DeepITE: Designing Variational Graph Autoencoders for Intervention Target Estimation

Authors: hongyuan  tao
hang  yu
jianguo  li
Venue: NeurIPS_cc_2024_Conference
Published: 2024-04-28 10:00:55

Abstract: Intervention Target Estimation (ITE) is vital for both understanding and decision-making in complex systems, yet it remains underexplored. Current ITE methods are hampered by their inability to learn from distinct intervention instances collaboratively and to incorporate rich insights from labeled data, which leads to inefficiencies such as the need for re-estimation of intervention targets with minor data changes or alterations in causal graphs. In this paper, we propose DeepITE, an innovative deep learning framework designed around a variational graph autoencoder. DeepITE can concurrently learn from both unlabeled and labeled data with different intervention targets and causal graphs, harnessing correlated information in a self or semi-supervised manner. The model's inference capabilities allow for the immediate identification of intervention targets on unseen samples and novel causal graphs, circumventing the need for retraining. Our extensive testing confirms that DeepITE not only surpasses 13 baseline methods in the Recall@k metric but also demonstrates expeditious inference times, particularly on large graphs. Moreover, incorporating a modest fraction of labeled data (5-10\%) substantially enhances DeepITE's performance, further solidifying its practical applicability. Our source code is available at https://github.com/alipay/DeepITE.

Main paper: 
 introduction: 
 Causal analysis in complex systems encompasses a series of steps beginning with causal discovery [1] , which aims to delineate the causal structure, followed by the identification and estimation of causal effects [2] . Within this framework, a critical yet often overlooked component is Intervention Target Estimation (ITE) [3] , alternatively known as Intervention Recognition [4] . ITE is the process of pinpointing which variables in a system have been subject to intervention, particularly when such interventions are opaque or not directly manipulable. This process not only fosters a deeper understanding of the causal mechanisms driving specific outcomes, which resonates with the principles of explainable AI (XAI), but also plays a pivotal role in recognizing variables that can be strategically altered to produce desired effects, aligning with the concept of algorithmic recourse [5] .To illustrate, consider the application of ITE in root cause analysis (RCA) within a microservices system. These systems consist of a network of services working in concert to deliver software functionality. When a service failure occurs, such as a system outage or performance degradation, it becomes imperative to identify the root cause. ITE is the key that unlocks definitive insight into the RCA process. It methodically pinpoints the specific services whose malfunctions-stemming from network issues, hardware failures, or security breaches-lead to the anomalies in question. ITE not• Extensive experiments show that DeepITE surpasses 13 baseline methods by a large margin on average in terms of Recall@k with competitive inference time, especially for large graphs.Question: Do the main claims made in the abstract and introduction accurately reflect the paper's contributions and scope?Answer: [Yes] Justification: We have outline our contributions and scopes in the abstract and introduction.Guidelines:• The answer NA means that the abstract and introduction do not include the claims made in the paper. • The abstract and/or introduction should clearly state the claims made, including the contributions made in the paper and important assumptions and limitations. A No or NA answer to this question will not be perceived well by the reviewers. • The claims made should match theoretical and experimental results, and reflect how much the results can be expected to generalize to other settings. • It is fine to include aspirational goals as motivation as long as it is clear that these goals are not attained by the paper. 
related works: 
 In this section, we briefly review the literature on ITE. Moreover, we notice that the realm of ITE is interconnected with causal explanations and RCA. These three concepts demonstrate a considerable degree of overlap (cf. [8, 4, 9] ), suggesting that methods from each domain can not only inform and enhance one another but also be utilized in a complementary fashion. We therefore refer the readers to Appendix B for further discussion on causal explanations and RCA.The limited literature on ITE approaches bifurcates, with one camp focusing on incidental estimation of intervention targets via causal discovery and the other dedicated solely to identifying intervention targets within a given causal framework. The former includes methods such as UT-IGSP [10] , which seeks to recover an interventional Markov equivalence class (I-MEC) through permutation searches but is hampered by sample inefficiency and limited scalability. Ghassami et al. [11] explore linear structural causal models (SCMs) yet may struggle with complexity in diverse data settings. For causal insufficient systems, Jaber et al. [12] propose Ψ-FCI for matching interventional distributions to causal graphs and intervention target pairs, contending with exponential growth in complexity as the number of variables increases. Mooij et al. [13] alternatively propose a method leveraging context variables for integrating interventional datasets, but this method suffers from scalability issues with large graphs. To overcome this problem, RCD [9] further adapts the Ψ-FCI algorithm in [12] to the Ψ-PC algorithm to expedite the process in causally sufficient systems. The second approach, exemplified by CITE [3] and PreDITEr [6] , zeros in on ITE by contrasting precision matrices from observational and interventional data, achieving scalability at the cost of being initially restricted to linear Gaussian SCMs. LIT [7] explores non-linear SCMs through non-linear ICA, still carrying quadratic complexity. Alternatively, CI-RCA [4] conducts ITE by detecting shifts in probability distributions of a variable conditioned on a variable's parents via hypothesis testing. Both groups of methods share critical disadvantages: they are vulnerable to even minor changes in data or causal graphs during both learning and inference, and they underutilize labeled data from controlled experiments.Question: Does the paper discuss the limitations of the work performed by the authors?Answer: [Yes] Justification: Please refer to Appendix H Guidelines:• The answer NA means that the paper has no limitation while the answer No means that the paper has limitations, but those are not discussed in the paper. • The authors are encouraged to create a separate "Limitations" section in their paper.• The paper should point out any strong assumptions and how robust the results are to violations of these assumptions (e.g., independence assumptions, noiseless settings, model well-specification, asymptotic approximations only holding locally). The authors should reflect on how these assumptions might be violated in practice and what the implications would be. • The authors should reflect on the scope of the claims made, e.g., if the approach was only tested on a few datasets or with a few runs. In general, empirical results often depend on implicit assumptions, which should be articulated. • The authors should reflect on the factors that influence the performance of the approach.For example, a facial recognition algorithm may perform poorly when image resolution is low or images are taken in low lighting. Or a speech-to-text system might not be used reliably to provide closed captions for online lectures because it fails to handle technical jargon. • The authors should discuss the computational efficiency of the proposed algorithms and how they scale with dataset size. • If applicable, the authors should discuss possible limitations of their approach to address problems of privacy and fairness. • While the authors might fear that complete honesty about limitations might be used by reviewers as grounds for rejection, a worse outcome might be that reviewers discover limitations that aren't acknowledged in the paper. The authors should use their best judgment and recognize that individual actions in favor of transparency play an important role in developing norms that preserve the integrity of the community. Reviewers will be specifically instructed to not penalize honesty concerning limitations. 
preliminaries: 
 This section lays the groundwork for our study by introducing SCMs and Pearl's Causal Hierarchy.Structural Causal Models (SCMs): Given a set of variables x = [x 1 , . . . , x d ], SCMs present a formal mechanism to represent causal relations among them. An SCM is composed of two primary components: a set of structural equations and a causal graph. The structural equations take the form:EQUATIONwhere f i is a deterministic function, Pa(x i ) denotes parent variables that exert direct causal influence on x i , and u i signifies unobserved exogenous variables capturing influences not represented by other variables in x. We typically invoke causal sufficiency, assuming the u i are jointly independent, thereby ruling out hidden confounders. The use of the assignment symbol ":=" instead of an equality sign underscores the asymmetry of the causal relationship. The corresponding causal graph G (see Figure 1 (a) for an example) induced by the SCM is typically a directed acyclic graph (DAG) with vertex set x ∪ u and directed edges from each variable on the right hand side (RHS) of a structural equation (1) to the variable on the left hand side, thus delineating the causal dependencies.Pearl's Causal Hierarchy (PCH): Under the SCMs framework, PCH categorizes causal inference into a three-tiered structure reflective of the cognitive processes of "seeing" (observational), "doing" (interventional), and "imagining" (counterfactual). The initial tier addresses observational queries using SCMs as conventional probabilistic models to describe statistical associations.Progressing to the second tier of PCH, SCMs distinguish themselves from standard probabilistic models by enabling the assessment of outcomes resulting from active interventions or manipulations, captured by the notions of do-operator and graph surgery. Here, the do-operator do(x i = x i ) represents an intervention that sets the variable x i to value x i , while graph surgery alters the corresponding causal graph by removing all incoming edges to the intervened-upon variable x i . Interventional queries are then addressed by performing probabilistic inference in the modified graph, which often reveals new conditional independencies due to the excision of edges. For example, the interventional The generative model then synthesizes x given these latent variables following Eq. ( 7) plus observation noise ϵ.distribution p(x 3 | do(x 2 = x 2 )) for the SCM in Figure 1 (b) is obtained via probabilistic inference with regard to (w.r.t.) the intervention graph:EQUATIONcontrasting with the conditional distribution in the original graph (i.e., Figure 1 (a)):EQUATIONThe key distinction is the marginal p(x 1 ) in (2) versus the conditional p(x 1 |x 2 = x 2 ) in (3), reflecting that the causal relationship between x 1 and x 2 is broken by the intervention do(x 2 = x 2 ).Finally, there are counterfactual queries about what would or could have been, given that something else was in fact observed. We refer the readers to [14] as this topic is beyond the scope of our paper.Question: For each theoretical result, does the paper provide the full set of assumptions and a complete (and correct) proof?Answer • Providing as much information as possible in supplemental material (appended to the paper) is recommended, but including URLs to data and code is permitted. 
problem formulation: 
 As discussed in the introduction, intervention target estimation (a.k.a. intervention recognition) is a pivotal component within the landscape of causal analysis, addressing the question of which nodes within a given causal system should be subjected to intervention in order to best explain the given interventional data. This inquiry draws upon the framework established by SCMs and operationalizes the principles enshrined in the second tier of Pearl's Causal Hierarchy. More formally, Definition 1. Given a causal graph G with variables x, the observational data, and the interventional data corresponding to a certain intervention on a subset of variables x I ⊆ x, the task of intervention target estimation is to identify x I .Here, we maintain the assumptions of causal sufficiency and the acyclicity of the causal graph. Note that while the DAG structure (i.e., the adjacency matrix A) is assumed to be known, the explicit forms of the structural equations remain unspecified. In comparison with the interventional queries mentioned in Section 3, which presuppose knowledge of where interventions have occurred and seek to determine their effects, ITE is the inverse process: it starts with the consequences of interventions and works backward to identify the sources of these perturbations. Essentially, we are solving for the origin of the observed interventional data, rather than predicting their impact.In this paper, we innovatively solve the problem of intervention target estimation from the perspective of graph surgery. Recognizing that the interventional data align best with the intervention graph (see Figure 1 (b)), our objective is to discover the subset of nodes x I such that, upon hypothetically removing the incoming edges to these nodes, the modified interventional model most accurately reflects the presented interventional data. Furthermore, We aim to create a singular model capable of pinpointing distinct sets of intervention targets for individual samples, each associated with its unique causal graph, while eliminating the need for observational data during inference. This represents a significant shift from conventional ITE methods that independently identify shared intervention targets for each intervention instance based on both observational and interventional data within the context of a fixed causal graph. Additionally, we seek to enhance model performance by incorporating labeling information during the training phase, which is a step forward in refining ITE processes. 
deepite: 
 To move forward to the above objectives, we present DeepITE, a VGAE that can estimate the probability of edge presence within the latent space. The architecture of DeepITE is showcased in Figure 1 (c). We will first introduce the generative and inference models within the VGAE. Subsequently, we will explicate the self and semi-supervised methods to train the inference model.The chief aim of the generative model is to recreate the observed variables x given the exogenous noise variables u, the adjacency matrix A of the causal DAG, and a set of nodes I that have been intervened upon. Notably, when I is an empty set, the model is capable of recovering the observational distribution.Specifically, when the structural equations are linear, they can be succinctly written as x = A T x + u. Therefore, given u and A, we can derive x through a linear decoder:EQUATION) Drawing inspiration from DAG-GNN [15] , we extend this formulation to non-linear scenarios with:EQUATIONwhere f 1 and f 2 are non-linear, component-wise learnable functions. In practice, these functions are executed by MLPs, which serve as universal approximators. Assuming f 2 is invertible, the aforementioned decoder corresponds to a conglomerate of non-linear structural equations [15] :EQUATIONThis setup implies that when f 1 and f -1 2 are suitably expressive, they can transform u and x into a space where their causal interrelations are aptly described by linear structural equations. The decoder, as specified in Eq. ( 5), exhibits inductiveness, enabling generalization to new nodes, edges, or graph schemas by only modifying the adjacency matrix A while preserving the learned functions f 1 and f 2 . This decoder displays a particular characteristic, ratified by the following proposition: Proposition 1. For a GNN layer as defined in Eq. (5), and denoting An(i) as the ancestor nodes of node i with the extension An * (i) = An(i) ∪ i, each output feature x i exclusively acquires information from its own and all ancestor input features u An * (i) . Proof. See Appendix C. Owing to this property, this decoder (5) satisfies causal factorization and captures causal intervention, as proven below. Proposition 2. (causal factorization) The decoder defined in Eq. (5) conforms to causal factorization p(x|u, A) = i p(x i |u An * (i) ), that is, each endogenous variable x i can be expressed as a function of its exogenous variable u i and those of its causal ancestors. Proposition 3. (causal intervention) The decoder defined in Eq. (5) captures causal interventions do(x I = x I ) by replacing the original adjacency matrix A in Eq. ( 5) with the one corresponding to the post-intervention graph after graph surgery. Proof. See Appendices D and E. As established in Section 4, ITE resides within the second tier of PCH. Within this framework, any model purporting to tackle the ITE challenge must adeptly manage both observational and interventional data. The above propositions bridge this requirement, affirming DeepITE's competency in fulfilling the ITE task. Specifically, these propositions serve as the key to unlocking the model's ability to honor the causal structure inherent in the data and to emulate the effects of interventions.In light of Proposition 3, to manipulate the intervened nodes I in the decoder (5), we introduce a Bernoulli distributed variable γ i for each node x i : γ i = 0 means x i is intervened, and thus, all incoming edges of x i is removed during the graph surgery. The variable γ i is henceforth referred to as the intervention indicator. The corresponding intervened adjacency matrix is given by A I = (γ T 1) ⊙ A, where 1 is a column vector of all ones and ⊙ denotes Hadamard product. As a result, the decoder, inclusive of interventions, is delineated as:EQUATIONWhen γ i = 1 for all i, there is no intervention (i.e., A I = A) and the above decoder can describe the observational distribution.To facilitate the reparameterization trick in VAE, we assume the exogenous variables u are standard normal distributions: u i ∼ N (0, 1). Finally, since we do not have access to the true structural equations, we introduce the observation noise ϵ ∼ N (0, ζ -1 ) to (7) , so as to account for the model uncertainty associated with the above decoder (7) . Here, ζ denotes the inverse variance of the noise, and we impose a non-informative Jeffrey's prior on ζ, that is,p(ζ) ∝ 1/ζ.Collectively, the overall generative model can be factorized as:EQUATIONwhere EQUATIONi := f i (Pa(x i ), u i ) with an updated version x i := f ′ i (Pa(x i ), u i ), where f i ̸ = f ′ i , thereby altering the generative process while maintaining the graph's structure. In our generative model, the intervention indicator γ i is a Bernoulli variable, allowing the learning of edge removal probability from data x. A probability of γ i = 0 being one indicates a hard intervention, whereas any other value suggests a soft intervention. This nuanced approach allows DeepITE to offer a spectrum between hard and soft interventions based on given data.The pinnacle goal of the inference model within DeepITE is to determine the probability that a node i has undergone an intervention based on the observed data, succinctly expressed as p(γ i = 1|x). To achieve this, we aim to compute the exact posterior p(u, γ, ζ|x, A). However, the intricate nature of this posterior necessitates approximation through a tractable inference model q(u, γ, ζ|x, A) [16, 17] . Specifically, the inference model can be factorized in a manner akin to the generative model as:EQUATION)The variational distributions on RHS are parametrized by:EQUATIONEQUATIONEQUATIONwhere the Bernoulli distribution (26) can be well approximated using the Gumbel-Softmax reparameterization trick [18, 19] . The parameters of the variational q distributions in ( 25)-( 27) are derived from a network based on Graph Attention Networks (GAT). While any inductive spatial GNN can be used as the inference network in DeepITE, we choose GAT since it provides the flexibility and scalability necessary for our model. This flexibility stems from GAT's ability to dynamically weigh the importance of different nodes, thus allowing the variational distribution given by the inference network better approximate the exact posterior distribution. This advantage is further demonstrated in Appendix G.6, where we replace the GAT encoder with the encoder of DAG-GNN.The architecture features an initial dual-layer GAT for feature extraction, followed by three specialized branches dedicated to the parameters of u, γ, and ζ. Note that the parameters of u and γ can be regarded as node-level features, while those of ζ as graph-level features. As such, the final ζ branch includes a pooling layer to yield the graph-level features. The complete inference network is depicted in Figure 1(c) .It is pertinent to mention that the graph associated with the GATs is undirected, in contrast to the directed nature of the causal graph. This design choice is motivated by the need for the variational update of a variable to account for all elements within its Markov blanket, which includes the parents, children, and co-parents of the node [20] . An undirected graph facilitates the message passing process within this Markov blanket by removing the constraints imposed by edge directionality. Moreover, the use of GAT ensures that the resulting model is inductive, enabling its application to new nodes within the graph and even entirely new graph structures.Relation to DAG-GNN [15] : DAG-GNN's objective is to infer the structure of a DAG (i.e., the zero pattern of A) from the provided data, a process known as causal discovery. The architecture of DAG-GNN employs a generative model expressed as x = f 2 ((I -A T ) -1 f 1 (u)) and an inference model as u = f 4 ((I -A T )f 3 (x)), both of which are differentiable with respect to A. This differentiability is crucial as it enables the learning of A through gradient descent. On the other hand, DeepITE enhances the generative model by integrating an intervention indicator, which facilitates the adaptation of the model to account for interventions via graph surgery. Furthermore, DeepITE's inference model seeks to closely approximate the true posterior p(u, γ, ζ|x, A). Unlike DAG-GNN, which may only collect messages from the parents of a node, DeepITE's model is designed to aggregate messages from all nodes within the Markov blanket of a given node i. This comprehensive approach ensures that DeepITE's inference model is not as restrictive as DAG-GNN's and is better suited for ITE tasks.Relation to VACA [21] : VACA sets out to perform causal queries utilizing observational data within the framework of the VGAE. It hinges on Message Passing Neural Networks (MPNNs) for both the generative and inference models. A prerequisite for VACA to perform observational and interventional queries is that the generative model's number of MPNN layers must at least be δ -1 given that δ is the graph diameter. 4 This criterion ensures that the information propagated within the graph can reach from one end to the other, thereby reflecting the global structure necessary for accurate causal inference. DeepITE aligns with this requirement for effectively performing ITE. However, DeepITE distinguishes itself by employing the generative model, specified in Eq. (7) . It keeps the number of GNN layers to be one regardless of graph diameter, while satisfying causal factorization and intervention conditions (cf. Proposition 2-3). DeepITE thereby overcomes the limitations imposed by VACA's dependence on graph diameter, offering a substantial benefit for collective learning on graphs with different sizes.DeepITE's learning strategies encompass self-supervised learning, which automates the identification of intervention targets from unlabeled data, and semi-supervised learning, which refines the model's performance by integrating labeled data. The training process is summarized in Algorithm 1.Self-Supervised Learning: Given the generative and inference model, we can learn their parameters jointly by maximizing the evidence lower bound (ELBO) of the log-likelihood of the given data x:EQUATIONwhere E q denotes expectation over the q distribution in ( 10) and H q denotes the entropy of the q distribution. The derivation of the ELBO can be found in Appendix F. Note that L can be maximized via stochastic gradient ascent after using the reparameterization trick for normal and Bernoulli distributions [22, 23, 19] .Semi-Supervised Learning: Information regarding intervention targets may often be available in practice. For instance, in the case of RCA in cloud-native systems, the ground truth of intervention targets can be derived from resolved incidents and chaos engineering exercises. This ground truth data can be utilized to train the inference network, enabling it to more accurately identify intervention targets. In particular, the term q(γ i |x, A) is replaced by the ground truth γ * i when computing the ELBO L, and an additional term is introduced to maximize the log-likelihood log q(γ * i |x, A). By taking advantage of both labeled and unlabeled data, we can effectively train the inference model.Once trained, the inference model of DeepITE becomes equipped to evaluate individual new samples against different causal graphs, directly deducing the intervention targets and thus circumventing the necessity of retraining for each new scenario. It can also distinguish between observational and interventional data directly as the former equates to the absence of intervention targets. Another significant feature of DeepITE is its independence from observational data during the testing phase; it relies solely on the interventional data input into the inference network. This is a distinct advantage over existing ITE methods, which consistently require observational data for ITE. In practice, we are primarily concerned with the intervention indicators γ. Hence, during inference, we only need to process x through the relevant branch of x, as highlighted by the red dashed box in Figure 1(c) , disregarding the other branches to optimize inference efficiency. 
experimental results: 
 In this section, we demonstrate the usefulness of DeepITE on three datasets, comprising one synthetically generated dataset, which provides a controlled environment to test the robustness and scalability of the framework, and two real-world datasets that introduce the complexity of genuine causal systems. We position DeepITE against 13 state-of-the-art (SOTA) methods, spanning three areas of relevance: Intervention Target Estimation (ITE), Explainable AI (XAI), and Root Cause Analysis (RCA), due to their intertwined nature (see more discussions in Section 2 and Appendix B).• ITE: We select 3 methods: UT-IGSP [10] , which learns intervention targets as a byproduct of causal discovery; CITE [3] and PreDITEr [6] , both of which are dedicated to ITE. • XAI: We opt for TreeExplainer [24] , ASV [25] , ShapleyFlow [26] , and PWSHAP [27] , 4 methods based on Shapley values. TreeExplainer only considers associations, whereas ASV, ShapleyFlow, and PWSHAP incorporate causation, accounting for the DAG structure. • RCA: We pick 6 methods: CauseInfer [28] , MicroHECL [29] , MicroRCA [30] , CausalRCA [31] , CI-RCA [4] , and RCD [9] . The last two aim to find intervention targets in a causal graph.To facilitate a fair comparison, all methods are provided with the same ground truth causal graph, eschewing the need for graph construction from data for some RCA methods. More implementation details can be found in Appendix G.1. The performance is quantified using the Recall@k metric.Recall@k measures the proportion of true intervention targets (ITs) that are successfully captured within the top k ranked candidates proposed by each method. This metric is widely adopted in the literature [4, 9, 29] . When k = 1, our goal is to pinpoint the intervention targets based on the highest-ranked candidate. We prioritize Recall@k because, in practice, false positives can be eliminated through further analysis, while false negatives are irrecoverable as they get lost among the numerous true negatives. All experiments report average results over 10 trials, with error bars representing a standard deviation (±1σ) from the mean.Synthetic Data: The synthetic data is generated following the method outlined in CI-RCA [4] and in Appendix G.2. We assess causal graphs with nodes ranging from 50 to 500 and corresponding edges from 100 to 5000, exhibiting different levels of complexity. In particular, DeepITE is evaluated in two configurations: DeepITE (sep), where separate models are trained for each graph size, and DeepITE (mix), where a single model is trained across all graph sizes and structures. Protein Signaling Dataset: The description of the dataset is presented in Appendix G.4. The results, shown in the second column of Table 2 , focus on the Recall@1 metric due to the graph's limited size.It is evident that DeepITE outshines competing methods, attributable to its capacity for collaborative learning across the entire dataset and its inherent adaptability. Traditional ITE and XAI methods trail closely behind, with their methodologies being particularly suited to smaller graphs that nevertheless have a substantial number of samples. In contrast, RCA methods exhibit weaker performance as techniques such as PageRank, DFS, BFS, or rank walk struggle to distinguish between nodes in such a compact network. Unlike these approaches, DeepITE demonstrates versatility in handling both small and large graphs, affirming its utility across a wide range of practical scenarios.The details of this dataset can be found in Appendix G.4. Note that the absence of purely observational data in this dataset precludes the application of the ITE methods including UT-IGSP, CITE, and PreDITEr. For our evaluation, we continue to employ Recall@1 and Recall@5 metrics and additionally consider accuracy and the root-cause score, the latter two being an official recommendation. The root-cause score is calculated by subtracting the number of false positives from the number of true positives and then dividing by the total number of true intervention targets. The results of this multifaceted assessment are presented in the last four columns of Table 2 . Once more, in comparison with the SOTA methods, DeepITE stands out by a large margin of above 20% in Recall@1, underscoring its applicability to real-world RCA challenges. Notably, CI-RCA and Shapley Flow emerge as close second-best performers, likely because both methods leverage causal rather than just correlational information, which appears to be advantageous in this context.Due to the page limit, we only present an overview of the major findings here. More details can be found in Appendix G.5-G.7. (i) Impact of Label Proportions: Incorporating even a modest amount (5-10%) of labeled data significantly enhances DeepITE's performance across various datasets, with recall improvements ranging from 4-20%. This approach provides substantial benefits in practical settings, unlike other baseline methods in the study that cannot utilize labeled data at all. (ii) Replacement of Encoder and Decoder: Modifying DeepITE's encoder to DAG-GNN's and its decoder to VACA's in two ablation designs shows that DeepITE-with its flexible generative and inference models-outperforms both modified versions and the original VACA [21] and DAG-GNN [15] . These observations, especially under conditions of increasing graph complexity, highlight Based on this evidence, we maintain that the amortization process across graphs does not significantly hinder the performance.We conducted a runtime analysis using four distinct datasets, with variable counts m ranging from 5 to 500, specifically m = [5, 10, 11, 20, 50, 100, 500] . For each value of m, we executed 10 trials on a set of 1000 samples and reported the average runtime. To ensure a fair comparison, we focused exclusively on the code pertinent to intervention identification. Timing commenced the moment the algorithm received the dataset and accompanying causal graph, if applicable, and ceased immediately upon delivery of the final results. This process ensured that our analysis exclusively measured the performance of the algorithm's core intervention-targeting functionality.The runtime performance of the various methods, relative to graph size, is depicted in Appendix Figure 3 . From the analysis, we note that DeepITE's runtime curve, represented in black, has the gentlest slope, implying that it boasts the lowest time complexity among all the methods. Notably, DeepITE secures the shortest runtime for graphs with more than 100 nodes. This heightened efficiency is attributable to DeepITE's inference process, which necessitates only a single pass through one branch of the inference network. In contrast, UT-IGSP exhibits the highest time complexity as it engages in an exponentially growing number of hypothesis tests to identify intervention targets. For instance, when handling graphs with m = 500 nodes, UT-IGSP requires nearly an hour to complete a single run.Question: Does the paper specify all the training and test details (e.g., data splits, hyperparameters, how they were chosen, type of optimizer, etc.) necessary to understand the results?Answer: [Yes]Justification: Please find the implementation details in Appendices G.1-G.4.Guidelines:• The answer NA means that the paper does not include experiments.• The experimental setting should be presented in the core of the paper to a level of detail that is necessary to appreciate the results and make sense of them. • The full details can be provided either with the code, in appendix, or as supplemental material. 
conclusion: 
 In this paper, we presented DeepITE, a novel VGAE for ITE. By carefully design the VGAE based on GNNs, DeepITE allows collaborative learning and amortized inference across data with a range of intervention targets and causal graphs. The model adeptly supports both self-supervised and semi-supervised learning modalities, effectively harnessing labeled data to refine ITE. Our comprehensive results demonstrate that DeepITE can be seamlessly adapted to a multitude of domains, accommodating diverse causal graph configurations while exhibiting superior performance in terms of both Recall@k metrics and computational efficiency. (•) variational q-distribution p(•) variational p-distribution N normal distribution Bern Bernoulli distribution Lognormal log-normal distribution u m × 1 latent variables for normal distribution γ m × 1 latent variables for Bernoulli distribution ϵ 1 × 1 global observation noise ζ 1 × 1 inverse variance of the noise µ i 1 × 1 mean of normal distribution of node i σ 2 i 1 × 1 variance of normal distribution of node i π 1 × 1 probaility of taking one in a Bernoulli distribution µ ζ m × 1 mean of log-normal distribution σ 2 ζ m × 1 variance of log-normal distribution µ i (x, A) 1 × 1 mean of the estimated normal distribution of node i σ 2 i (x, A) 1 × 1 variance of the estimated Normal distribution of node i ω i (x, A) 1 × 1 estimated probaility of taking one in a Bernoulli distribution of node i µ ζ (x, A) 1 × 1 mean of the estimated log-normal distribution σ 2 ζ (x, A) 1 × 1 variance of the estimated log-normal distribution p(x, u, γ, ζ|A)the proposed gernerative model q(u, γ, ζ|x, A) the proposed inference model E q expectation over the q-distribution H q entropy of the q-distribution L the evidence lower bound (ELBO) D KL q||p) KL divergence between distributions q and p Dec(u, γ, A) the proposed decoderQuestion: Does the paper report error bars suitably and correctly defined or other appropriate information about the statistical significance of the experiments?Answer: [Yes] Justification: All experiments report average results over 10 trials, with error bars representing a standard deviation (±1σ) from the mean.Guidelines:• The answer NA means that the paper does not include experiments.• The authors should answer "Yes" if the results are accompanied by error bars, confidence intervals, or statistical significance tests, at least for the experiments that support the main claims of the paper. • The factors of variability that the error bars are capturing should be clearly stated (for example, train/test split, initialization, random drawing of some parameter, or overall run with given experimental conditions). • The method for calculating the error bars should be explained (closed form formula, call to a library function, bootstrap, etc.) • The assumptions made should be given (e.g., Normally distributed errors).• It should be clear whether the error bar is the standard deviation or the standard error of the mean. Guidelines:• The answer NA means that the authors have not reviewed the NeurIPS Code of Ethics.• If the authors answer No, they should explain the special circumstances that require a deviation from the Code of Ethics. • The authors should make sure to preserve anonymity (e.g., if there is a special consideration due to laws or regulations in their jurisdiction). 
broader impacts: 
 Question: Does the paper discuss both potential positive societal impacts and negative societal impacts of the work performed?Answer: [NA] Justification: This paper aims to contribute to the advancement of intervention target estimation, a fundamental research area not specific to any application. As such, we do not anticipate any direct societal impact resulting from our work.Guidelines:• The answer NA means that there is no societal impact of the work performed.• If the authors answer NA or No, they should explain why their work has no societal impact or why the paper does not address societal impact.• Examples of negative societal impacts include potential malicious or unintended uses (e.g., disinformation, generating fake profiles, surveillance), fairness considerations (e.g., deployment of technologies that could make decisions that unfairly impact specific groups), privacy considerations, and security considerations. • The conference expects that many papers will be foundational research and not tied to particular applications, let alone deployments. However, if there is a direct path to any negative applications, the authors should point it out. For example, it is legitimate to point out that an improvement in the quality of generative models could be used to generate deepfakes for disinformation. On the other hand, it is not needed to point out that a generic algorithm for optimizing neural networks could enable people to train models that generate Deepfakes faster. • The authors should consider possible harms that could arise when the technology is being used as intended and functioning correctly, harms that could arise when the technology is being used as intended but gives incorrect results, and harms following from (intentional or unintentional) misuse of the technology. • If there are negative societal impacts, the authors could also discuss possible mitigation strategies (e.g., gated release of models, providing defenses in addition to attacks, mechanisms for monitoring misuse, mechanisms to monitor how a system learns from feedback over time, improving the efficiency and accessibility of ML). 
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 Appendix: See Table 3 .Causal Explanations: We also briefly review causal explanations as they are related to ITE. AI explainability endeavors to demystify model decisions, a pursuit encompassing feature attribution and contrastive explanations. Feature attribution methods initially focused on associations, revealing how input features correlate with predictions [24] . Moving beyond mere correlations, recent approaches integrate causality to enhance interpretability: CXPlain [32] employs supervised learning to discern the causal impact of features on model predictions, though computational demands escalate with the need for repeated model evaluations. Generative Causal Explanations (GCE) [33] introduce disentangled latent factors to isolate causal effects, yet ensuring these factors accurately reflect the data distribution is complex. Asymmetric Shapley Value (ASV) [25] , Shapley Flows [26] , and PWSHAP [27] further this trend by considering the causal graphs, with the former adapting Shapley values to reflect causal structures and the latter two focusing on the causal relationships signified by the graph's edges and paths. On the other hand, Contrastive explanations, illustrated by Counterfactual Explanations (CE) [34] and Causal Algorithmic Recourse (CAR) [35, 36] [44] and DAG-GNN [31] , or it is derived from domain-specific knowledge like topology graphs [45, 46, 29, 47, 48, 49, 30] .The second stage then leverages algorithms such as PageRank [46, 31] , breadth-first or depthfirst search [28, 37, 38, 29] , and random walk [50, 40, 41, 42, 43, 30] for root cause localization within the graph. Despite their utility, the second stage tends to focus on association rather than causation, assigning a higher correlation to the connections between a node and its parents over those between the node and its children to consider the directionality in the causal graph. In contrast, as highlighted in the preceding sections, CI-RCA [4] emphasizes causation, utilizing linear regressionbased hypothesis testing to pinpoint intervention targets. As an alternative, RCD [9] incorporates the Ψ-PC algorithm in a hierarchical fashion, intertwining the learning of intervention targets with graph structure discovery. These approaches not only improve root cause identification but also harmonize with ITE goals, fostering a causally informed analysis in RCA. However, as noted earlier, these methods lack collaborative learning and are fully unsupervised, necessitating complete inference for each RCA instance from scratch and failing to utilize labeling information.According to the Neumann power series for the matrix inverse, we can obtain:EQUATIONwhere A k denotes the k-th power of the matrix A, which involves multiplying the matrix A by itself k times. In the above expression, entry (i, j) in the k-th power of A can be elaborated as:EQUATIONwhere the sum encapsulates all paths (i, w 1 , w 2 , . . . , w k-1 , j) from i to j with length k. In directed graphs, these paths must observe edge directionality. Consequently, for DAGs, the matrix A k becomes a zero matrix when k surpasses the graph diameter δ, as no paths of length k exist between any two nodes within such graphs. Substitute (15) into (5), and the GNN layer is recast as:EQUATIONBy multiplying (A k ) T with f 1 (u) as in (17) , node i can receive information from its ancestors that have a path of length k connecting to i. As k goes from 0 to ∞, node i accrues information from the input features of its own and all its ancestors. On the other hand, paths only exist between node i and one of its ancestors. Conversely, such paths are non-existent between node i and non-ancestral nodes; hence, node i exclusively assimilates inputs from its ancestors, thereby concluding the proof.In consideration of Proposition 1 and given the decoder in Eq. ( 5), it is evident that x i is a function solely of u An * (i) for all indices i. Consequently, the probability distribution p(x|u, A) can be factorized into:EQUATIONwhich logically concludes the proof.The essence of a causal intervention lies in severing all the incoming edges to the intervened nodes. Therefore, the decoder stipulated in Eq. ( 5) can faithfully represent causal interventions only if it encompasses all possible causal pathways; otherwise, severing certain pathways would exert no influence on the resulting intervention configuration. The decoder in Eq. ( 5) does indeed model all causally relevant paths, as corroborated by Proposition 1, thereby completing the proof.Recall that the generative model (i.e., the p distribution) can be factorized as:EQUATIONwhere p(u i ) = N (0, 1), ∀i,EQUATIONEQUATIONEQUATION, and the inference model (i.e., the q distribution) can be factorized as:EQUATIONwhereEQUATIONEQUATIONEQUATIONNote that the parameters of the above q distributions are explicit functions of the given sample of the endogenous variables x and the adjacency matrix A, which is parameterized by the GAT-based inference network. By substituting the p (19) and q distributions (24) into the ELBO (14), we can obtain:EQUATIONwhere D KL denotes the KL (Kullback-Leibler) divergence between two distributions. We now delve into the expectation term in the above expression, which is given by:EQUATIONThe remaining three KL divergence terms can be written as:EQUATIONEQUATIONEQUATION)Require: Causal graph G, adjacency matrix A, endogenous variables x {1:m} , labels of intervention targets γ {1:m} true if available. Ensure: Parameters of the inference network ϕ, parameters of the generative network θ;1: Initialize ϕ, θ randomly; 2: repeat 3: Pass x {1:m} and A through the inference network to get the parameters for q(u|x {1:m} , A), q(γ|x {1:m} , A), q(ζ|x {1:m} , A); 4:Draw samples from the Normal distribution q(u|x {1:m} , A); 5:Draw samples from the Bernoulli distribution q(γ|x {1:m} , A) using the gumbel-softmax reparameterization trick; 6:Draw samples from the Log Normal distribution q(ζ|x {1:m} , A); 7:x {1:m} ← Dec(u {1:m} , γ Unless otherwise specified, in all of our experiments for DeepITE, we set the hidden dimension in GAT and MLP to 64. For optimization, we used NAdam [52] with a learning rate 1 × 10 -4 . We conducted training for 1000 epochs and select the checkpoints with the lowest training loss. The temperature t for gumbel-softmax [23] is calculated by t = 101 -0.2e when epoch e <= 500 and t = 0.5/(e -500) for epoch e > 500. All the training runs on 4 NVIDIA TESLA P100 GPUs with 50GB of VRAM. All the inference runs on a MacBook Pro 16 inch with a 6-core Intel i7 CPU and 16 GB of RAM.The key assumptions and characteristics of the comparative methods, as well as the time complexity in the inference process, are summarized in the table 4 and table 5 To facilitate a fair comparison, all methods (including ITE, RCA, and XAI) are provided with the same ground truth causal graph, Table 4 : Key assumptions and characteristics of comparing methods. Here, m and n denote the number of nodes and edges in the DAG, p∆ is the number of intervention targets given by the precision different estimation algorithm, and finally, T , L, and D represent the number of trees, the depth of the trees, and the number of leaf nodes in the gradient-boosted trees.O(m 3 ) PWSHAP Given No Soft Yes No < 100 O(m 3 )Table 5 : Time Complexity during Inference. Here, m and n denote the number of nodes and edges in the DAG, p∆ is the number of intervention targets given by the precision different estimation algorithm, and finally, T , L, and D represent the number of trees, the depth of the trees, and the number of leaf nodes in the gradient-boosted trees.O(2 m-1 ) CITE [3] O (2 p∆ ) PreDITEr [6] O (2 p∆ ) CauseInfer [28] O(m 2 ) MicroHECL [29] O(m 2 ) MicroRCA [30] O(m 2 ) + O(m + n) CausalRCA [31] O(m 2 ) CI-RCA [4] O(m 2 ) RCD [9] O(m 3 ) TreeExplainer [51] O T LD 2 ASV [25] O(m 3 ) ShapleyFlow [26] O(m 3 ) PWSHAP [27] O(m 3 )DeepITE O(m + n)eschewing the need for graph construction from data for some RCA methods. Within the realm of XAI, constructing a forward predictive model is a prerequisite for backward attribution analysis-the process used to identify the intervention targets. To facilitate this, we construct a predictive model using gradient-boosted trees. This forward model is trained to predict whether the graph is intervened based on the full set of node features x, in a supervised manner. During inference, we extract the intervention targets by identifying the top k nodes that yield the highest attribution scores.The generation process begins by creating a random adjacency matrix A, which is structured to be upper-triangular to ensure the resulting DAG is indeed acyclic. The matrix's non-zero entries are uniformly distributed across the range [-2, -0.5] ∪ [0.5, 2], representing the possible strengths of causal relationships between nodes. For each node within the DAG, time series data are synthesized according to a model that captures causal dependencies, as inspired by the linear decoder equation:x(t) = (I -A T ) -1 (u(t) + βx(t -1)), where t indicates the discrete time steps, and β denotes the autoregressive coefficient, influencing the temporal consistency of the data.Interventions are then introduced in the time series at time t, with the set of intervention nodes I being randomly selected from all non-root nodes, and the size of I adhering to a Poisson distribution.For nodes within I, we augment the corresponding exogenous noise, adhering to the three-sigma rule for significant deviation. Each generated time series spans 1000 time steps, with interventions 0.999 ± 0.000 1.000 ± 0.000 1.000 ± 0.000 1.000 ± 0.000 0.998 ± 0.001 1.000 ± 0.000 0.999 ± 0.000 0.999 ± 0.000 occurring randomly between time steps 100 and 900. Data preceding the intervention time t are labeled as observational, while data from t onwards are categorized as interventional. We explore causal graphs of varying complexity, with 50, 100, and 500 nodes, and associated edge counts of 100, 500, and 5000, respectively. To ensure a comprehensive assessment, 10 unique graphs are generated for each size, and for each graph, we create 100 distinct instances with varying intervention targets. The dataset is partitioned with an 85:5:10 ratio for training, validation, and testing.For an equitable evaluation with existing ITE approaches, we further devise experiments on synthetically generated datasets tailored to classical ITE configurations, using dataset generation scripts from VACA [21] . Our setup included two linear and two non-linear SCMs. Initially, we generate 10,000 observational samples from each SCM. Subsequently, we perform ten distinct interventions on randomly selected variables, mimicking the procedures followed by ITE methods. Each intervention resulted in the creation of 1,000 samples. Throughout these interventions, we maintain the SCMs' modularity and provid the causal graph with the data. We divide the dataset into training, validation, and testing batches with an 85:5:10 ratio, respectively.Table 6 reveals that DeepITE consistently surpasses competing methods in performance. Notably, traditional ITE approaches like UT-IGSP, CITE, and PreDITEr benefit significantly from an adequate pool of observational samples on small-scale graphs, reflecting a marked improvement in their effectiveness. Similarly, XAI techniques-ShapleyFlow in particular-demonstrate commendable performance, proving to be well-adapted for smaller graphs where their capabilities can be fully leveraged. Conversely, RCA methods exhibit weaker results, a trend that may be linked to their design inclination towards larger-scale graphs. These larger configurations are often seen in complex environments such as microservice diagnosis, suggesting that RCA methods' strengths are not fully utilized in smaller or less complex scenarios highlighted in this comparison.Furthermore, it is evident that models based on the premise of linear SCMs, such as CITE, PreDITEr, and CI-RCA, tend to underperform in settings that demand an understanding of non-linear dynamics. In contrast, DeepITE, which utilizes learnable SCMs, demonstrates impressive versatility by effectively addressing both linear and non-linear scenarios.Protein Signaling Dataset: The well-known protein signaling dataset, which originates from Sachs et al. [53] , investigates the complex interactions within T-4 cell signaling networks. The dataset comprises 11 nodes and 16 edges, with a collection of 1755 observational and 4091 interventional samples derived from five different experimental environments where various drugs were used to modulate signaling proteins. We harness an accepted ground truth network structure in [54] , and the preprocessing steps outlined in [10] , to benchmark DeepITE's performance with other models. The dataset is partitioned with an 85:5:10 ratio for training, validation, and testing. 0.850 ± 0.003 0.920 ± 0.001 0.994 ± 0.001 0.9964 ± 0.0000 0.9524 ± 0.0000 DeepITE (25%) 0.849 ± 0.002 0.922 ± 0.001 0.994 ± 0.000 0.9964 ± 0.0000 0.9524 ± 0.0000 DeepITE (50%) 0.868 ± 0.002 0.925 ± 0.000 0.995 ± 0.000 0.9964 ± 0.0000 0.9524 ± 0.0000 DeepITE (75%) 0.863 ± 0.002 0.924 ± 0.001 0.995 ± 0.000 0.9964 ± 0.0000 0.9524 ± 0.0000 DeepITE (100%) 0.872 ± 0.001 0.925 ± 0.000 0.995 ± 0.000 0.9964 ± 0.0000 0.9524 ± 0.0000 ICASSP-SPGC 20225 : The ICASSP-SPGC 2022 dataset [55] , derived from active 5G networks, is a real-world telecommunications dataset for RCA comprising 2984 samples and 23 variables that represent various Key Performance Indicators (KPIs). Human experts have verified the accompanying causal graph, yet only around 45% of the data are explicitly labeled with root cause faults. Unlike the previously mentioned dataset, where interventions are directly known from labels, the root causes here are represented by unobserved variables outside the causal graph. However, experts provide a mapping of each root cause to observable causal variables. During training with labeled data, we treat these associated variables as if they had been intervened upon. Additionally, 600 extra samples are provided for testing purposes.In this section, we delve into the influence of labeled data on the efficacy of DeepITE, with our findings summarized in Tables 7 8 . Across all datasets under consideration, it is clear that the incorporation of labeled data yields a substantial enhancement in DeepITE's performance, with improvements in Recall@1 ranging between 4% to 20%, depending on the dataset. Notably, the most pronounced gains are observed when the initial 5% to 10% of labeled data are integrated, with the rate of improvement tapering off beyond this point. This suggests that even a modest quantity of labeled data can lead to significant performance boosts, a fact that bears particular relevance in practical scenarios where acquiring a limited amount of labeled data is typically feasible and can offer considerable benefits to DeepITE. Conversely, the other baseline methods in our study do not possess the capability to leverage such labeling information to their advantage.The ablation study of DeepITE, in comparison to VACA and DAG-GNN, is presented in Table 9 . In Section 5.2, we have delved into the relationships between DeepITE, DAG-GNN, and VACA. We highlighted the limitations of DAG-GNN's inference model and VACA's generative model and illustrated how DeepITE overcomes these shortcomings. DAG-GNN utilizes an inference model represented as u = f 4 ((I -A T )f 3 (x)), which has constraints as it can only gather messages from a node's parents. On the other hand, DeepITE's inference model is crafted to aggregate messages from all nodes within the Markov blanket of a given node, ensuring a more flexible inference model tailored for ITE tasks. VACA employs a generative model with a minimum requirement of δ -1 MPNN layers, where δ represents the graph diameter. This limitation restricts the propagation distance of information within the graph, hindering its performance in estimating distributions over large graphs. DeepITE distinguishes itself by employing the generative model, specified in Eq. ( 7), thereby overcomes the limitations imposed by VACA's dependence on graph diameter.To demonstrate the superiority of DeepITE's generative and inference models, we devised two ablation designs by seperately modifying DeepITE's encoder layers to DAG-GNN's encoder and DeepITE's decoder layers to VACA's decoder. These settings were compared alongside VACA and DAG-GNN. Based on the synthetic data in Appendix G.2, we combined the observational and interventional data and fed them into the model along with the adjacency matrix A for observational data, which is exactly how ITE works. Since VACA and DAG-GNN do not directly output ITE results, we utilized Maximum Mean Discrepancy (MMD) and the standard deviation of the squared error (SSE) between the true and estimated values for our evalutaion, providing another dimension to gauge their effectiveness in estimating ITE. MMD was calculated separately for observational and interventional data, even though this information was unknown to the models.The results, as shown in Table 9 , revealed DeepITE outperforming the other models, validating the excellence of DeepITE's generative and inference models. Due to its relatively inflexible model design, DAG-GNN struggles to effectively reconstruct the biases associated with intervention points. The constraint of minimal number decoder layers limits VACA's capability in capturing long-range dependencies and interactions within the graph structure, leading to a significant decrease in its performance as the number of graph nodes increase. Although the ablation methods showed suboptimal performance, the flexibility introduced by the ITE indicator γ enabled them to outperform the origin VACA and DAG-GNN. This underscores the adaptability of our approach for ITE tasks despite its limitations in certain scenarios.To address the challenges of root cause analysis in complex systems with interconnected variables, we conducted a case study on the real-world dataset ICASSP-SPGC 2022, evaluating the performance of DeepITE in comparison to other methods. The groundtruth causal graph is provided in [55] . Recall that we focus on the RCA problem and we aim to identify and present the root causes of the system to users. Note that while we have labels for the root causes in our testing data, we only possess observations for the observable variables represented in the graph. Consequently, all methodologies employed can only localize observable variables as intervention targets (ITs), rather than directly identifying the root causes. For instance, RootCause 2 (a weak signal in marginal areas) can influence feature19, feature X, and feature Y. However, RootCause 3 also affects feature X. As a result, when configuration when it is not known, the joint pursuit of determining both the graph structure and the intervention targets simultaneously offers a tantalizing challenge for future exploration. Finally, proving the consistency and identifiability of DeepITE, and more broadly in the application of VGAEs for ITE, remains an interesting avenue for future work. Notably, such theoretical guarantees have been established for VGAEs in the context of causal inference (both observational and interventional) in [56] .NeurIPS Paper ChecklistWe define an intervention instance as one manipulation on the causal system. We can then collect a set of data with the same intervention targets for this instance.The diameter of a graph is the length of the shortest path between the most distanced endogenous nodes.https://www.aiops.sribd.cn/home/statement 


Decision: I recommend the work "DeepITE" for acceptance based on its significant contributions and overall positive feedback. The work introduces a novel framework for intervention target estimation using a variational graph autoencoder (VGAE) and is empirically validated to outperform baseline methods, demonstrating superior scalability and efficiency. The paper is well-written and connects the new model to existing methods. 

The score of this work has benefited a lot from the discussion between authors and reviewers. Many points have been successfully and extensively clarified and addressed by the authors. 

However, there are some weaknesses that need to be addressed before the final camera-ready version. These include , clarifying assumptions related to the causal graph and intervention types, improving the theoretical analysis concerning scalability and confounder handling and providing accessible implementation code to enhance reproducibility. Addressing these points will strengthen the paper and ensure its contribution is fully validated.

Reviews: review: paper_summary: paper_summary: Given a causal graph, this paper describes an autoencoder-based approach specifically designed for the purpose of designing intervention targets. This algorithm aims to be data and computation-efficient by by-passing the task of having to recover the causal graph, and also by incorporating specific architectural designs for the auto-encoder.
strength_weakness: strength_weakness: The weaknesses of this paper are as follows: 

1. The code is not available -- the main contributions of this work are experiments and empirical evaluation, which are quite strong. In order to truly assess this work, code availability, while not the only factor, is very important. 

2. Lack of clarity: a) There is lack of clarity in terms of the datasets and evaluations (see questions below); b) there is lack of clarity on the competing methods and how this method fits within the general framework. For example, it would be great if RCA, and the main ITE baselines can be formally described in mathematical terms through a simple example (either in the main text or the appendix). 

3. Evaluation: the authors seem to not discuss a very trivial and intuitive baseline regarding prediction methods with sparsity such as Lasso (please see questions below).
questions: questions: I have a few questions for the authors: 

1. What is the purpose of the noise variable \zeta, and why is it modeled as a separate variable from the \mathbf{u} variable? From my experience, the exogenous variables are simply independent noise terms that are provided as input to the functional causal model. 

2. How do the authors know the true intervention targets of the protein dataset? 

3. Have the authors considered the following baseline: given M interventional datasets and an observational dataset, label each point with label G corresponding to which interventional dataset it comes from. Then, train a sparse classification (feature selection) method such as sparse logistic regression to predict G from the features X when combining an interventional and an observational dataset. Then, the selected features will be the Markov Blanket of G. I was wondering what the author's thoughts are on this simple baseline.  

4. In line 300, the authors mention: "Once trained, the inference model of DeepITE becomes equipped to evaluate individual new samples
against different causal graphs, directly deducing the intervention targets and thus circumventing
the necessity of retraining for each new scenario...."; could the authors elaborate on this point? My understanding is that the model assumes a given causal graph.
limitations: limitations: From what I see, there is no discussion on this model's limitation in the text.
paper_summary: paper_summary: This paper proposes a deep learning approach for Intervention Target Estimation (ITE) which is an important problem in causal discovery and inference. The authors argue that traditional methods in this area can only independently process each instance and is computationally inefficient. To address these limitations, the authors propose a variational graph auto-encoder whose key components involve an encoder and a decoder that are specially designed to accommodate the properties of causal factorization/intervention. The authors also discuss how to instantiate the encoder and decoder with modern GNNs and use the variational inference for deriving the objective. Experiments on synthetic datasets and two real-world datasets verify the effectiveness of the model against several state-of-the-art baselines.
strength_weakness: strength_weakness: The model section is not entirely clear, and some parts need further explanation.

The technical novelty is somehow weakened given that the direct usage of DAG-GNN in Sec 5.1.

The experiments lack qualitative analysis or case study to verify the model.

The presentation can be improved, especially the descriptions about prior art and the motivation in Sec. 1 (the third and fourth para are too long and involved).
questions: questions: 1. What precisely the semi-supervised learning is conducted using the model? How the labeled data is incorporated into the ELBO?

2. Can the authors provide more explanations why Recall is used as the only metric for evaluation?

3. Given the studied problem, maybe more qualitative analysis or case study are expected to further verify the model.

Minor: 

1. The authors argue that GAT enables inductiveness and consider this as the advantage of GAT over other GNNs. This arguement seems problematic, since in the context of the proposed framework, the GAT can be in principle replaced by other off-the-shelf GNNs, such as basically GCN and SGC. Maybe more explanations or ablation studies are needed for jusitification on this design choice.

2. Some typos for reference: 

line 106: "but this too suffers from scalability issues with large graphs"

line 109: "zeroes in on ITE"
limitations: limitations: The limitations are properly discussed in the appendix.
paper_summary: paper_summary: The paper presents DeepITE, a novel deep learning framework designed for Intervention Target Estimation (ITE) in complex systems. DeepITE addresses these issues by employing a variational graph autoencoder (VGAE) that can learn from both unlabeled and labeled data across various intervention targets and causal graphs. The framework is capable of self-supervised and semi-supervised learning, allowing it to identify intervention targets without the need for retraining with new instances. It demonstrates improved performance in Recall@k metrics and faster inference times, especially for large graphs.
strength_weakness: strength_weakness: While the paper presents a significant contribution with the introduction of DeepITE, there are several areas where the work could be improved towards its stated goals:
1. **Theoretical Depth**: The paper could benefit from a more thorough theoretical analysis, particularly in understanding the limitations of the VGAE approach compared to traditional causal inference methods. For instance, a deeper discussion on the assumptions made by DeepITE and how they compare to assumptions in established causal frameworks would be valuable.
2. **Scalability Analysis**: While the paper mentions the efficiency of DeepITE, a more detailed analysis of its scalability with respect to the size of the graph and the number of interventions would be beneficial. This could include profiling the computational complexity and memory usage for very large graphs.
3. **Intervention Types**: DeepITE is designed to handle interventions, but the paper could provide more details on the types of interventions it can effectively estimate. For example, it would be useful to know how the model performs with different mixes of hard and soft interventions.
4. **Confounding Factors**: The paper assumes the absence of confounders, which may not hold in real-world scenarios. Future work could explore extensions of DeepITE to handle potential confounding, possibly through the integration of domain knowledge or advanced causal inference techniques.
questions: questions: 1. **Identifiability**: Does DeepITE have decidability, and can it guarantee that the optimal set of intervention variables can always be recovered from the data?
2. **Sample size**: Since this method is based on deep networks, are there any specific requirements for the amount of data samples?
3. **Robustness to random initialization**: according to algorithm 1,  this method need to be initialized by some random parameters. Does it robustness to the random initialization?
limitations: limitations: NA
paper_summary: paper_summary: The paper introduces a deep learning framework for identifying intervention targets in causal systems by amortizing the problem, although assuming that the causal graph is known. The framework, called DeepITE, employs a variational graph autoencoder (VGAE) that learns from both labeled and unlabeled data across different intervention targets and causal graphs. The model can quickly identify intervention targets in new samples without the need for retraining, addressing the inefficiencies of current methods which require frequent re-estimations with minor data changes. DeepITE is validated through comprehensive testing against 13 baseline methods, showing superior performance.
strength_weakness: strength_weakness: 1. The authors should make it explicit from the introduction that their framework assumes that the graph is known (but not the full SCM). As far as I understand, this is not the case in Yang et al. [7]. I believe the manuscript would be clearer if it had a table summarizing the different efforts for RCA and ITE, explaining for each paper what they assume (wrt knowledge of causal model, nature of intervention, max number of nodes targeted, and any other relevant assumptions), so that a reader may situate the work more carefully.
2. The claim that the model can handle soft interventions seems uninstantiated. I quote "A probability of gamma_i = 0 being one indicates a hard intervention, whereas any other value suggests a soft intervention". Given that there are many different layers of complexity at play here, I do not believe this is a reasonable claim. For example, this is a clear instance of model misspecification, in which I do not expect there there would be consistency. For certain type of soft interventions, it is plausible that the proposed model (based on hard interventions) would erroneously predict the set of intervened nodes. Additionally, the model's inference strategy uses variational approximations, and differentiable relaxation of discrete distributions, which makes it very hard to assess whether "probability of gamma_i = 0 [equals] one".
3. I wish to have seen some form of consistency theory for the proposed method. So far it has little to no theoretical backing, even though I understand that the authors have explained well why the generative model has a nice causal semantic.
4. A main advantage of the method is to amortize across different settings, but I am not sure this claim is perfectly justified. For example, DeepITE mix performs worse than the sep variant and it performs worse than CI-RCA in table 1 (unlike written in the text!). Additionally, the authors didn't quite explain how many graphs were put together, and I didn't see in the main text the existence of an ablation study to show that with more graphs, the method performs better. I wish to have seen a assessment of the amortization to justify that it actually works.  
5. It would be great if the authors could explain when they expect the model to perform well, or not, and which components are helpful for its empirical success.
questions: questions: - Can you clarify whether the framework assumes the causal graph is known a priori, as this seems to differ from approaches like Yang et al. [7]? Would it be possible to include a table summarizing key assumptions of different RCA and ITE efforts for clearer comparative context?
- Can you substantiate the claim that the model can handle soft interventions, given the complexities associated with different types of interventions and the potential for model misspecification?
- Is there any consistency theory or additional theoretical backing for the proposed method, especially regarding its generative model and causal semantics?
- How do you justify the claim about the model's ability to amortize across different settings, particularly given the mixed performance of DeepITE in various configurations as noted in your results?
- Could you discuss under what conditions the model is expected to perform well, which components significantly contribute to its empirical success, and any limitations in its current design?
limitations: limitations: N/A

Comments: title: Reply to Reviewer HUbk
Reply to Reviewer GccQ
Reply to Reviewer q8ww
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comment: Thank you very much for your positive feedback. We greatly appreciate your time and thoughtful review.
We greatly appreciate your valuable suggestions and the time you've taken to provide detailed feedback. We will carefully incorporate the case study results and clarifications into our paper.

> For the different from DAG-GNN, the main theoretical results of this paper are from DAG-GNN. While this work applies the method to different problem settings, the technical novelty and contributions would be limited in this sense.

We would like to clarify that DAG-GNN **does not prove any of the theorems presented in our paper**, even within their problem settings. Instead, DAG-GNN provides two theorems specifically related to their proposed acyclicity constraints.

> For Recall metric, the authors use different metrics for different datasets without enough justification. I understand what Recall means, but the rebuttal fails to properly justify why only Recall is used for Protein/Synthetic and the other metrics are used for ICASSP. This questions the robustness of the results.

Thank you for raising this concern. The additional metrics used for the ICASSP dataset were selected due to the unique characteristics and requirements of this particular dataset. As a result, these additional metrics **could not be applied to to the Protein/Synthetic datasets** in our study.

As explained in our rebuttal, we prioritize Recall@k because, in practice, false positives can be eliminated through further analysis, while **false negatives are irrecoverable** as they get lost among the numerous true negatives. This approach ensures that critical detections are not overlooked, which is why Recall@k is emphasized for certain datasets in our study.

On the other hand, it’s important to note that Recall@k **inherently includes a ranking among all candidate intervention targets** (ITs). A higher Recall@1 indicates that the true IT is ranked first, which implies that, with an appropriate threshold, the precision will also be very high. This is another reason why we focused on Recall@k in our analysis.

> The argument that GAT is inductive is not rigorously correct, since common GNNs (e.g., GCN and SGC) are all applicable for inductive learning. The inductiveness is not a unique advantage of GAT.

Thank you for pointing this out. We agree that GCN and SGC are also inductive, as they, along with GAT, fall under the category of spatial GNNs rather than spectral GNNs, making them all applicable for inductive learning. 

As mentioned in our rebuttal, we **choose GAT** not because only GAT is inductive, but **because it is more flexible compared to GCN and SGC** [R3]. This flexibility stems from GAT's ability to dynamically weigh the importance of different nodes, thus allowing the variational distribution given by the inference network better approximate the exact posterior distribution. This point is also validated in our experiments in Appendix A.6.

Once again, we sincerely thank you for your thoughtful feedback.
Thank you very much for your valuable feedback.

>Regarding Q5:

>- I think we may have a misunderstanding. If G is an auxiliary discrete variable (with discrete values denoting the interventional environment a data point came from), which has the same value for each point in the same interventional environment, a method like Lasso would indeed find all variables that are associated with G (it will yield the variables in the Markov Blanket of G, we can term them MB(G)). One can also assume that G is always a cause (by definition it cannot be an effect of any variable). Then, MB(G) will be either the direct effects of G, or parents of the direct effects. Then, one can think about using the known causal graph to distinguish these sets of variables.

Thank you very much for your clarification. We now understand that this is quite similar to the method implemented in [3], and we have compared DeepITE with it in our analysis.

>Regarding Q6:

>- Can the authors briefly elaborate why it is possible to generalize to new, previously-unseen, causal graphs when using their framework?

Sure. In simple words, after training the VGAE collaboratively using graphs with different sets of intervention targets, different structures, and even different sizes, the inference model (i.e., the encoder) in the VGAE successfully learns a mapping whose input is the observed data $\mathbf{x}$ and the adjacency matrix $A$ and output is the distribution of intervention indicator $\gamma$. As a result, when we replace the adjacency matrix $A$ by that of an unseen graph, the encoder can still output the distribution of the intervention indicator.

Thank you again for your thoughtful response, as they have provided valuable insights for improving our paper.
Thanks for the discussions. Please incorporate the case study results and clarification into the paper.

For the different from DAG-GNN, the main theoretical results of this paper are from DAG-GNN. While this work applies the method to different problem settings, the technical novelty and contributions would be limited in this sense.

For Recall metric, the authors use different metrics for different datasets without enough justification. I understand what Recall means, but the rebuttal fails to properly justify why only Recall is used for Protein/Synthetic and the other metrics are used for ICASSP. This questions the robustness of the results.

The argument that GAT is inductive is not rigorously correct, since common GNNs (e.g., GCN and SGC) are all applicable for inductive learning. The inductiveness is not a unique advantage of GAT.
I thank the reviewers for detailed responses to my questions, and for addressing some of my concerns. 

Regarding Q5: 
- I think we may have a misunderstanding. If G is an auxiliary discrete variable (with discrete values denoting the interventional environment a data point came from), which has the same value for each point in the same interventional environment, a method like Lasso would indeed find all variables that are associated with G (it will yield the variables in the Markov Blanket of G, we can term them MB(G)). One can also assume that G is always a cause (by definition it cannot be an effect of any variable). Then, MB(G) will be either the direct effects of G, or parents of the direct effects. Then, one can think about using the known causal graph to distinguish these sets of variables. 

Regarding Q6: 
- Can the authors briefly elaborate why it is possible to generalize to new, previously-unseen, causal graphs when using their framework? 

Thank you very much.
I would like to thank the authors for their detailed response, and the additional experiments. I do not have additional questions, and will consider changing my score while discussing with other reviewers.
Dear Reviewer HUbk,

We wanted to kindly check in on the status of the rebuttal, as there are 2 days remaining for the rebuttal period. Please let us know if there is anything else we can provide to contribute to our work. We would greatly appreciate it if you could provide your insights at your earliest convenience.

Thank you for your time and consideration.

Best regards,

Authors of DeepITE
Dear Reviewer bhQC,

We wanted to kindly check in on the status of the rebuttal, as there are 2 days remaining for the rebuttal period. Please let us know if there is anything else we can provide to contribute to our work. We would greatly appreciate it if you could provide your insights at your earliest convenience.

Thank you for your time and consideration.

Best regards,

Authors of DeepITE
Dear Reviewer GccQ,

We wanted to kindly check in on the status of the rebuttal, as there are 2 days remaining for the rebuttal period. Please let us know if there is anything else we can provide to contribute to our work. We would greatly appreciate it if you could provide your insights at your earliest convenience. 

Thank you for your time and consideration.

Best regards,

Authors of DeepITE
Dear Reviewer q8ww,

We wanted to kindly check in on the status of the rebuttal, as there are 2 days remaining for the rebuttal period. Please let us know if there is anything else we can provide to contribute to our work. We would greatly appreciate it if you could provide your insights at your earliest convenience. 

Thank you for your time and consideration.

Best regards,

Authors of DeepITE