REVIEW 4 major objections 4 minor 44 references
Why Does Dropping Edges Usually Outperform Adding Edges in Graph Contrastive Learning?
T0 review · 4 major / 4 minor · reviewed 2026-08-11 · deepseek-v4-flash
Pith's one-line read The paper claims that the relative stability of edge dropping versus edge adding in graph contrastive learning is governed by the Error Passing Rate, with the change proportional to a degree-based coefficient and the threshold set by an…
desk verdict A genuinely good question and a working algorithm, but the central theoretical explanation rests on an unstated extra assumption, so the main claim is not established in the current form. read the letter →
The pith
A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.
The reading
What carries the argument
The central object is the Error Passing Rate (EPR), $r_G=M_{\mathrm{wp}}/M$, the proportion of messages in GCN aggregation that travel along error edges, i.e. edges linking different classes. The load-bearing identity is $\delta_{G,G'}=m\,m'\,(r_G-r_{G'})=(k-\xi)\,\alpha_{ij}\,m$ under Assumption 3.4, where $\alpha_{ij}$ is the degree-normalized coefficient $2/\sqrt{(d_i+1)(d_j+1)}$ for an added edge and $2/\sqrt{d_i d_j}$ for a dropped edge. This identity reduces the effect of a single edge perturbation to a product of a universal error fraction, a class-concordance indicator, and a degree factor, which is what lets the paper compare the stability of adding and dropping without labels. It also supplies the algorithmic pre-screening criterion: candidate edges can be ranked by $\alpha$ and perturbed only when the EPR impact is small.
What would settle it
Use ground-truth labels on a benchmark graph to compute each node's error fraction $M_{\mathrm{wp},i}/M_i$ and check whether the values are nearly constant; if they vary widely, the uniform-$k$ assumption behind Theorem 3.5 does not hold. Alternatively, measure EPR after adding and dropping edges with known $\alpha$ values and test whether the change is proportional to $\alpha$ as predicted.
Extended reading notes
Core claim
The paper's central claim is that the relative stability of edge dropping versus edge adding in graph contrastive learning is governed by an Error Passing Rate (EPR), defined as the ratio of GCN message-passing traffic that flows between different classes. For a graph $G$ and a graph $G'$ obtained by adding edge $(v_i,v_j)$, the paper proves the identity $\delta_{G,G'} = m\,m'\,(r_G - r_{G'}) = (k-\xi)\,\alpha_{ij}\,m$, where $k$ is the assumed uniform per-node error fraction, $\xi=1$ exactly when the endpoints have different classes, and $\alpha_{ij}=2/\sqrt{(d_i+1)(d_j+1)}$. For dropping the same edge the sign reverses, $\delta_{G',G}=(\xi-k)\alpha_{ij}m$, with $\alpha_{ij}=2/\sqrt{d_i d_j}$ in the original graph. The magnitudes are therefore $k\alpha/m'$ for a same-class addition, $(1-k)\alpha/m'$ for a cross-class addition, and the mirror image for drops. Because most real graphs have $k<0.5$ and because almost all non-edges are cross-class, this explains why dropping edges usually hurts less than adding edges; the paper goes on to construct an augmentation method that samples edges according to these $\alpha$ weights.
Load-bearing premise
The entire quantitative comparison rests on the assumption that every node receives the same fraction $k$ of erroneous messages during aggregation, a condition real graphs will only approximate.
Editorial extensions
If this is right
- Under $k<0.5$ in homophilic graphs, the expected EPR damage of a random edge addition ($(1-k)\alpha/m'$ for the typical cross-class non-edge) exceeds that of a random edge drop ($k\alpha/m$ for the typical same-class edge), which is the paper's quantitative explanation for the empirical rule.
- Because non-edges vastly outnumber edges, blind edge adding is almost always a cross-class move and therefore raises EPR; limiting additions to non-edges with small $\alpha$ should make adding competitive with dropping.
- Low-degree node pairs have larger $\alpha$, so their perturbation changes EPR more; augmentation policies that frequently drop low-degree edges are predicted to be higher-variance, a prediction the paper verifies against importance-based edge dropping.
- A symmetric use of added edges is beneficial in only one of the two contrastive views; the paper's EPAGCL uses add-and-drop for one view and drop-only for the other, and reports lower standard deviation as well as higher accuracy.
Reading between the lines
- If Assumption 3.4 is replaced by node-dependent error fractions $k_i$, the clean proportionality in the paper's Eq. (5) should become a weighted average; a per-node version of the theorem could predict which local neighborhoods benefit from drops versus adds.
- The predicted reversal at $k=0.5$ is directly testable: on a heterophilic or dense graph with EPR above one half, the theory says edge adding should become the stable augmentation, turning EPR into a practical guide for augmentation choice.
- The analysis treats one edge perturbation at a time; an extension to simultaneous perturbations or deeper GNNs would show whether the $\alpha$-based edge ranking survives interactions, which is the assumption the EPAGCL sampling procedure effectively makes.
Signed reviews
Editorial analysis
A structured set of objections, weighed in public.
Referee Report
Summary. The paper asks why dropping edges is usually a more stable graph augmentation than adding edges in graph contrastive learning. It introduces a metric called Error Passing Rate (EPR), which measures the fraction of message-passing mass that flows along edges connecting different classes in a GCN. The authors derive formulas for the change in EPR when an edge is added or dropped, concluding that, under an assumption of uniform per-node error rates, the change is proportional to alpha_ij = 2/sqrt((d_i+1)(d_j+1)) or 2/sqrt(d_i d_j), and that for graphs with EPR below 0.5 dropping edges is more stable. Based on this analysis they propose EPAGCL, an augmentation method that adds and drops edges with probabilities derived from alpha_ij. Experiments on seven benchmark datasets report competitive or improved accuracy relative to several GCL baselines, together with ablation and efficiency studies.
Significance. The question addressed is relevant and the proposed EPR viewpoint is interpretable: it gives a concrete, label-free-in-principle measure of how well a graph structure matches a GNN's message-passing scheme. If the theoretical derivation were sound, the paper would provide a useful explanation for a widely observed empirical phenomenon and a principled basis for designing augmentations. The paper also ships code and includes a reasonably broad experimental comparison, ablations, efficiency measurements, and appendices with EPR values for real datasets. The main weakness is that the central theorem supporting the paper's explanation contains a derivation gap that is not fixed by the stated assumptions, and the key uniformity assumption is neither justified nor empirically checked. Until these points are repaired, the paper's contribution is primarily an empirical augmentation method rather than an established theoretical explanation.
major comments (4)
- [Appendix B / Eq. (5)] The derivation of Eq. (5) from Assumption 3.4 is incomplete. Assumption 3.4 states Mwp,i/Mi = k for every node, which gives e2 = k m2 and e3 = k m3 for the edge sets incident to vi and vj, but for the set E1 (edges with neither endpoint equal to vi or vj) it gives only the aggregate constraint 2e1 + C_err = k(2m1 + C_tot), where C_err and C_tot are the error and total message masses on the cut between {vi,vj} and the remaining nodes. The equality e1 = k m1 used in Appendix B therefore requires the additional, unstated condition C_err = k C_tot. Since Eq. (5) and hence Theorem 3.5 are derived entirely from this step, the paper's central explanation for why dropping edges is more stable than adding edges is not established even under Assumption 3.4.
- [Section 3.3 / Appendix F] Assumption 3.4 is load-bearing for Theorem 3.5 but is never justified or tested. Table 6 reports only the global EPR rG for benchmark graphs; a global value below 0.5 is compatible with arbitrarily large per-node variation in Mwp,i/Mi, so it does not support the uniformity assumption or the inference that 'k < 0.5 for most graphs' in the sense required by Theorem 3.5. The authors should report the empirical distribution of per-node error fractions on the datasets used in Section 4, or replace Assumption 3.4 with a condition that can actually be checked on real graphs.
- [Theorem 3.3 / Appendix A] Theorem 3.3.2 as stated is false without an additional assumption. The proof introduces Assumption A.2 (at least one same-class edge) only in the appendix and uses it to rule out the equality case t1 = t2 = t3 = 1. If every edge of G connects different classes, then adding a different-class edge leaves rG unchanged, so delta_G,G' = 0 rather than < 0. The theorem statement in Section 3.3 must include this condition or a replacement, and the main text should state it explicitly rather than burying it in the proof.
- [Section 4 / Theorem 3.3] The benchmark datasets used in the experiments do not satisfy the degree condition dmax <= 4 dmin - 1 assumed by Theorem 3.3. For example, Cora has a maximum degree far above 4 dmin - 1, so the experiments in Section 4 cannot be said to validate Theorem 3.3 on these graphs. If the intended validation target is instead Theorem 3.5, this should be stated explicitly, since Theorem 3.5 does not inherit the degree condition from Theorem 3.3.
minor comments (4)
- [Proposition 3.2 / Eq. (2)] In Eq. (2) the numerator and denominator are written with the same symbol E, which is confusing: the numerator should be the sum over the error edge set (edges connecting different classes), while the denominator is the sum over all edges. Please use distinct notation, e.g. an overline or a calligraphic symbol for the error edge set, throughout the paper.
- [Appendix E / Table 5] The Wilcoxon signed-rank test is applied after repeating each of the 5 runs five times to obtain 25 observations. This pseudo-replication violates the independence assumption of the test and inflates the reported significance levels. The test should be run on the original 5 paired observations, or a different procedure should be used.
- [Section 3.3 / Appendix B] The symbol for the class-indicator term is xi in Eq. (5) in the main text but becomes s in Appendix B; please standardize the notation.
- [Throughout] There are several typographical errors, including 'recursivly' in Section 3.2, 'summarzied' before Theorem 3.3, and 'Memroy' in Table 3; a careful proofread is needed.
Circularity Check
No significant circularity: the EPR derivation is self-contained and the self-citations are inspirational rather than load-bearing.
full rationale
The central derivation (Eq. 5 and Theorem 3.5) starts from Definition 3.1 and Assumption 3.4, neither of which is fitted to the claims. Under Assumption 3.4, e2 = k m2 and e3 = k m3 are exactly the per-node constraints at vi and vj, and subtracting these from the summed per-node constraints over all nodes yields e1 = k m1; hence Appendix B's reduction delta = (k - xi) alpha m follows from the stated assumptions rather than from a hidden fit. EPR is introduced as a definition, not as a renamed known result, and Theorems 3.3 and 3.5 are derived inequalities with stated degree conditions. The alpha weights used in the algorithm are computed from graph degrees, not fitted to performance. Citations to Li (2022) and Zhang et al. (2024), which share authors with this paper, are used only as inspiration and related-work context; the EPR analysis does not depend on them. The empirical EPR values in Appendix F validate the k < 0.5 assumption on benchmarks but are not used as fitted inputs to the derivation. Therefore no equation in the paper reduces by construction to its own inputs. The main scientific weaknesses, namely the uniform per-node k assumption and the degree condition d_max <= 4 d_min - 1 being violated by benchmark graphs, are concerns about assumption validity, not circularity, and are outside this pass.
Assumptions & free parameters
free parameters (5)
- padd =
grid-searched, not tied to theory
- pdrop (edge dropping rates pe1, pe2) =
grid-searched over {0.1..0.6}
- feature mask rates pf1, pf2 =
grid-searched over {0.1,0.3,0.5}
- temperature tau =
grid-searched over {0.3,0.4,0.5}
- candidate node threshold =
top sqrt(2|E|) highest-degree nodes
assumptions (4)
- ad hoc to paper Assumption 3.4: Mwp,i/Mi = k for all nodes i
- domain assumption Degree regularity: dmax <= 4 dmin - 1
- domain assumption Assumption A.2: at least one same-class edge exists
- domain assumption Ground-truth class labels exist for defining the error edge set E
invented entities (1)
-
Error Passing Rate (EPR)
independent evidence
Cite this review
Pith. "Pith review of Why Does Dropping Edges Usually Outperform Adding Edges in Graph Contrastive Learning?." pith.science (2026). https://pith.science/paper/KTZONL7F
@misc{pith2026241208128,
author = {Pith},
title = {Pith review of: Why Does Dropping Edges Usually Outperform Adding Edges in Graph Contrastive Learning?},
year = {2026},
howpublished = {\url{https://pith.science/paper/KTZONL7F}},
note = {Machine review of arXiv:2412.08128}
}
read the original abstract
Graph contrastive learning (GCL) has been widely used as an effective self-supervised learning method for graph representation learning. However, how to apply adequate and stable graph augmentation to generating proper views for contrastive learning remains an essential problem. Dropping edges is a primary augmentation in GCL while adding edges is not a common method due to its unstable performance. To our best knowledge, there is no theoretical analysis to study why dropping edges usually outperforms adding edges. To answer this question, we introduce a new metric, namely Error Passing Rate (EPR), to quantify how a graph fits the network. Inspired by the theoretical conclusions and the idea of positive-incentive noise, we propose a novel GCL algorithm, Error-PAssing-based Graph Contrastive Learning (EPAGCL), which uses both edge adding and edge dropping as its augmentations. To be specific, we generate views by adding and dropping edges based on the weights derived from EPR. Extensive experiments on various real-world datasets are conducted to validate the correctness of our theoretical analysis and the effectiveness of our proposed algorithm. Our code is available at: https://github.com/hyzhang98/EPAGCL.
Figures
Reference graph
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Reviewed August 11, 2026 · model on record in the stance chip above.
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