28, 2022 |
|---|
|
PONE-D-22-09166 Decomposing past and future: Integrated information decomposition based on shared probability mass exclusions PLOS ONE Dear Dr. Thomas Varely, As before we thank you for your patience in the reviewing process. Also, thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Both referees are positive about the general ideas and direction of the paper. The first only suggest a minor revision a minor revision regarding the way "negative atoms" are considered within the paper. The second reviewer, however, has an extremely detailed list of a number of points that should be addressed before the paper is accepted. Please submit your revised manuscript by 10/22/2022. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Benjamin Z. Webb, Ph.D. Academic Editor PLOS ONE ournal requirements: When submitting your revision, we need you to address these additional requirements. 1.Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2.For this single-authored manuscript, please replace "we" with "I". 3. Please update your submission to use the PLOS LaTeX template. The template and more information on our requirements for LaTeX submissions can be found at http://journals.plos.org/plosone/s/latex. 4.Thank you for stating the following in the Acknowledgments Section of your manuscript: “T.F.V is supported by NSF-NRT grant 1735095, Interdisciplinary Training in Complex Networks and Systems at Indiana University Bloomington. I would like to thank Dr. John Beggs & Dr. Olaf Sporns for mentorship and feedback on this project. I would also like to thank Dr. Abolfazl Alipour and Mr. Leandro Fosque for providing the dissociated culture data.” We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5.In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The article introduces a novel metric of double redundancy and evaluates it in various scenarios. The manuscript is very well written, the proposed metric has a number of desirable properties, and the presented analyses are very interesting. As I believe this is a good contribution to the field, I strongly suggest the manuscript to be accepted for publication. My main suggestion is the following. It seems to me that this type of information decomposition do not consider negative atoms as a bug, but actually embrace them and provide an explanation for their meaning. If this is the case, I'd like to see that important feature highlighted more through the text. Additionally, it would be nice if this feature could be illustrated a bit more extensively in the analysis of the three synthetic models, where I would have liked to see a bit more of explanation of the meaning of various results. Besides, it seems to me that this Phi-I-D could be readily extended for a local version, i.e. one could use these ideas to define an information decomposition that can be applied to individual datapoints. That could open an exciting line of research studying dynamics with these tools, which perhaps could be mentioned in the discussion? Also, it seems to me that such extension would be more natural than if one tries to do the same with other Phi-I-D decompositions? Finally, I'd suggest to try to introduce the acronym "Phi-I" (which I guess stands for integrated information atom) in the introduction, just to make the reading easier. Reviewer #2: * Summary This paper builds upon the recently introduced Integrated Information Decomposition (phi-ID) from Mediano et al. More specifically, it takes the proposed measure of redundant information I_sx from Makkeh et al., which was originally introduced for the Partial Information Decomposition (PID), and proposes a modified measure I_Tsx such that it is now compatible with Phi-ID. The paper discusses some of the properties of the resulting decomposition, and applied it to several examples. Have reviewed the paper, I have identified 10 significant issues that would need to be addressed before the paper could be accepted. As such, I am recommending that this paper undergo major revisions. * MAJOR ISSUES / COMMENTS 1. It is not clear to me if Phi-ID is meant purely for the analysis of timeseries, or can it be applied to any random variables (as per PID). Some clarification on this point would be good. 2. You state that the desire to decompose the excess entropy into separate components associated with the particular elements of the system is the main motivation behind this work, and you describe how such a decomposition could perhaps be used to understand and quantify hitherto weakly defined concepts such as downward and upward causation. This motivation is perfectly reasonable and is of broad interest to the scientific community. You briefly discuss PID before ruling it out because it is only applicable to a single target variable. However, based on what you have written, I don't understand why this is so problematic. In PID, the target is privileged in the sense we are decomposing the information that the source variables provide about this particular variable. There is no restriction that requires the target variable to be univariate, so in this regard, PID is not limited to a single target variable. Of course, you are well aware of this since (as mentioned at the bottom of page 8) you describe your own work (ref. [18]) which uses PID to decompose the information provided by each state in the past about the entire system in the future. At top of page 9, you state that PID provides no insights into how parts of the system constrain each other, as the future state is aggregated into a single unitary whole. (Actually, you might want to reconsider describing a multivariate variable as a unitary whole.) The problem I have is that clearly PID can also be used to decompose the information provided by each state in the past about any particular state in the future, or indeed about any collection of states in the future. If your application of PID in ref. [18] provides insights into how the states of particular elements collectively constrain the future of the whole system, then why would PID not be able to provide insights into how the states of particular elements constrain particular parts of the system in the future? To me, it seems that you just need to replace the target variable representing the future state of the entire system with a target variable representing the future state of the particular part that you are interested in. Hence, I do not understand how this is supposed to be a fundamental limitation as you describe it. So, either I misunderstand the problem based on your the description of the problem, in which case you should improve the description, or it is not quite the limitation that you describe. 3. Following up on the prior point, it seems to me that your problem might perhaps be that decomposing the information provided by each state in the past about a particular state in the future would not strictly speaking be a decomposition of the excess entropy. However, I don't really see how this is a problem. Nevertheless, if it is a problem, then it is worth noting that certain approaches to information decomposition satisfy a chain rule for the target variable. In effect, this means that there is consistency between the decomposition of the information provided by each state in the past about the entire system in the future, and the separate decompositions of the information provided by each state in the past about the particular states in the future. That is to say, if the decomposition satisfying a target chain rule, then the separate decompositions of the information provided by each state in the past about the future state of each particular part in the future, must be consistent with the full decomposition of the full decomposition of the information provided by each state in the past about the future state of the entire system in the future, i.e. the decomposition of the excess entropy. In fact, to me, this consistency seems like a very natural requirement. To summarise, I don't understand the problem that you say is a limitation of PID, and furthermore, a PID with a target chain rule seems like a much more important problem, as this would me that there is a consistency between the decompositions of the information provided by the past state of the parts about future states of the various parts,and the decomposition of the information provided by the past state of the parts about future state of the entire system. Perhaps you could discuss the relevance of a target chain rule to the problem of decomposition the future states of various parts of the system versus the future state of the entire system. 4. PID is not yet a well-accepted methodology in information theory. This lack of acceptance is largely down to a lack of a single, well-accepted measure of redundant information that is compatible with the Williams and Beer Axioms. Nevertheless, if one accepts that the Williams and Beer Axioms are reasonable properties for a measure of redundant information, then the derived redundancy lattice cannot be dismissed. To be specific, Williams and Beer start with the Axioms for I_cap, and then show how this axioms reduce the domain of I_cap to the set of all antichains of the inclusion lattice, i.e. the set A(R) in their notation. They then use the axioms to show that the elements of this set are partially ordered, and that these elements, together with the partial order, form a lattice structure which they call the redundancy lattice. In other words, if you accept the axioms, then you arrive at the redundancy lattice and this is not something that is disputed. Furthermore, Williams and Beer then show how the axioms lead to a two nice properties: specifically, that I_cap is nonnegative and an increasing function on the redundancy lattice. In this regard, PID is theoretically sound and the fact that we do not yet have a unique measure of redundant information is not problematic until you actually want to evaluate the atoms in the lattice. Similar to PID, Phi-ID is not generally accepted. However, unlike PID, Phi-ID does not have a simple axiomatic basis. Reference [8] seems to provide two axioms, namely compatibility and partial ordering. It seems to me that the compatibility axiom also contains the original Williams and Beer axioms (although this is not very clearly stated), and so this axiom effectively just states that we have the original Williams and Beer axioms. The second axiom, i.e. partial ordering, however, is not so elegant. In effect, it is a requirement that this double redundancy function satisfies a certain partial ordering, and there isn't much justification provided for this axiom as far as I can tell. Contrast this to PID, where Williams and Beer started with three very simple axioms and then subsequently showed that any function which satisfies these axioms would necessarily be partially ordered. That is to say, in the Williams and Beer approach, the lattice is derived from three simple properties of the redundancy function, whereas in Phi-ID the lattice is effectively introduced as an axiom itself without much justification. In fact, I am actually confused as to how exactly Reference [8] arrives at this lattice structure from their axioms. It seems to come from Proposition 1 in Reference [8], but I do not see any proof of this proposition in their paper. Strictly speaking, this is a problem with Reference [8] rather than your paper. However, since Reference [8] is not a published paper, this is also problematic for your paper. Since your paper aims to build upon this work, I think it is important that you clarify how exactly the double-redundancy lattice is obtained. 5. Following on from the prior point, you would also need to show that the double-redundancy function that you define satisfies these axioms. If you can't (i) show that the double-redundancy lattice can be derived from the axioms and then (ii) show that your double-redundancy function satisfies these axioms, then you have no justification for later some of the later steps such as the Moebius inversion. You will notice that almost all of the existing proposals for a measure of redundancy for PID first start out by showing that the proposed measure satisfies the Williams and Beer Axioms, or variants thereof. 6. Since you are building so directly upon i_sx, I think you need to improved the description of the motivation behind its introduction. As it is, there isn't much beyond the sentence appearing before equation (15). There is a great deal of discussion motivating i_sx in the original papers, so it should be expanded since you are basically just extending this approach to make it compatible with Phi-ID. 7. Similarly, when you introduce I_Tau-sx, you do not provide much of a description of the motivation behind this particular definition. In particular, you should be justifying the replacement that you make in your definition relative to the original definition of i_sx provided in equation (15). Furthermore, is this change obvious? I am not saying that it is, but since the original i_sx was proposed for PID rather than Phi-ID, then i_sx would clearly also need to be modified. Perhaps the change you have made it a trivial change, or maybe it is more significant in some way. Either case is fine, but you really aught to be discussing this change and justifying why you have defined this generalisation in this particular way. 8. You are proposing a decomposition that is based on the local mutual information, which is a non-negative function. The justification for doing this seems to come from reference [35] which gets around this issue by decomposing the local entropy instead of the local mutual information, i.e. the local mutual information is first decomposed into two non-negative local entropies, and then each of these local entropies are decomposed separately. Thus, really you have two separate information decompositions (i.e. two separate decompositions of the local entropy), and you are combining the corresponding atoms of these two separate decompositions quantities to get local-mutual-information-like quantities. In other words, you are not really decomposition the local mutual information, but rather you are decomposing the two local entropies. You present your decomposition as though it is a decomposition of the local mutual information, and make it sound like the decomposition of the local entropies is an additional feature. To me, it seems like it is actually a decomposition of the local entropy, and you are also combining corresponding atoms of these two separate decompositions quantities to get local-mutual-information-like quantities. This difference is important as the results from the recombine atoms really should be seen as the results obtained from combining quantities from two separate decompositions, rather than a decomposition in its own right. This problem is also present in reference [10]. 9. The synthetic systems that you use here in this paper: where do they come from? Are you introducing them for the first time here, or are they well known within the field of IIT? Do we know what the actual results should be or are their certain results which are seen as desirable based on intuition? In general, your description of obtain results does not give me the impression that the results are well understood. For instance, when it comes to describing the result for the disintegrated system, you describe the the element-wise storage atoms as being the "strongest" while the pairwise transfer atoms are negative. You describe this latter result as being "consistent with the notion of the system as a disintegrated structure", but I don't see how this is the case and you do not provide any further clarification. You say that there are more positive interactions(?) between individual elements and higher-order synergistic joint states than anticipated. However, you never described or justified your anticipated result, so this is not a helpful comment to make. The fact that you describe this result as "curious" does not fill me with confidence that the results are indeed sensible or helpful. These results are all local mutual informations, but as described in point 7, these values are really obtained from separate decompositions of the two local entropies, so I suspect these results would be less mysterious if you looked at these values. Similarly, you are also a bit vague and uncertain about the results obtained from the integrated system. Do we know what the results should be, or are is there some kind of intuitive result that you would like to see? Describing some of the obtained results as a "surprise" when you are considering synthetic examples that should have some definite result is quite problematic to me. This could be fine if you provide an explanation for the surprising results, but I don't see any justification that explains these results to me. This kind of description would be absolutely fine if this was a well established method and you were applying it to some empirical data from some system that is not well understood. It is troubling, however, when these are the results that you obtain from applying this to synthetic examples which really should be justifying the theoretical definition that you have introduced. Regarding the heterogeneous system, I am not really sure what we are supposed to take away from this example. You were actually a bit more explicit in stating your expectation for this example, in that you said that you expected to see multiple types of information atoms present, and indeed, this is the result that you obtained. However, what does it really tell us to learn that a randomly generated example produces a dynamic which is associated with a small amount of information associated with each of the atoms? Without further guidance, I am not sure what exactly I should take away from this. 10. The empirical example using a dissociated neural culture: I don't want to be overly negative here because I think the analysis of this kind of data is an interesting scientific endeavour, and I think that information-theoretic methodologies are an appropriate way of potentially understanding this kind of system. However, this entire section to me, is not helpful for a paper that aims to propose a novel theoretical approach. It is interesting, but I think that this work would be far more appropriate as a separate paper after this theoretical method has been accepted in its own right. The theoretical result should be interesting based on its own merits. You should propose the theoretical measure, provide the motivation for the definition, and justify it using well-understood examples. Typically, for this kind of proposal, you would typically use synthetic examples (indeed, as you have aimed to do with your synthetic examples). This is certainly true for all of the PID based approaches, although perhaps it is more tricky for Phi-ID (see point 1). The problem here is that the motivation for defining your measure is not very clear (see points 6 and 7), and I think there are some notable theoretical shortcomings (see points 4, 5 and 8). Then the results the you obtain for the synthetic examples are not clear or convincing (see point 9). With all of this in mind, I do not see what value the empirical example where there is no well-established ground truth. If the results can't be fully explained for the synthetic examples that are designed to exhibit certain features or characteristics, then I don't see how we can trust the results when applied to real empirical data. On the flip side, it is you paper, so I don't want to say that this analysis must be removed. Rather, I am saying that it needs much better theoretical justification before we can trust the results, or draw inference from the results when applied to empirical data. To reiterate, the theoretical results should be interesting in there own right, and should stand on their own two feet (to use an idiom). In my opinion, the level of detail required achieve this level of theoretical rigour would result in a paper in its own right, and then this example could potentially go in a separate empirical paper that uses the newly establish theoretical framework. Whether or not you want to keep the empirical example in this paper, you must improve the rigour of the theoretical results before this paper is suitable for publication. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 1 |
|
Decomposing past and future: Integrated information decomposition based on shared probability mass exclusions PONE-D-22-09166R1 Dear Thomas Varley , We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Benjamin Z. Webb, Ph.D. Academic Editor PLOS ONE P.S. There are just a few comments by the second referee that could be addressed in a slightly revised version of the paper but whether these changes are placed in the final version of the paper is up to the author. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #2: (No Response) Reviewer #3: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2: Yes Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes Reviewer #3: (No Response) ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #2: Yes Reviewer #3: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #2: Yes Reviewer #3: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #2: * Summary The author has greatly improved the manuscript, and my recommendation is that the paper can go to publication pending minor revisions. The author has addressed the 10 issues that I previously mentioned insofar as can reasonably demanded. I am still sceptical of the \\Phi-ID framework regarding the specific issues that were raised in the prior round. However, the author cannot be expected to solve all weaknesses or shortcoming in existing research. I would urge the author to have a further think about these issues going forward, but this certainly should not stop the publication of this work. I have also added one additional point regarding the bar | notation used at a certain point in this paper. However, the fix is straightforward. * PRIOR ISSUES and COMMENTS 1. Okay, this is interesting to know! However, I am still confused by something here: if you are applying it to random variables (instead of timeseries), then what is the meaning of each of the atoms? For instance, in Fig. 2, you say that {1}{2}->{1} corresponds to information that is redundantly disclosed by X^1 and X^2 at time t-\\tau that is then only uniquely disclosed by X^1 at time t. What does the atom {1}{2}->{1} corresponds to if there is no sense of time in the data? I suppose I am saying that I find your response interesting, and it leaves me with even more questions. I don't feel very strongly that you need to address this point, however. This really is something that aught to be addressed by the authors who introduced \\phi-ID. 2. I am a bit confused by the response. I find it natural to query the composition of the information provided by the past states of each component about the future states of the entire system. For example, in a two component system, we would have a decomposition based on I(X^1_-\\tau; \\bm{X}_t) and I(X^2_-\\tau; \\bm{X}_t), which tells us what the past states of X^1 and X^2 tell us about the future states of the entire system (X^1,X^2) in terms of what the past states of each component uniquely, redundantly and synergistically tell us about the future states of the system. Of course, this does not consider the unique, redundant and synergistic interactions between the system in the future. In order to consider these, we would have to slide our time window along, say, k steps into the future, i.e. by evaluating a decomposition based on I(X^1_-\\tau+k; \\bm{X}_t+k) and I(X^2_-\\tau+k; \\bm{X}_t+k). I don't see why we should expect a quantity based on the time t to tell us about the interactions into the future beyond t. I can see why it would be nice to have such a quantity. However, that does not mean that such a quantity has to exist. The critique here is strongly related to my fourth point; that is, I find the axiomatic basis of \\phi-ID very weak compared to PID. The PID lattice and hence the atoms are a consequence of some rather simple axioms. In contrast, as far as I can tell, the second \\phi-ID axiom effectively introduces the \\phi-ID lattice as an axiom itself without much justification. As such, I don't find the associated atoms very natural, which is why I say it might be nice to have these quantities, but the \\phi-ID axioms don't provide much of a justification to me. However, this is more a critique of \\phi-ID itself that the content of this paper. The contribution that you make here is perfectly reasonable (and indeed very good) if I suppose that \\phi-ID is itself theoretical sound, so I would not like this point to block you from publishing this work. 3. The point I was making about the target chain rule is that it could be used to consider the how each time point in the future contributes to each atom of information about the entire future. If we consider the future states over time, i.e. \\bm{X}_t = {\\bm{X}t_1, \\bm{X}t_2, ...}, then a decomposition with a target chain rule could be used to consider how each atom of information at each time point in the future contributes to each of the corresponding atom of information for the entire future. For example, the you could look at what the past states redundantly tell us about the future states R(X^1_-\\tau,X^2_-\\tau; \\bm{X}_t) and consider how each time point t_1, t_2... contributes by looking at R(X^1_-\\tau,X^2_-\\tau; \\bm{X}_{t_1}), R(X^1_-\\tau,X^2_-\\tau; \\bm{X}_{t_2} | \\bm{X}_{t_1}) and R(X^1_-\\tau,X^2_-\\tau; \\bm{X}_{t_3} | \\bm{X}_{t_1}, \\bm{X}_{t_2},), etc, via the chain rule: R(X^1_-\\tau,X^2_-\\tau; \\bm{X}_{t_1}) = R(X^1_-\\tau,X^2_-\\tau;\\bm{X}_{t_2} | \\bm{X}_{t_1}) + R(X^1_-\\tau,X^2_-\\tau; \\bm{X}_{t_3} | \\bm{X}_{t_1}, \\bm{X}_{t_2},) + ... If you have a target chain rule for the redundancy, then you also have it of the synergy. Thus, for instance, you could use a PID with a chain rule to understand how the (total) synergy in the future is composed of synergies at each particular time point in the future. This to me seems like a natural way of using PID to address the problem that you seem interested in regarding point 2. Similar to before, this is more a critique of the \\phi-ID framework than of your contribution to here, which is perfectly reasonable. 4. This is really the main issue that I have, i.e. the weakness that I see in the \\phi-ID approach. However, as I said above, I think your contribution to the literature is very worthwhile. I think it is also worth saying I have no issue with basing your research on an unpublished paper. \\phi-ID is certainly getting enough attention to merit further work. However, the fact that many people are using \\phi-ID does not make this weakness in the axiomatic basis go away. Personally, I would be far more worried about fixing the weak foundations before trying to build more work on top of it. However, it is perfectly reasonable for you to do this and I would not like this point to prevent you from publishing your worthwhile findings. 5. Your response to point 4 addresses this point perfectly. 6. Your response addresses this point. 7. I did not mean to say that the contribution is not significant -- it is very worthwhile! I more meant that I think you should comment on how natural it is as a generalisation, and your additional comment addresses this perfectly. 8. The changes you have made fully address this point. 9. The new version is much improved. The motivation behind each of the synthetic systems is greatly improved. Now that I understand the motivation behind them, this section is much stronger to me. I think your earlier caution along with the weaker description of the motivation gave me the sense that the results were not well-understood. This improved description together with the improvement regarding point 8 has much improved this section. The intuition is more clear, and I much prefer this section. I am still a little sceptic of some of the interpretations, but this all comes from my scepticism of the terms in the \\phi-ID lattice rather than anything that is said here. 10. Given the improvements to the section regarding the synthetic examples, my main problem with this section has been resolved. (When the results of the synthetic examples where no clear, this application seemed to be an attempt at justifying the method rather than an example of how it can be used.) I perhaps was not explicit enough in saying that my comment here was not to say that I thought this section must be removed. * NEW ISSUE 1. The notation that you have used for the unique information is quite problematic. Specifically, you have used the bar | to denote which variable the information is unique with respect to, e.g. Unq(X^1;Y|X^2) is the unique information that X^1 provides about Y with respect to X^2. It is standard practice to use the bar | to denote conditional probabilities, and this notation is naturally inherited by information theory as a subset of probability theory. Thus, it is very confusing to use the bar notation for the unique information. The problem with you choice is that, in probability theory, you can always replace a probability with a conditional probability, and so any function defined based on some probability can also have a conditional variant. So, for instance, instead of decomposing the information that X^1 and X^2 provide about Y which is associated with P(X^1,X^2,Y), as you have denoted in eq. (4), you could decompose the information that X^1 and X^2 provide about Y given that you know variable Z, which is associated with P(X^1,X^2,Y | Z), yielding the decomposition, I(X^1,X^2,Y|Z) = Red(X^1,X^2;Y | Z) + Unq(X^1; Y \\ X^2 | Z) + Unq(X^2; Y \\ X^1 | Z) + Syn(X^1,X^2;Y | Z). If you use the bar for unique information too, then how could you represent the above decomposition? I think this issue is also in the original \\phi-ID paper, so it probably just came directly from there without noticing this issue. I suggest switching to the set difference \\ notation used by Bertschinger et al 'Quantifying Unique Information', as this is much less problematic, as demonstrated here. Reviewer #3: (No Response) ********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #2: No Reviewer #3: No **********
|
| Formally Accepted |
|
PONE-D-22-09166R1 Decomposing past and future: Integrated information decomposition based on shared probability mass exclusions. Dear Dr. Varley: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Benjamin Z. Webb Academic Editor PLOS ONE |
Open letter on the publication of peer review reports
PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.
We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.
Learn more at ASAPbio .