The calibration of a reservoir model with observed transient data of fluid pressures and rates is a key task in obtaining a predictive model of the flow and transport behaviour of the earth's subsurface. The model calibration task, commonly referred to as "history matching", can be formalised as an ill-posed inverse problem where we aim to find the underlying spatial distribution of petrophysical properties that explain the observed dynamic data. We use a generative adversarial network pretrained on geostatistical object-based models to represent the distribution of rock properties for a synthetic model of a hydrocarbon reservoir. The dynamic behaviour of the reservoir fluids is modelled using a transient two-phase incompressible Darcy formulation. We invert for the underlying reservoir properties by first modeling property distributions using the pre-trained generative model then using the adjoint equations of the forward problem to perform gradient descent on the latent variables that control the output of the generative model. In addition to the dynamic observation data, we include well rock-type constraints by introducing an additional objective function. Our contribution shows that for a synthetic test case, we are able to obtain solutions to the inverse problem by optimising in the latent variable space of a deep generative model, given a set of transient observations of a non-linear forward problem.

Despite the recent successes in robotic locomotion control, the design of robot relies heavily on human engineering. Automatic robot design has been a long studied subject, but the recent progress has been slowed due to the large combinatorial search space and the difficulty in evaluating the found candidates. To address the two challenges, we formulate automatic robot design as a graph search problem and perform evolution search in graph space. We propose Neural Graph Evolution (NGE), which performs selection on current candidates and evolves new ones iteratively. Different from previous approaches, NGE uses graph neural networks to parameterize the control policies, which reduces evaluation cost on new candidates with the help of skill transfer from previously evaluated designs. In addition, NGE applies Graph Mutation with Uncertainty (GM-UC) by incorporating model uncertainty, which reduces the search space by balancing exploration and exploitation. We show that NGE significantly outperforms previous methods by an order of magnitude. As shown in experiments, NGE is the first algorithm that can automatically discover kinematically preferred robotic graph structures, such as a fish with two symmetrical flat side-fins and a tail, or a cheetah with athletic front and back legs. Instead of using thousands of cores for weeks, NGE efficiently solves searching problem within a day on a single 64 CPU-core Amazon EC2 machine.

Variational inference for Bayesian deep neural networks (DNNs) requires specifying priors and approximate posterior distributions for neural network weights. Specifying meaningful weight priors is a challenging problem, particularly for scaling variational inference to deeper architectures involving high dimensional weight space. We propose Bayesian MOdel Priors Extracted from Deterministic DNN (MOPED) method for stochastic variational inference to choose meaningful prior distributions over weight space using deterministic weights derived from the pretrained DNNs of equivalent architecture. We evaluate the proposed approach on multiple datasets and real-world application domains with a range of varying complex model architectures to demonstrate MOPED enables scalable variational inference for Bayesian DNNs. The proposed method achieves faster training convergence and provides reliable uncertainty quantification, without compromising on the accuracy provided by the deterministic DNNs. We also propose hybrid architectures to Bayesian DNNs where deterministic and variational layers are combined to balance computation complexity during prediction phase and while providing benefits of Bayesian inference. We will release the source code for this work.

Multi-hop reading comprehension requires the model to explore and connect relevant information from multiple sentences/documents in order to answer the question about the context. To achieve this, we propose an interpretable 3-module system called Explore-Propose-Assemble reader (EPAr). First, the Document Explorer iteratively selects relevant documents and represents divergent reasoning chains in a tree structure so as to allow assimilating information from all chains. The Answer Proposer then proposes an answer from every root-to-leaf path in the reasoning tree. Finally, the Evidence Assembler extracts a key sentence containing the proposed answer from every path and combines them to predict the final answer. Intuitively, EPAr approximates the coarse-to-fine-grained comprehension behavior of human readers when facing multiple long documents. We jointly optimize our 3 modules by minimizing the sum of losses from each stage conditioned on the previous stage's output. On two multi-hop reading comprehension datasets WikiHop and MedHop, our EPAr model achieves significant improvements over the baseline and competitive results compared to the state-of-the-art model. We also present multiple reasoning-chain-recovery tests and ablation studies to demonstrate our system's ability to perform interpretable and accurate reasoning.

Collaborative representation is a popular feature learning approach, which encoding process is assisted by variety types of information. In this paper, we propose a collaborative representation restricted Boltzmann Machine (CRRBM) for modeling binary data and a collaborative representation Gaussian restricted Boltzmann Machine (CRGRBM) for modeling realvalued data by applying a collaborative representation strategy in the encoding procedure. We utilize Locality Sensitive Hashing (LSH) to generate similar sample subsets of the instance and observed feature set simultaneously from input data. Hence, we can obtain some mini blocks, which come from the intersection of instance and observed feature subsets. Then we integrate Contrastive Divergence and Bregman Divergence methods with mini blocks to optimize our CRRBM and CRGRBM models. In their training process, the complex collaborative relationships between multiple instances and features are fused into the hidden layer encoding. Hence, these encodings have dual characteristics of concealment and cooperation. Here, we develop two deep collaborative encoder frameworks (DCEF) based on the CRRBM and CRGRBM models: one is a DCEF with Gaussian linear visible units (GDCEF) for modeling real-valued data, and the other is a DCEF with binary visible units (BDCEF) for modeling binary data. We explore the collaborative representation capability of the hidden features in every layer of the GDCEF and BDCEF framework, especially in the deepest hidden layer. The experimental results show that the GDCEF and BDCEF frameworks have more outstanding performances than the classic Autoencoder framework for unsupervised clustering task on the MSRA-MM2.0 and UCI datasets, respectively.

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.

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.