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In this section we motivate the design choices and inductive biases that we encode into our neural encoder network e, which is the network that is used to model the relative accuracies of the weak supervision sources λ. Recall that we model the probability of a particular sample x X having the class label y Y = {1,...,C}as Pθ(y|λ) = softmax(s)yP(y), (4) s = θ(λ,x)Tλ RC . Connection to prior PGM models We now motivate this choice by deriving a less expressive variant of it from the standard Markov Random Field (MRF) used in the related work. If we view the attention scores θ(λ,x) Rm, that assign sample-dependent accuracies to each labeling function, as sample-independent parameters θ1 and, by that, drop the features from the equation - as is done in the related work [30, 32, 19, 11] - we can rewrite Eq. 4 as exp θT1 1 {λ = y} P We can recognize Pθ as a distribution from the exponential familiy, and more specifically as a pairwise MRF, or factor graph, with canonical parameters θ = (θ1,θ2) and corresponding sufficient statistics, or factors, φ(λ,y) = (φ1(λ,y),φ2(λ)), as well as the log partition function Zθ. The accuracy factors and parameters φ1,θ1 are the core component of this model and sometimes take the form φ1(λy) = λy in binary models as in [30, 19, 11]. The label-independent factors φ2(λ) have, as can be seen from the derivation above, no direct influence on the latent label posterior, but are often used to model labeling propensities 1 {λ 6= 0}and correlation dependencies 1 {λi = λj}, which can be important for PGM parameter learning, but are susceptible to misspecifications [39, 11, 8].

In Figure 1 we demonstrate the common neighbor (CN) distribution among positive and negative test samples for ogbl-collab, ogbl-ppa, and ogbl-citation2. These results demonstrate that a vast majority of negative samples have no CNs. Since CNs is a typically good heuristic, this makes it easy to identify most negative samples. We further present the CN distribution of Cora, Citeseer, Pubmed, and ogbl-ddi in Figure 3. The CN distribution of Cora, Citeseer, and Pubmed are consistent with our previous observations on the OGB datasets in Figure 1.

Link prediction attempts to predict whether an unseen edge exists based on only a portion of edges of a graph. A flurry of methods have been introduced in recent years that attempt to make use of graph neural networks (GNNs) for this task. Furthermore, new and diverse datasets have also been created to better evaluate the effectiveness of these new models. However, multiple pitfalls currently exist that hinder our ability to properly evaluate these new methods. These pitfalls mainly include: (1) Lower than actual performance on multiple baselines, (2) A lack of a unified data split and evaluation metric on some datasets, and (3) An unrealistic evaluation setting that uses easy negative samples. To overcome these challenges, we first conduct a fair comparison across prominent methods and datasets, utilizing the same dataset and hyperparameter search settings. We then create a more practical evaluation setting based on a Heuristic Related Sampling Technique (HeaRT), which samples hard negative samples via multiple heuristics. The new evaluation setting helps promote new challenges and opportunities in link prediction by aligning the evaluation with real-world situations.

A.1 Majority Voting The Majority Voting (MV) is the most intuitive algorithm for aggregate LFs' annotations. We omit this case for simplicity. A.3 Snorkel MeTaL The parameters µof Snorkel MeTaL [31] are given by Bayes' theorem we have: pµ(y = c,λ = m) = pµ(λ = m | y = c)p(y = c) = Consider a label model g(L(x),x) F in arbitrary functional class F, e.g., neural network, and having additional dependency on data feature x4, we can still approximate such complicated function with identity function-based label model g W(x)(L(x)) similar to the aforementioned one except that W(x): X RM (C+1) C is a similarly complicated function, e.g., neural network, that maps each data x X to a unique label model parameter W(x). We leave the exploration of more complicated form of label models into future work. B.1 Case 1: identity function We define the loss with reweighted sample as, Instead of employing the decomposing loss function, we introduce a more general influence estimation method - weight-moving Influence, which get ride of the loss decomposition and approximation and is agnostic to the selection of σ() function.

Programmatic Weak Supervision (PWS) aggregates the source votes of multiple weak supervision sources into probabilistic training labels, which are in turn used to train an end model. With its increasing popularity, it is critical to have some tool for users to understand the influence of each component (e.g., the source vote or training data) in the pipeline and interpret the end model behavior. To achieve this, we build on Influence Function (IF) and propose source-aware IF2, which leverages the generation process of the probabilistic labels to decompose the end model's training objective and then calculate the influence associated with each (data, source, class) tuple. These primitive influence score can then be used to estimate the influence of individual component of PWS, such as source vote, supervision source, and training data. On datasets of diverse domains, we demonstrate multiple use cases: (1) interpreting incorrect predictions from multiple angles that reveals insights for debugging the PWS pipeline, (2) identifying mislabeling of sources with a gain of 9%-37% over baselines, and (3) improving the end model's generalization performance by removing harmful components in the training objective (13%-24% better than ordinary IF).

We formalize and generalize the notation of Section 4.1 and prove the results. For the remainder of this section, we fix a dimension D (e.g. The D-dimensional SSM will be a map from a function u: D! to y: D!. Definition 2 (Indexing notation). Given a subset I [D], let I denote its complement [D]\I. Given a 2 N1 and b 2 N2, let a b 2 N1 N2 be defined as (a b)n1,n2 = an1bn2.