Adaptive Perturbation-Based Gradient Estimation for Discrete Latent Variable Models

The integration of discrete algorithmic components in deep learning architectures has numerous applications. Recently, Implicit Maximum Likelihood Estimation (IMLE, Niepert, Minervini, and Franceschi 2021), a class of gradient estimators for discrete exponential family distributions, was proposed by combining implicit differentiation through perturbation with the path-wise gradient estimator. However, due to the finite difference approximation of the gradients, it is especially sensitive to the choice of the finite difference step size which needs to be specified by the user. In this work, we present Adaptive IMLE (AIMLE) the first adaptive gradient estimator for complex discrete distributions: it adaptively identifies the target distribution for IMLE by trading off the density of gradient information with the degree of bias in the gradient estimates. We empirically evaluate our estimator on synthetic examples, as well as on Learning to Explain, Discrete Variational Auto-Encoders, and Neural Relational Inference tasks. In our experiments, we show that our adaptive gradient estimator can produce faithful estimates while requiring orders of magnitude fewer samples than other gradient estimators.

Ordered Subgraph Aggregation Networks

Numerous subgraph-enhanced graph neural networks (GNNs) have emerged recently, provably boosting the expressive power of standard (message-passing) GNNs. However, there is a limited understanding of how these approaches relate to each other and to the Weisfeiler--Leman hierarchy. Moreover, current approaches either use all subgraphs of a given size, sample them uniformly at random, or use hand-crafted heuristics instead of learning to select subgraphs in a data-driven manner. Here, we offer a unified way to study such architectures by introducing a theoretical framework and extending the known expressivity results of subgraph-enhanced GNNs. Concretely, we show that increasing subgraph size always increases the expressive power and develop a better understanding of their limitations by relating them to the established $k\text{-}\mathsf{WL}$ hierarchy. In addition, we explore different approaches for learning to sample subgraphs using recent methods for backpropagating through complex discrete probability distributions. Empirically, we study the predictive performance of different subgraph-enhanced GNNs, showing that our data-driven architectures increase prediction accuracy on standard benchmark datasets compared to non-data-driven subgraph-enhanced graph neural networks while reducing computation time.

Integrating diverse extraction pathways using iterative predictions for Multilingual Open Information Extraction

In this paper we investigate a simple hypothesis for the Open Information Extraction (OpenIE) task, that it may be easier to extract some elements of an triple if the extraction is conditioned on prior extractions which may be easier to extract. We successfully exploit this and propose a neural multilingual OpenIE system that iteratively extracts triples by conditioning extractions on different elements of the triple leading to a rich set of extractions. The iterative nature of MiLIE also allows for seamlessly integrating rule based extraction systems with a neural end-to-end system leading to improved performance. MiLIE outperforms SOTA systems on multiple languages ranging from Chinese to Galician thanks to it's ability of combining multiple extraction pathways. Our analysis confirms that it is indeed true that certain elements of an extraction are easier to extract than others. Finally, we introduce OpenIE evaluation datasets for two low resource languages namely Japanese and Galician.

AnnIE: An Annotation Platform for Constructing Complete Open Information Extraction Benchmark

Open Information Extraction (OIE) is the task of extracting facts from sentences in the form of relations and their corresponding arguments in schema-free manner. Intrinsic performance of OIE systems is difficult to measure due to the incompleteness of existing OIE benchmarks: the ground truth extractions do not group all acceptable surface realizations of the same fact that can be extracted from a sentence. To measure performance of OIE systems more realistically, it is necessary to manually annotate complete facts (i.e., clusters of all acceptable surface realizations of the same fact) from input sentences. We propose AnnIE: an interactive annotation platform that facilitates such challenging annotation tasks and supports creation of complete fact-oriented OIE evaluation benchmarks. AnnIE is modular and flexible in order to support different use case scenarios (i.e., benchmarks covering different types of facts). We use AnnIE to build two complete OIE benchmarks: one with verb-mediated facts and another with facts encompassing named entities. Finally, we evaluate several OIE systems on our complete benchmarks created with AnnIE. Our results suggest that existing incomplete benchmarks are overly lenient, and that OIE systems are not as robust as previously reported. We publicly release AnnIE under non-restrictive license.

BenchIE: Open Information Extraction Evaluation Based on Facts, Not Tokens

Intrinsic evaluations of OIE systems are carried out either manually -- with human evaluators judging the correctness of extractions -- or automatically, on standardized benchmarks. The latter, while much more cost-effective, is less reliable, primarily because of the incompleteness of the existing OIE benchmarks: the ground truth extractions do not include all acceptable variants of the same fact, leading to unreliable assessment of models' performance. Moreover, the existing OIE benchmarks are available for English only. In this work, we introduce BenchIE: a benchmark and evaluation framework for comprehensive evaluation of OIE systems for English, Chinese and German. In contrast to existing OIE benchmarks, BenchIE takes into account informational equivalence of extractions: our gold standard consists of fact synsets, clusters in which we exhaustively list all surface forms of the same fact. We benchmark several state-of-the-art OIE systems using BenchIE and demonstrate that these systems are significantly less effective than indicated by existing OIE benchmarks. We make BenchIE (data and evaluation code) publicly available.

VEGN: Variant Effect Prediction with Graph Neural Networks

Genetic mutations can cause disease by disrupting normal gene function. Identifying the disease-causing mutations from millions of genetic variants within an individual patient is a challenging problem. Computational methods which can prioritize disease-causing mutations have, therefore, enormous applications. It is well-known that genes function through a complex regulatory network. However, existing variant effect prediction models only consider a variant in isolation. In contrast, we propose VEGN, which models variant effect prediction using a graph neural network (GNN) that operates on a heterogeneous graph with genes and variants. The graph is created by assigning variants to genes and connecting genes with an gene-gene interaction network. In this context, we explore an approach where a gene-gene graph is given and another where VEGN learns the gene-gene graph and therefore operates both on given and learnt edges. The graph neural network is trained to aggregate information between genes, and between genes and variants. Variants can exchange information via the genes they connect to. This approach improves the performance of existing state-of-the-art models.

Implicit MLE: Backpropagating Through Discrete Exponential Family Distributions

Integrating discrete probability distributions and combinatorial optimization problems into neural networks has numerous applications but poses several challenges. We propose Implicit Maximum Likelihood Estimation (I-MLE), a framework for end-to-end learning of models combining discrete exponential family distributions and differentiable neural components. I-MLE is widely applicable: it only requires the ability to compute the most probable states; and does not rely on smooth relaxations. The framework encompasses several approaches, such as perturbation-based implicit differentiation and recent methods to differentiate through black-box combinatorial solvers. We introduce a novel class of noise distributions for approximating marginals via perturb-and-MAP. Moreover, we show that I-MLE simplifies to maximum likelihood estimation when used in some recently studied learning settings that involve combinatorial solvers. Experiments on several datasets suggest that I-MLE is competitive with and often outperforms existing approaches which rely on problem-specific relaxations.

Uncertainty Estimation and Calibration with Finite-State Probabilistic RNNs

Uncertainty quantification is crucial for building reliable and trustable machine learning systems. We propose to estimate uncertainty in recurrent neural networks (RNNs) via stochastic discrete state transitions over recurrent timesteps. The uncertainty of the model can be quantified by running a prediction several times, each time sampling from the recurrent state transition distribution, leading to potentially different results if the model is uncertain. Alongside uncertainty quantification, our proposed method offers several advantages in different settings. The proposed method can (1) learn deterministic and probabilistic automata from data, (2) learn well-calibrated models on real-world classification tasks, (3) improve the performance of out-of-distribution detection, and (4) control the exploration-exploitation trade-off in reinforcement learning.

Explaining Neural Matrix Factorization with Gradient Rollback

Explaining the predictions of neural black-box models is an important problem, especially when such models are used in applications where user trust is crucial. Estimating the influence of training examples on a learned neural model's behavior allows us to identify training examples most responsible for a given prediction and, therefore, to faithfully explain the output of a black-box model. The most generally applicable existing method is based on influence functions, which scale poorly for larger sample sizes and models. We propose gradient rollback, a general approach for influence estimation, applicable to neural models where each parameter update step during gradient descent touches a smaller number of parameters, even if the overall number of parameters is large. Neural matrix factorization models trained with gradient descent are part of this model class. These models are popular and have found a wide range of applications in industry. Especially knowledge graph embedding methods, which belong to this class, are used extensively. We show that gradient rollback is highly efficient at both training and test time. Moreover, we show theoretically that the difference between gradient rollback's influence approximation and the true influence on a model's behavior is smaller than known bounds on the stability of stochastic gradient descent. This establishes that gradient rollback is robustly estimating example influence. We also conduct experiments which show that gradient rollback provides faithful explanations for knowledge base completion and recommender datasets.