Many applications of machine learning in science and medicine, including molecular property and protein function prediction, can be cast as problems of predicting some properties of graphs, where having good graph representations is critical. However, two key challenges in these domains are (1) extreme scarcity of labeled data due to expensive lab experiments, and (2) needing to extrapolate to test graphs that are structurally different from those seen during training. In this paper, we explore pre-training to address both of these challenges. In particular, working with Graph Neural Networks (GNNs) for representation learning of graphs, we wish to obtain node representations that (1) capture similarity of nodes' network neighborhood structure, (2) can be composed to give accurate graph-level representations, and (3) capture domain-knowledge. To achieve these goals, we propose a series of methods to pre-train GNNs at both the node-level and the graph-level, using both unlabeled data and labeled data from related auxiliary supervised tasks. We perform extensive evaluation on two applications, molecular property and protein function prediction. We observe that performing only graph-level supervised pre-training often leads to marginal performance gain or even can worsen the performance compared to non-pre-trained models. On the other hand, effectively combining both node- and graph-level pre-training techniques significantly improves generalization to out-of-distribution graphs, consistently outperforming non-pre-trained GNNs across 8 datasets in molecular property prediction (resp. 40 tasks in protein function prediction), with the average ROC-AUC improvement of 7.2% (resp. 11.7%).

The causes underlying unfair decision making are complex, being internalised in different ways by decision makers, other actors dealing with data and models, and ultimately by the individuals being affected by these decisions. One frequent manifestation of all these latent causes arises in the form of missing values: protected groups are more reluctant to give information that could be used against them, delicate information for some groups can be erased by human operators, or data acquisition may simply be less complete and systematic for minority groups. As a result, missing values and bias in data are two phenomena that are tightly coupled. However, most recent techniques, libraries and experimental results dealing with fairness in machine learning have simply ignored missing data. In this paper, we claim that fairness research should not miss the opportunity to deal properly with missing data. To support this claim, (1) we analyse the sources of missing data and bias, and we map the common causes, (2) we find that rows containing missing values are usually fairer than the rest, which should not be treated as the uncomfortable ugly data that different techniques and libraries get rid of at the first occasion, and (3) we study the trade-off between performance and fairness when the rows with missing values are used (either because the technique deals with them directly or by imputation methods). We end the paper with a series of recommended procedures about what to do with missing data when aiming for fair decision making.

Neuromorphic Computing is a nascent research field in which models and devices are designed to process information by emulating biological neural systems. Thanks to their superior energy efficiency, analog neuromorphic systems are highly promising for embedded, wearable, and implantable systems. However, optimizing neural networks deployed on these systems is challenging. One main challenge is the so-called timescale mismatch: Dynamics of analog circuits tend to be too fast to process real-time sensory inputs. In this thesis, we propose a few working solutions to slow down dynamics of on-chip spiking neural networks. We empirically show that, by harnessing slow dynamics, spiking neural networks on analog neuromorphic systems can gain non-trivial performance boosts on a battery of real-time signal processing tasks.

Neuroscientists have enjoyed much success in understanding brain functions by constructing brain connectivity networks using data collected under highly controlled experimental settings. However, these experimental settings bear little resemblance to our real-life experience in day-to-day interactions with the surroundings. To address this issue, neuroscientists have been measuring brain activity under natural viewing experiments in which the subjects are given continuous stimuli, such as watching a movie or listening to a story. The main challenge with this approach is that the measured signal consists of both the stimulus-induced signal, as well as intrinsic-neural and non-neuronal signals. By exploiting the experimental design, we propose to estimate stimulus-locked brain network by treating non-stimulus-induced signals as nuisance parameters. In many neuroscience applications, it is often important to identify brain regions that are connected to many other brain regions during cognitive process. We propose an inferential method to test whether the maximum degree of the estimated network is larger than a pre-specific number. We prove that the type I error can be controlled and that the power increases to one asymptotically. Simulation studies are conducted to assess the performance of our method. Finally, we analyze a functional magnetic resonance imaging dataset obtained under the Sherlock Holmes movie stimuli.

We consider learning ancestral causal relationships in high dimensions. Our approach is driven by a supervised learning perspective, with discrete indicators of causal relationships treated as labels to be learned from available data. We focus on the setting in which some causal (ancestral) relationships are known (via background knowledge or experimental data) and put forward a general approach that scales to large problems. This is motivated by problems in human biology which are characterized by high dimensionality and potentially many latent variables. We present a case study involving interventional data from human cells with total dimension $p \! \sim \! 19{,}000$. Performance is assessed empirically by testing model output against previously unseen interventional data. The proposed approach is highly effective and demonstrably scalable to the human genome-wide setting. We consider sensitivity to background knowledge and find that results are robust to nontrivial perturbations of the input information. We consider also the case, relevant to some applications, where the only prior information available concerns a small number of known ancestral relationships.

When recruiting job candidates, employers rarely observe their underlying skill level directly. Instead, they must administer a series of interviews and/or collate other noisy signals in order to estimate the worker's skill. Traditional economics papers address screening models where employers access worker skill via a single noisy signal. In this paper, we extend this theoretical analysis to a multi-test setting, considering both Bernoulli and Gaussian models. We analyze the optimal employer policy both when the employer sets a fixed number of tests per candidate and when the employer can set a dynamic policy, assigning further tests adaptively based on results from the previous tests. To start, we characterize the optimal policy when employees constitute a single group, demonstrating some interesting trade-offs. Subsequently, we address the multi-group setting, demonstrating that when the noise levels vary across groups, a fundamental impossibility emerges whereby we cannot administer the same number of tests, subject candidates to the same decision rule, and yet realize the same outcomes in both groups.

Deep generative models (DGMs) of images are now sufficiently mature that they produce nearly photorealistic samples and obtain scores similar to the data distribution on heuristics such as Frechet Inception Distance. These results, especially on large-scale datasets such as ImageNet, suggest that DGMs are learning the data distribution in a perceptually meaningful space, and can be used in downstream tasks. To test this latter hypothesis, we use class-conditional generative models from a number of model classes---variational autoencoder, autoregressive models, and generative adversarial networks---to infer the class labels of real data. We perform this inference by training the image classifier using only synthetic data, and using the classifier to predict labels on real data. The performance on this task, which we call Classification Accuracy Score (CAS), highlights some surprising results not captured by traditional metrics and comprise our contributions. First, when using a state-of-the-art GAN (BigGAN), Top-5 accuracy decreases by 41.6% compared to the original data and conditional generative models from other model classes, such as high-resolution VQ-VAE and Hierarchical Autoregressive Models, substantially outperform GANs on this benchmark. Second, CAS automatically surfaces particular classes for which generative models failed to capture the data distribution, and were previously unknown in the literature. Third, we find traditional GAN metrics such as Frechet Inception Distance neither predictive of CAS nor useful when evaluating non-GAN models. Finally, we introduce Naive Augmentation Score, a variant of CAS where the image classifier is trained on both real and synthetic data, to demonstrate that naive augmentation improves classification performance in limited circumstances. In order to facilitate better diagnoses of generative models, we open-source the proposed metric.

Despite the tremendous progress in the estimation of generative models, the development of tools for diagnosing their failures and assessing their performance has advanced at a much slower pace. Recent developments have investigated metrics that quantify which parts of the true distribution are modeled well, and, on the contrary, what the model fails to capture, akin to precision and recall in information retrieval. In this paper, we present a general evaluation framework for generative models that measures the trade-off between precision and recall using R\'enyi divergences. Our framework provides a novel perspective on existing techniques and extends them to more general domains. As a key advantage, it allows for efficient algorithms that are directly applicable to continuous distributions directly without discretization. We further showcase the proposed techniques on a set of image synthesis models.

In this paper, we consider the nonparametric least square regression in a Reproducing Kernel Hilbert Space (RKHS). We propose a new randomized algorithm that has optimal generalization error bounds with respect to the square loss, closing a long-standing gap between upper and lower bounds. Moreover, we show that our algorithm has faster finite-time and asymptotic rates on problems where the Bayes risk with respect to the square loss is small. We state our results using standard tools from the theory of least square regression in RKHSs, namely, the decay of the eigenvalues of the associated integral operator and the complexity of the optimal predictor measured through the integral operator.

Online learning algorithms update models via one sample per iteration, thus efficient to process large-scale datasets and useful to detect malicious events for social benefits, such as disease outbreak and traffic congestion on the fly. However, existing algorithms for graph-structured models focused on the offline setting and the least square loss, incapable for online setting, while methods designed for online setting cannot be directly applied to the problem of complex (usually non-convex) graph-structured sparsity model. To address these limitations, in this paper we propose a new algorithm for graph-structured sparsity constraint problems under online setting, which we call \textsc{GraphDA}. The key part in \textsc{GraphDA} is to project both averaging gradient (in dual space) and primal variables (in primal space) onto lower dimensional subspaces, thus capturing the graph-structured sparsity effectively. Furthermore, the objective functions assumed here are generally convex so as to handle different losses for online learning settings. To the best of our knowledge, \textsc{GraphDA} is the first online learning algorithm for graph-structure constrained optimization problems. To validate our method, we conduct extensive experiments on both benchmark graph and real-world graph datasets. Our experiment results show that, compared to other baseline methods, \textsc{GraphDA} not only improves classification performance, but also successfully captures graph-structured features more effectively, hence stronger interpretability.