De novo molecule generation can suffer from data inefficiency; requiring large amounts of training data or many sampled data points to conduct objective optimization. The latter is a particular disadvantage when combining deep generative models with computationally expensive molecule scoring functions (a.k.a. oracles) commonly used in computer-aided drug design. Recent works have therefore focused on methods to improve sample efficiency in the context of de novo molecule drug design, or to benchmark it. In this work, we discuss and adapt a recent sample efficiency benchmark to better reflect realistic goals also with respect to the quality of chemistry generated, which must always be considered in the context of small-molecule drug design; we then re-evaluate all benchmarked generative models. We find that accounting for molecular weight and LogP with respect to the training data, and the diversity of chemistry proposed, re-orders the ranking of generative models. In addition, we benchmark a recently proposed method to improve sample efficiency (Augmented Hill-Climb) and found it ranked top when considering both the sample efficiency and chemistry of molecules generated. Continual improvements in sample efficiency and chemical desirability enable more routine integration of computationally expensive scoring functions on a more realistic timescale.
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For medical image segmentation, contrastive learning is the dominant practice to improve the quality of visual representations by contrasting semantically similar and dissimilar pairs of samples. This is enabled by the observation that without accessing ground truth label, negative examples with truly dissimilar anatomical features, if sampled, can significantly improve the performance. In reality, however, these samples may come from similar anatomical features and the models may struggle to distinguish the minority tail-class samples, making the tail classes more prone to misclassification, both of which typically lead to model collapse. In this paper, we propose ARCO, a semi-supervised contrastive learning (CL) framework with stratified group sampling theory in medical image segmentation. In particular, we first propose building ARCO through the concept of variance-reduced estimation, and show that certain variance-reduction techniques are particularly beneficial in medical image segmentation tasks with extremely limited labels. Furthermore, we theoretically prove these sampling techniques are universal in variance reduction. Finally, we experimentally validate our approaches on three benchmark datasets with different label settings, and our methods consistently outperform state-of-the-art semi- and fully-supervised methods. Additionally, we augment the CL frameworks with these sampling techniques and demonstrate significant gains over previous methods. We believe our work is an important step towards semi-supervised medical image segmentation by quantifying the limitation of current self-supervision objectives for accomplishing medical image analysis tasks.
Self-supervised learning (SSL) pipelines differ in many design choices such as the architecture, augmentations, or pretraining data. Yet SSL is typically evaluated using a single metric: linear probing on ImageNet. This does not provide much insight into why or when a model is better, now how to improve it. To address this, we propose an SSL risk decomposition, which generalizes the classical supervised approximation-estimation decomposition by considering errors arising from the representation learning step. Our decomposition consists of four error components: approximation, representation usability, probe generalization, and encoder generalization. We provide efficient estimators for each component and use them to analyze the effect of 30 design choices on 169 SSL vision models evaluated on ImageNet. Our analysis gives valuable insights for designing and using SSL models. For example, it highlights the main sources of error and shows how to improve SSL in specific settings (full- vs few-shot) by trading off error components. All results and pretrained models are at //github.com/YannDubs/SSL-Risk-Decomposition.
We present a generative document-specific approach to character analysis and recognition in text lines. Our main idea is to build on unsupervised multi-object segmentation methods and in particular those that reconstruct images based on a limited amount of visual elements, called sprites. Our approach can learn a large number of different characters and leverage line-level annotations when available. Our contribution is twofold. First, we provide the first adaptation and evaluation of a deep unsupervised multi-object segmentation approach for text line analysis. Since these methods have mainly been evaluated on synthetic data in a completely unsupervised setting, demonstrating that they can be adapted and quantitatively evaluated on real text images and that they can be trained using weak supervision are significant progresses. Second, we demonstrate the potential of our method for new applications, more specifically in the field of paleography, which studies the history and variations of handwriting, and for cipher analysis. We evaluate our approach on three very different datasets: a printed volume of the Google1000 dataset, the Copiale cipher and historical handwritten charters from the 12th and early 13th century.
Estimating causal effects from large experimental and observational data has become increasingly prevalent in both industry and research. The bootstrap is an intuitive and powerful technique used to construct standard errors and confidence intervals of estimators. Its application however can be prohibitively demanding in settings involving large data. In addition, modern causal inference estimators based on machine learning and optimization techniques exacerbate the computational burden of the bootstrap. The bag of little bootstraps has been proposed in non-causal settings for large data but has not yet been applied to evaluate the properties of estimators of causal effects. In this paper, we introduce a new bootstrap algorithm called causal bag of little bootstraps for causal inference with large data. The new algorithm significantly improves the computational efficiency of the traditional bootstrap while providing consistent estimates and desirable confidence interval coverage. We describe its properties, provide practical considerations, and evaluate the performance of the proposed algorithm in terms of bias, coverage of the true 95% confidence intervals, and computational time in a simulation study. We apply it in the evaluation of the effect of hormone therapy on the average time to coronary heart disease using a large observational data set from the Women's Health Initiative.
Deep generative models have gained popularity in recent years due to their ability to accurately replicate inherent empirical distributions and yield novel samples. In particular, certain advances are proposed wherein the model engenders data examples following specified attributes. Nevertheless, several challenges still exist and are to be overcome, i.e., difficulty in extrapolating out-of-sample data and insufficient learning of disentangled representations. Structural causal models (SCMs), on the other hand, encapsulate the causal factors that govern a generative process and characterize a generative model based on causal relationships, providing crucial insights for addressing the current obstacles in deep generative models. In this paper, we present a comprehensive survey of Causal deep Generative Models (CGMs), which combine SCMs and deep generative models in a way that boosts several trustworthy properties such as robustness, fairness, and interpretability. We provide an overview of the recent advances in CGMs, categorize them based on generative types, and discuss how causality is introduced into the family of deep generative models. We also explore potential avenues for future research in this field.
Graphs are important data representations for describing objects and their relationships, which appear in a wide diversity of real-world scenarios. As one of a critical problem in this area, graph generation considers learning the distributions of given graphs and generating more novel graphs. Owing to their wide range of applications, generative models for graphs, which have a rich history, however, are traditionally hand-crafted and only capable of modeling a few statistical properties of graphs. Recent advances in deep generative models for graph generation is an important step towards improving the fidelity of generated graphs and paves the way for new kinds of applications. This article provides an extensive overview of the literature in the field of deep generative models for graph generation. Firstly, the formal definition of deep generative models for the graph generation and the preliminary knowledge are provided. Secondly, taxonomies of deep generative models for both unconditional and conditional graph generation are proposed respectively; the existing works of each are compared and analyzed. After that, an overview of the evaluation metrics in this specific domain is provided. Finally, the applications that deep graph generation enables are summarized and five promising future research directions are highlighted.
The dominating NLP paradigm of training a strong neural predictor to perform one task on a specific dataset has led to state-of-the-art performance in a variety of applications (eg. sentiment classification, span-prediction based question answering or machine translation). However, it builds upon the assumption that the data distribution is stationary, ie. that the data is sampled from a fixed distribution both at training and test time. This way of training is inconsistent with how we as humans are able to learn from and operate within a constantly changing stream of information. Moreover, it is ill-adapted to real-world use cases where the data distribution is expected to shift over the course of a model's lifetime. The first goal of this thesis is to characterize the different forms this shift can take in the context of natural language processing, and propose benchmarks and evaluation metrics to measure its effect on current deep learning architectures. We then proceed to take steps to mitigate the effect of distributional shift on NLP models. To this end, we develop methods based on parametric reformulations of the distributionally robust optimization framework. Empirically, we demonstrate that these approaches yield more robust models as demonstrated on a selection of realistic problems. In the third and final part of this thesis, we explore ways of efficiently adapting existing models to new domains or tasks. Our contribution to this topic takes inspiration from information geometry to derive a new gradient update rule which alleviate catastrophic forgetting issues during adaptation.
Modern neural network training relies heavily on data augmentation for improved generalization. After the initial success of label-preserving augmentations, there has been a recent surge of interest in label-perturbing approaches, which combine features and labels across training samples to smooth the learned decision surface. In this paper, we propose a new augmentation method that leverages the first and second moments extracted and re-injected by feature normalization. We replace the moments of the learned features of one training image by those of another, and also interpolate the target labels. As our approach is fast, operates entirely in feature space, and mixes different signals than prior methods, one can effectively combine it with existing augmentation methods. We demonstrate its efficacy across benchmark data sets in computer vision, speech, and natural language processing, where it consistently improves the generalization performance of highly competitive baseline networks.
This paper focuses on two fundamental tasks of graph analysis: community detection and node representation learning, which capture the global and local structures of graphs, respectively. In the current literature, these two tasks are usually independently studied while they are actually highly correlated. We propose a probabilistic generative model called vGraph to learn community membership and node representation collaboratively. Specifically, we assume that each node can be represented as a mixture of communities, and each community is defined as a multinomial distribution over nodes. Both the mixing coefficients and the community distribution are parameterized by the low-dimensional representations of the nodes and communities. We designed an effective variational inference algorithm which regularizes the community membership of neighboring nodes to be similar in the latent space. Experimental results on multiple real-world graphs show that vGraph is very effective in both community detection and node representation learning, outperforming many competitive baselines in both tasks. We show that the framework of vGraph is quite flexible and can be easily extended to detect hierarchical communities.
It is a common paradigm in object detection frameworks to treat all samples equally and target at maximizing the performance on average. In this work, we revisit this paradigm through a careful study on how different samples contribute to the overall performance measured in terms of mAP. Our study suggests that the samples in each mini-batch are neither independent nor equally important, and therefore a better classifier on average does not necessarily mean higher mAP. Motivated by this study, we propose the notion of Prime Samples, those that play a key role in driving the detection performance. We further develop a simple yet effective sampling and learning strategy called PrIme Sample Attention (PISA) that directs the focus of the training process towards such samples. Our experiments demonstrate that it is often more effective to focus on prime samples than hard samples when training a detector. Particularly, On the MSCOCO dataset, PISA outperforms the random sampling baseline and hard mining schemes, e.g. OHEM and Focal Loss, consistently by more than 1% on both single-stage and two-stage detectors, with a strong backbone ResNeXt-101.
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