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.

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 purely probabilistic model. We show the model's competitiveness on scarce supervision scenarios, handling missing data, and 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.

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.

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.

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.

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

PDEBENCH: An Extensive Benchmark for Scientific Machine Learning

Machine learning-based modeling of physical systems has experienced increased interest in recent years. Despite some impressive progress, there is still a lack of benchmarks for Scientific ML that are easy to use but still challenging and representative of a wide range of problems. We introduce PDEBench, a benchmark suite of time-dependent simulation tasks based on Partial Differential Equations (PDEs). PDEBench comprises both code and data to benchmark the performance of novel machine learning models against both classical numerical simulations and machine learning baselines. Our proposed set of benchmark problems contribute the following unique features: (1) A much wider range of PDEs compared to existing benchmarks, ranging from relatively common examples to more realistic and difficult problems; (2) much larger ready-to-use datasets compared to prior work, comprising multiple simulation runs across a larger number of initial and boundary conditions and PDE parameters; (3) more extensible source codes with user-friendly APIs for data generation and baseline results with popular machine learning models (FNO, U-Net, PINN, Gradient-Based Inverse Method). PDEBench allows researchers to extend the benchmark freely for their own purposes using a standardized API and to compare the performance of new models to existing baseline methods. We also propose new evaluation metrics with the aim to provide a more holistic understanding of learning methods in the context of Scientific ML. With those metrics we identify tasks which are challenging for recent ML methods and propose these tasks as future challenges for the community. The code is available at https://github.com/pdebench/PDEBench.

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.

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.