arXiv subjects

Mathias Niepert

Publications and source records attributed to Mathias Niepert.

At least 73 records · Page 4Linked to original sources

arXiv2024

L2XGNN: Learning to Explain Graph Neural Networks

Graph Neural Networks (GNNs) are a popular class of machine learning models. Inspired by the learning to explain (L2X) paradigm, we propose L2XGNN, a framework for explainable GNNs which provides faithful explanations by design. L2XGNN learns a mechanism for selecting explanatory subgraphs (motifs) which are exclusively used in the GNNs message-passing operations. L2XGNN is able to select, for each input graph, a subgraph with specific properties such as being sparse and connected. Imposing such constraints on the motifs often leads to more interpretable and effective explanations. Experiments on several datasets suggest that L2XGNN achieves the same classification accuracy as baseline methods using the entire input graph while ensuring that only the provided explanations are used to make predictions. Moreover, we show that L2XGNN is able to identify motifs responsible for the graph's properties it is intended to predict.

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arXiv2024

SIMPLE: A Gradient Estimator for $k$-Subset Sampling

$k$-subset sampling is ubiquitous in machine learning, enabling regularization and interpretability through sparsity. The challenge lies in rendering $k$-subset sampling amenable to end-to-end learning. This has typically involved relaxing the reparameterized samples to allow for backpropagation, with the risk of introducing high bias and high variance. In this work, we fall back to discrete $k$-subset sampling on the forward pass. This is coupled with using the gradient with respect to the exact marginals, computed efficiently, as a proxy for the true gradient. We show that our gradient estimator, SIMPLE, exhibits lower bias and variance compared to state-of-the-art estimators, including the straight-through Gumbel estimator when $k = 1$. Empirical results show improved performance on learning to explain and sparse linear regression. We provide an algorithm for computing the exact ELBO for the $k$-subset distribution, obtaining significantly lower loss compared to SOTA.

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arXiv2024

Probabilistically Rewired Message-Passing Neural Networks

Message-passing graph neural networks (MPNNs) emerged as powerful tools for processing graph-structured input. However, they operate on a fixed input graph structure, ignoring potential noise and missing information. Furthermore, their local aggregation mechanism can lead to problems such as over-squashing and limited expressive power in capturing relevant graph structures. Existing solutions to these challenges have primarily relied on heuristic methods, often disregarding the underlying data distribution. Hence, devising principled approaches for learning to infer graph structures relevant to the given prediction task remains an open challenge. In this work, leveraging recent progress in exact and differentiable $k$-subset sampling, we devise probabilistically rewired MPNNs (PR-MPNNs), which learn to add relevant edges while omitting less beneficial ones. For the first time, our theoretical analysis explores how PR-MPNNs enhance expressive power, and we identify precise conditions under which they outperform purely randomized approaches. Empirically, we demonstrate that our approach effectively mitigates issues like over-squashing and under-reaching. In addition, on established real-world datasets, our method exhibits competitive or superior predictive performance compared to traditional MPNN models and recent graph transformer architectures.

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arXiv2024

Tractable Probabilistic Graph Representation Learning with Graph-Induced Sum-Product Networks

We introduce Graph-Induced Sum-Product Networks (GSPNs), a new probabilistic framework for graph representation learning that can tractably answer probabilistic queries. Inspired by the computational trees induced by vertices in the context of message-passing neural networks, we build hierarchies of sum-product networks (SPNs) where the parameters of a parent SPN are learnable transformations of the a-posterior mixing probabilities of its children's sum units. Due to weight sharing and the tree-shaped computation graphs of GSPNs, we obtain the efficiency and efficacy of deep graph networks with the additional advantages of a probabilistic model. We show the model's competitiveness on scarce supervision scenarios, under missing data, and for graph classification in comparison to popular neural models. We complement the experiments with qualitative analyses on hyper-parameters and the model's ability to answer probabilistic queries.

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arXiv2023

LVM-Med: Learning Large-Scale Self-Supervised Vision Models for Medical Imaging via Second-order Graph Matching

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

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arXiv2023

On the Out of Distribution Robustness of Foundation Models in Medical Image Segmentation

Constructing a robust model that can effectively generalize to test samples under distribution shifts remains a significant challenge in the field of medical imaging. The foundational models for vision and language, pre-trained on extensive sets of natural image and text data, have emerged as a promising approach. It showcases impressive learning abilities across different tasks with the need for only a limited amount of annotated samples. While numerous techniques have focused on developing better fine-tuning strategies to adapt these models for specific domains, we instead examine their robustness to domain shifts in the medical image segmentation task. To this end, we compare the generalization performance to unseen domains of various pre-trained models after being fine-tuned on the same in-distribution dataset and show that foundation-based models enjoy better robustness than other architectures. From here, we further developed a new Bayesian uncertainty estimation for frozen models and used them as an indicator to characterize the model's performance on out-of-distribution (OOD) data, proving particularly beneficial for real-world applications. Our experiments not only reveal the limitations of current indicators like accuracy on the line or agreement on the line commonly used in natural image applications but also emphasize the promise of the introduced Bayesian uncertainty. Specifically, lower uncertainty predictions usually tend to higher out-of-distribution (OOD) performance.

eess.IV↗

arXiv2023

Continual Invariant Risk Minimization

Empirical risk minimization can lead to poor generalization behavior on unseen environments if the learned model does not capture invariant feature representations. Invariant risk minimization (IRM) is a recent proposal for discovering environment-invariant representations. IRM was introduced by Arjovsky et al. (2019) and extended by Ahuja et al. (2020). IRM assumes that all environments are available to the learning system at the same time. With this work, we generalize the concept of IRM to scenarios where environments are observed sequentially. We show that existing approaches, including those designed for continual learning, fail to identify the invariant features and models across sequentially presented environments. We extend IRM under a variational Bayesian and bilevel framework, creating a general approach to continual invariant risk minimization. We also describe a strategy to solve the optimization problems using a variant of the alternating direction method of multiplier (ADMM). We show empirically using multiple datasets and with multiple sequential environments that the proposed methods outperform or is competitive with prior approaches.

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arXiv2023

Approximate Answering of Graph Queries

Knowledge graphs (KGs) are inherently incomplete because of incomplete world knowledge and bias in what is the input to the KG. Additionally, world knowledge constantly expands and evolves, making existing facts deprecated or introducing new ones. However, we would still want to be able to answer queries as if the graph were complete. In this chapter, we will give an overview of several methods which have been proposed to answer queries in such a setting. We will first provide an overview of the different query types which can be supported by these methods and datasets typically used for evaluation, as well as an insight into their limitations. Then, we give an overview of the different approaches and describe them in terms of expressiveness, supported graph types, and inference capabilities.

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arXiv2023

Learning Disentangled Discrete Representations

Recent successes in image generation, model-based reinforcement learning, and text-to-image generation have demonstrated the empirical advantages of discrete latent representations, although the reasons behind their benefits remain unclear. We explore the relationship between discrete latent spaces and disentangled representations by replacing the standard Gaussian variational autoencoder (VAE) with a tailored categorical variational autoencoder. We show that the underlying grid structure of categorical distributions mitigates the problem of rotational invariance associated with multivariate Gaussian distributions, acting as an efficient inductive prior for disentangled representations. We provide both analytical and empirical findings that demonstrate the advantages of discrete VAEs for learning disentangled representations. Furthermore, we introduce the first unsupervised model selection strategy that favors disentangled representations.

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arXiv2023

Efficient Learning of Discrete-Continuous Computation Graphs

Numerous models for supervised and reinforcement learning benefit from combinations of discrete and continuous model components. End-to-end learnable discrete-continuous models are compositional, tend to generalize better, and are more interpretable. A popular approach to building discrete-continuous computation graphs is that of integrating discrete probability distributions into neural networks using stochastic softmax tricks. Prior work has mainly focused on computation graphs with a single discrete component on each of the graph's execution paths. We analyze the behavior of more complex stochastic computations graphs with multiple sequential discrete components. We show that it is challenging to optimize the parameters of these models, mainly due to small gradients and local minima. We then propose two new strategies to overcome these challenges. First, we show that increasing the scale parameter of the Gumbel noise perturbations during training improves the learning behavior. Second, we propose dropout residual connections specifically tailored to stochastic, discrete-continuous computation graphs. With an extensive set of experiments, we show that we can train complex discrete-continuous models which one cannot train with standard stochastic softmax tricks. We also show that complex discrete-stochastic models generalize better than their continuous counterparts on several benchmark datasets.

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arXiv2023

Learning Neural PDE Solvers with Parameter-Guided Channel Attention

Scientific Machine Learning (SciML) is concerned with the development of learned emulators of physical systems governed by partial differential equations (PDE). In application domains such as weather forecasting, molecular dynamics, and inverse design, ML-based surrogate models are increasingly used to augment or replace inefficient and often non-differentiable numerical simulation algorithms. While a number of ML-based methods for approximating the solutions of PDEs have been proposed in recent years, they typically do not adapt to the parameters of the PDEs, making it difficult to generalize to PDE parameters not seen during training. We propose a Channel Attention mechanism guided by PDE Parameter Embeddings (CAPE) component for neural surrogate models and a simple yet effective curriculum learning strategy. The CAPE module can be combined with neural PDE solvers allowing them to adapt to unseen PDE parameters. The curriculum learning strategy provides a seamless transition between teacher-forcing and fully auto-regressive training. We compare CAPE in conjunction with the curriculum learning strategy using a popular PDE benchmark and obtain consistent and significant improvements over the baseline models. The experiments also show several advantages of CAPE, such as its increased ability to generalize to unseen PDE parameters without large increases inference time and parameter count.

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arXiv2023

Learning Sparsity of Representations with Discrete Latent Variables

Deep latent generative models have attracted increasing attention due to the capacity of combining the strengths of deep learning and probabilistic models in an elegant way. The data representations learned with the models are often continuous and dense. However in many applications, sparse representations are expected, such as learning sparse high dimensional embedding of data in an unsupervised setting, and learning multi-labels from thousands of candidate tags in a supervised setting. In some scenarios, there could be further restriction on degree of sparsity: the number of non-zero features of a representation cannot be larger than a pre-defined threshold $L_0$. In this paper we propose a sparse deep latent generative model SDLGM to explicitly model degree of sparsity and thus enable to learn the sparse structure of the data with the quantified sparsity constraint. The resulting sparsity of a representation is not fixed, but fits to the observation itself under the pre-defined restriction. In particular, we introduce to each observation $i$ an auxiliary random variable $L_i$, which models the sparsity of its representation. The sparse representations are then generated with a two-step sampling process via two Gumbel-Softmax distributions. For inference and learning, we develop an amortized variational method based on MC gradient estimator. The resulting sparse representations are differentiable with backpropagation. The experimental evaluation on multiple datasets for unsupervised and supervised learning problems shows the benefits of the proposed method.

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arXiv2023

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.

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arXiv2022

State-Regularized Recurrent Neural Networks to Extract Automata and Explain Predictions

Recurrent neural networks are a widely used class of neural architectures. They have, however, two shortcomings. First, they are often treated as black-box models and as such it is difficult to understand what exactly they learn as well as how they arrive at a particular prediction. Second, they tend to work poorly on sequences requiring long-term memorization, despite having this capacity in principle. We aim to address both shortcomings with a class of recurrent networks that use a stochastic state transition mechanism between cell applications. This mechanism, which we term state-regularization, makes RNNs transition between a finite set of learnable states. We evaluate state-regularized RNNs on (1) regular languages for the purpose of automata extraction; (2) non-regular languages such as balanced parentheses and palindromes where external memory is required; and (3) real-word sequence learning tasks for sentiment analysis, visual object recognition and text categorisation. We show that state-regularization (a) simplifies the extraction of finite state automata that display an RNN's state transition dynamic; (b) forces RNNs to operate more like automata with external memory and less like finite state machines, which potentiality leads to a more structural memory; (c) leads to better interpretability and explainability of RNNs by leveraging the probabilistic finite state transition mechanism over time steps.

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arXiv2022

Joint Multilingual Knowledge Graph Completion and Alignment

Knowledge graph (KG) alignment and completion are usually treated as two independent tasks. While recent work has leveraged entity and relation alignments from multiple KGs, such as alignments between multilingual KGs with common entities and relations, a deeper understanding of the ways in which multilingual KG completion (MKGC) can aid the creation of multilingual KG alignments (MKGA) is still limited. Motivated by the observation that structural inconsistencies -- the main challenge for MKGA models -- can be mitigated through KG completion methods, we propose a novel model for jointly completing and aligning knowledge graphs. The proposed model combines two components that jointly accomplish KG completion and alignment. These two components employ relation-aware graph neural networks that we propose to encode multi-hop neighborhood structures into entity and relation representations. Moreover, we also propose (i) a structural inconsistency reduction mechanism to incorporate information from the completion into the alignment component, and (ii) an alignment seed enlargement and triple transferring mechanism to enlarge alignment seeds and transfer triples during KGs alignment. Extensive experiments on a public multilingual benchmark show that our proposed model outperforms existing competitive baselines, obtaining new state-of-the-art results on both MKGC and MKGA tasks. We publicly release the implementation of our model at https://github.com/vinhsuhi/JMAC

cs.CL↗

arXiv2022

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.

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arXiv2022

milIE: Modular & Iterative Multilingual Open Information Extraction

Open Information Extraction (OpenIE) is the task of extracting (subject, predicate, object) triples from natural language sentences. Current OpenIE systems extract all triple slots independently. In contrast, we explore the hypothesis that it may be beneficial to extract triple slots iteratively: first extract easy slots, followed by the difficult ones by conditioning on the easy slots, and therefore achieve a better overall extraction. Based on this hypothesis, we propose a neural OpenIE system, milIE, that operates in an iterative fashion. Due to the iterative nature, the system is also modular -- it is possible to seamlessly integrate rule based extraction systems with a neural end-to-end system, thereby allowing rule based systems to supply extraction slots which milIE can leverage for extracting the remaining slots. We confirm our hypothesis empirically: milIE outperforms SOTA systems on multiple languages ranging from Chinese to Arabic. Additionally, we are the first to provide an OpenIE test dataset for Arabic and Galician.

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arXiv2022

BenchIE: A Framework for Multi-Faceted Fact-Based Open Information Extraction Evaluation

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 the 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 is fact-based, i.e., it takes into account informational equivalence of extractions: our gold standard consists of fact synsets, clusters in which we exhaustively list all acceptable surface forms of the same fact. Moreover, having in mind common downstream applications for OIE, we make BenchIE multi-faceted; i.e., we create benchmark variants that focus on different facets of OIE evaluation, e.g., compactness or minimality of extractions. 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 on https://github.com/gkiril/benchie.

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