In the world of Natural Language Processing (NLP), the most basic models are based on Bag of Words. But such models fail to capture the syntactic relations between words. For example, suppose we build a sentiment analyser based on only Bag of Words. Such a model will not be able to capture the difference between "I like you", where "like" is a verb with a positive sentiment, and "I am like you", where "like" is a preposition with a neutral sentiment. So this leaves us with a question -- how do we improve on this Bag of Words technique?

We present a novel approach to train pixel resolution segmentation models on whole slide images in a weakly supervised setup. The model is trained to classify patches extracted from slides. This leads the training to be made under noisy labeled data. We solve the problem with two complementary strategies. First, the patches are sampled online using the model's knowledge by focusing on regions where the model's confidence is higher. Second, we propose an extension of the KL divergence that is robust to noisy labels. Our preliminary experiment on CAMELYON 16 data set show promising results.

Quantifying and measuring uncertainty in deep neural networks, despite recent important advances, is still an open problem. Bayesian neural networks are a powerful solution, where the prior over network weights is a design choice, often a normal distribution or other distribution encouraging sparsity. However, this prior is agnostic to the generative process of the input data, which might lead to unwarranted generalization for out-of-distribution tested data. We suggest treating the generative process of the input data as a confounder for the relation between the input and the discriminative function, thereby conditioning the prior of the network weights on the distribution of the input. We propose an algorithm for modeling this confounder through neural connectivity patterns. This approach is ultimately translated into a new deep architecture---a compact hierarchy of networks. We demonstrate that sampling networks from this hierarchy, proportionally to their posterior, is efficient and enables estimating various types of uncertainties. Empirical evaluations of our method demonstrate significant improvement compared to state-of-the-art calibration and out-of-distribution detection methods.

Diagnosis and treatment guidance are aided by detecting relevant biomarkers in medical images. Although supervised deep learning can perform accurate segmentation of pathological areas, it is limited by requiring a-priori definitions of these regions, large-scale annotations, and a representative patient cohort in the training set. In contrast, anomaly detection is not limited to specific definitions of pathologies and allows for training on healthy samples without annotation. Anomalous regions can then serve as candidates for biomarker discovery. Knowledge about normal anatomical structure brings implicit information for detecting anomalies. We propose to take advantage of this property using bayesian deep learning, based on the assumption that epistemic uncertainties will correlate with anatomical deviations from a normal training set. A Bayesian U-Net is trained on a well-defined healthy environment using weak labels of healthy anatomy produced by existing methods. At test time, we capture epistemic uncertainty estimates of our model using Monte Carlo dropout. A novel post-processing technique is then applied to exploit these estimates and transfer their layered appearance to smooth blob-shaped segmentations of the anomalies. We experimentally validated this approach in retinal optical coherence tomography (OCT) images, using weak labels of retinal layers. Our method achieved a Dice index of 0.789 in an independent anomaly test set of age-related macular degeneration (AMD) cases. The resulting segmentations allowed very high accuracy for separating healthy and diseased cases with late wet AMD, dry geographic atrophy (GA), diabetic macular edema (DME) and retinal vein occlusion (RVO). Finally, we qualitatively observed that our approach can also detect other deviations in normal scans such as cut edge artifacts.

Complex classification performance metrics such as the F${}_\beta$-measure and Jaccard index are often used, in order to handle class-imbalanced cases such as information retrieval and image segmentation. These performance metrics are not decomposable, that is, they cannot be expressed in a per-example manner, which hinders a straightforward application of the M-estimation widely used in supervised learning. In this paper, we consider \emph{linear-fractional metrics}, which are a family of classification performance metrics that encompasses many standard metrics such as the F${}_\beta$-measure and Jaccard index, and propose methods to directly maximize performances under those metrics. A clue to tackle their direct optimization is a \emph{calibrated surrogate utility}, which is a tractable lower bound of the true utility function representing a given metric. We characterize necessary conditions which make the surrogate maximization coincide with the maximization of the true utility. To the best of our knowledge, this is the first surrogate calibration analysis for the linear-fractional metrics. We also propose gradient-based optimization algorithms and show their practical usefulness in experiments.

In this paper, we consider recommender systems with side information in the form of graphs. Existing collaborative filtering algorithms mainly utilize only immediate neighborhood information and have a hard time taking advantage of deeper neighborhoods beyond 1-2 hops. The main caveat of exploiting deeper graph information is the rapidly growing time and space complexity when incorporating information from these neighborhoods. In this paper, we propose using Graph DNA, a novel Deep Neighborhood Aware graph encoding algorithm, for exploiting deeper neighborhood information. DNA encoding computes approximate deep neighborhood information in linear time using Bloom filters, a space-efficient probabilistic data structure and results in a per-node encoding that is logarithmic in the number of nodes in the graph. It can be used in conjunction with both feature-based and graph-regularization-based collaborative filtering algorithms. Graph DNA has the advantages of being memory and time efficient and providing additional regularization when compared to directly using higher order graph information. We conduct experiments on real-world datasets, showing graph DNA can be easily used with 4 popular collaborative filtering algorithms and consistently leads to a performance boost with little computational and memory overhead.

Models leak information about their training data. This enables attackers to infer sensitive information about their training sets, notably determine if a data sample was part of the model's training set. The existing works empirically show the possibility of these tracing (membership inference) attacks against complex models with a large number of parameters. However, the attack results are dependent on the specific training data, can be obtained only after the tedious process of training the model and performing the attack, and are missing any measure of the confidence and unused potential power of the attack. A model designer is interested in identifying which model structures leak more information, how adding new parameters to the model increases its privacy risk, and what is the gain of adding new data points to decrease the overall information leakage. The privacy analysis should also enable designing the most powerful inference attack. In this paper, we design a theoretical framework to analyze the maximum power of tracing attacks against high-dimensional models, with the focus on probabilistic graphical models. We provide a tight upper-bound on the power (true positive rate) of these attacks, with respect to their error (false positive rate). The bound, as it should be, is independent of the knowledge and algorithm of any specific attack, as well as the values of particular samples in the training set. It provides a measure of the potential leakage of a model given its structure, as a function of the structure complexity and the size of training set.

We study the denoising of piecewise smooth graph signals that exhibit inhomogeneous levels of smoothness over a graph, where the value at each node can be vector-valued. We extend the graph trend filtering framework to denoising vector-valued graph signals with a family of non-convex regularizers that exhibit superior recovery performance over existing convex regularizers. We establish the statistical error rates of first-order stationary points of the proposed non-convex method for generic graphs using oracle inequalities. We further present an ADMM-based algorithm to solve the proposed method and analyze its convergence. We present numerical experiments on both synthetic and real-world data for denoising, support recovery, and semi-supervised classification.

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.