Times series classification can be successfully tackled by jointly learning a shapelet-based representation of the series in the dataset and classifying the series according to this representation. However, although the learned shapelets are discriminative, they are not always similar to pieces of a real series in the dataset. This makes it difficult to interpret the decision, i.e. difficult to analyze if there are particular behaviors in a series that triggered the decision. In this paper, we make use of a simple convolutional network to tackle the time series classification task and we introduce an adversarial regularization to constrain the model to learn more interpretable shapelets. Our classification results on all the usual time series benchmarks are comparable with the results obtained by similar state-of-the-art algorithms but our adversarially regularized method learns shapelets that are, by design, interpretable.

People can learn a new concept and use it compositionally, understanding how to "blicket twice" after learning how to "blicket." In contrast, powerful sequence-to-sequence (seq2seq) neural networks fail such tests of compositionality, especially when composing new concepts together with existing concepts. In this paper, I show that neural networks can be trained to generalize compositionally through meta seq2seq learning. In this approach, models train on a series of seq2seq problems to acquire the compositional skills needed to solve new seq2seq problems. Meta se2seq learning solves several of the SCAN tests for compositional learning and can learn to apply rules to variables.

Machine learning and deep learning have gained popularity and achieved immense success in Drug discovery in recent decades. Historically, machine learning and deep learning models were trained on either structural data or chemical properties by separated model. In this study, we proposed an architecture training simultaneously both type of data in order to improve the overall performance. Given the molecular structure in the form of SMILES notation and their label, we generated the SMILES-based feature matrix and molecular descriptors. These data was trained on an deep learning model which was also integrated with the Attention mechanism to facilitate training and interpreting. Experiments showed that our model could raise the performance of model. With the maximum MCC 0.56 and AUC 91% by cross-validation on EGFR inhibitors dataset, our architecture was outperforming the referring model. We also successfully integrated Attention mechanism into our model, which helped to interpret the contribution of chemical structures on bioactivity.

Adversarial attacks on deep neural networks traditionally rely on a constrained optimization paradigm, where an optimization procedure is used to obtain a single adversarial perturbation for a given input example. Here, we instead view adversarial attacks as a generative modelling problem, with the goal of producing entire distributions of adversarial examples given an unperturbed input. We show that this generative perspective can be used to design a unified encoder-decoder framework, which is domain-agnostic in that the same framework can be employed to attack different domains with minimal modification. Across three diverse domains---images, text, and graphs---our approach generates whitebox attacks with success rates that are competitive with or superior to existing approaches, with a new state-of-the-art achieved in the graph domain. Finally, we demonstrate that our generative framework can efficiently generate a diverse set of attacks for a single given input, and is even capable of attacking unseen test instances in a zero-shot manner, exhibiting attack generalization.

Many applications for classification methods not only require high accuracy but also reliable estimation of predictive uncertainty. However, while many current classification frameworks, in particular deep neural network architectures, provide very good results in terms of accuracy, they tend to underestimate their predictive uncertainty. In this paper, we propose a method that corrects the confidence output of a general classifier such that it approaches the true probability of classifying correctly. This classifier calibration is, in contrast to existing approaches, based on a non-parametric representation using a latent Gaussian process and specifically designed for multi-class classification. It can be applied to any classification method that outputs confidence estimates and is not limited to neural networks. We also provide a theoretical analysis regarding the over- and underconfidence of a classifier and its relationship to calibration. In experiments we show the universally strong performance of our method across different classifiers and benchmark data sets in contrast to existing classifier calibration techniques.

We present a meta-learning approach based on learning an adaptive, high-dimensional loss function that can generalize across multiple tasks and different model architectures. We develop a fully differentiable pipeline for learning a loss function targeted at maximizing the performance of an optimizee trained using this loss function. We observe that the loss landscape produced by our learned loss significantly improves upon the original task-specific loss. We evaluate our method on supervised and reinforcement learning tasks. Furthermore, we show that our pipeline is able to operate in sparse reward and self-supervised reinforcement learning scenarios.

This thesis presents new methods for unsupervised learning of distributed representations of words and entities from text and knowledge bases. The first algorithm presented in the thesis is a multi-view algorithm for learning representations of words called Multiview Latent Semantic Analysis (MVLSA). By incorporating up to 46 different types of co-occurrence statistics for the same vocabulary of english words, I show that MVLSA outperforms other state-of-the-art word embedding models. Next, I focus on learning entity representations for search and recommendation and present the second method of this thesis, Neural Variational Set Expansion (NVSE). NVSE is also an unsupervised learning method, but it is based on the Variational Autoencoder framework. Evaluations with human annotators show that NVSE can facilitate better search and recommendation of information gathered from noisy, automatic annotation of unstructured natural language corpora. Finally, I move from unstructured data and focus on structured knowledge graphs. I present novel approaches for learning embeddings of vertices and edges in a knowledge graph that obey logical constraints.

Understanding temporal and causal relations between events is a fundamental natural language understanding task. Because a cause must be before its effect in time, temporal and causal relations are closely related and one relation even dictates the other one in many cases. However, limited attention has been paid to studying these two relations jointly. This paper presents a joint inference framework for them using constrained conditional models (CCMs). Specifically, we formulate the joint problem as an integer linear programming (ILP) problem, enforcing constraints inherently in the nature of time and causality. We show that the joint inference framework results in statistically significant improvement in the extraction of both temporal and causal relations from text.

Transportation cost is an attractive similarity measure between probability distributions due to its many useful theoretical properties. However, solving optimal transport exactly can be prohibitively expensive. Therefore, there has been significant effort towards the design of scalable approximation algorithms. Previous combinatorial results [Sharathkumar, Agarwal STOC '12, Agarwal, Sharathkumar STOC '14] have focused primarily on the design of strongly polynomial multiplicative approximation algorithms. There has also been an effort to design approximate solutions with additive errors [Cuturi NIPS '13, Altschuler et. al NIPS '17, Dvurechensky et al., ICML '18, Quanrud, SOSA '19] within a time bound that is linear in the size of the cost matrix and polynomial in $C/\delta$; here $C$ is the largest value in the cost matrix and $\delta$ is the additive error. We present an adaptation of the classical graph algorithm of Gabow and Tarjan and provide a novel analysis of this algorithm that bounds its execution time by $O(\frac{n^2 C}{\delta}+ \frac{nC^2}{\delta^2})$. Our algorithm is extremely simple and executes, for an arbitrarily small constant $\varepsilon$, only $\lfloor \frac{2C}{(1-\varepsilon)\delta}\rfloor + 1$ iterations, where each iteration consists only of a Dijkstra search followed by a depth-first search. We also provide empirical results that suggest our algorithm significantly outperforms existing approaches in execution time.

We study how language on social media is linked to diseases such as atherosclerotic heart disease (AHD), diabetes and various types of cancer. Our proposed model leverages state-of-the-art sentence embeddings, followed by a regression model and clustering, without the need of additional labelled data. It allows to predict community-level medical outcomes from language, and thereby potentially translate these to the individual level. The method is applicable to a wide range of target variables and allows us to discover known and potentially novel correlations of medical outcomes with life-style aspects and other socioeconomic risk factors.