We describe ChemBO, a Bayesian Optimization framework for generating and optimizing organic molecules for desired molecular properties. This framework is useful in applications such as drug discovery, where an algorithm recommends new candidate molecules; these molecules first need to be synthesized and then tested for drug-like properties. The algorithm uses the results of past tests to recommend new ones so as to find good molecules efficiently. Most existing data-driven methods for this problem do not account for sample efficiency and/or fail to enforce realistic constraints on synthesizability. In this work, we explore existing kernels for molecules in the literature as well as propose a novel kernel which views a molecule as a graph. In ChemBO, we implement these kernels in a Gaussian process model. Then we explore the chemical space by traversing possible paths of molecular synthesis. Consequently, our approach provides a proposal synthesis path every time it recommends a new molecule to test, a crucial advantage when compared to existing methods. In our experiments, we demonstrate the efficacy of the proposed approach on several molecular optimization problems.
Global routing has been a historically challenging problem in electronic circuit design, where the challenge is to connect a large and arbitrary number of circuit components with wires without violating the design rules for the printed circuit boards or integrated circuits. Similar routing problems also exist in the design of complex hydraulic systems, pipe systems and logistic networks. Existing solutions typically consist of greedy algorithms and hard-coded heuristics. As such, existing approaches suffer from a lack of model flexibility and non-optimum solutions. As an alternative approach, this work presents a deep reinforcement learning method for solving the global routing problem in a simulated environment. At the heart of the proposed method is deep reinforcement learning that enables an agent to produce an optimal policy for routing based on the variety of problems it is presented with leveraging the conjoint optimization mechanism of deep reinforcement learning. Conjoint optimization mechanism is explained and demonstrated in details; the best network structure and the parameters of the learned model are explored. Based on the fine-tuned model, routing solutions and rewards are presented and analyzed. The results indicate that the approach can outperform the benchmark method of a sequential A* method, suggesting a promising potential for deep reinforcement learning for global routing and other routing or path planning problems in general. Another major contribution of this work is the development of a global routing problem sets generator with the ability to generate parameterized global routing problem sets with different size and constraints, enabling evaluation of different routing algorithms and the generation of training datasets for future data-driven routing approaches.
Current state-of-the-art NMT systems use large neural networks that are not only slow to train, but also often require many heuristics and optimization tricks, such as specialized learning rate schedules and large batch sizes. This is undesirable as it requires extensive hyperparameter tuning. In this paper, we propose a curriculum learning framework for NMT that reduces training time, reduces the need for specialized heuristics or large batch sizes, and results in overall better performance. Our framework consists of a principled way of deciding which training samples are shown to the model at different times during training, based on the estimated difficulty of a sample and the current competence of the model. Filtering training samples in this manner prevents the model from getting stuck in bad local optima, making it converge faster and reach a better solution than the common approach of uniformly sampling training examples. Furthermore, the proposed method can be easily applied to existing NMT models by simply modifying their input data pipelines. We show that our framework can help improve the training time and the performance of both recurrent neural network models and Transformers, achieving up to a 70% decrease in training time, while at the same time obtaining accuracy improvements of up to 2.2 BLEU.
Bayesian Optimisation (BO), refers to a suite of techniques for global optimisation of expensive black box functions, which use introspective Bayesian models of the function to efficiently find the optimum. While BO has been applied successfully in many applications, modern optimisation tasks usher in new challenges where conventional methods fail spectacularly. In this work, we present Dragonfly, an open source Python library for scalable and robust BO. Dragonfly incorporates multiple recently developed methods that allow BO to be applied in challenging real world settings; these include better methods for handling higher dimensional domains, methods for handling multi-fidelity evaluations when cheap approximations of an expensive function are available, methods for optimising over structured combinatorial spaces, such as the space of neural network architectures, and methods for handling parallel evaluations. Additionally, we develop new methodological improvements in BO for selecting the Bayesian model, selecting the acquisition function, and optimising over complex domains with different variable types and additional constraints. We compare Dragonfly to a suite of other packages and algorithms for global optimisation and demonstrate that when the above methods are integrated, they enable significant improvements in the performance of BO. The Dragonfly library is available at dragonfly.github.io.
We describe the construction of end-to-end jet image classifiers based on simulated low-level detector data to discriminate quark- vs. gluon-initiated jets with high-fidelity simulated CMS Open Data. We highlight the importance of precise spatial information and demonstrate competitive performance to existing state-of-the-art jet classifiers. We further generalize the end-to-end approach to event-level classification of quark vs. gluon di-jet QCD events. We compare the fully end-to-end approach to using hand-engineered features and demonstrate that the end-to-end algorithm is robust against the effects of underlying event and pile-up.
Optimizing an expensive-to-query function is a common task in science and engineering, where it is beneficial to keep the number of queries to a minimum. A popular strategy is Bayesian optimization (BO), which leverages probabilistic models for this task. Most BO today uses Gaussian processes (GPs), or a few other surrogate models. However, there is a broad set of Bayesian modeling techniques that we may want to use to capture complex systems and reduce the number of queries. Probabilistic programs (PPs) are modern tools that allow for flexible model composition, incorporation of prior information, and automatic inference. In this paper, we develop ProBO, a framework for BO using only standard operations common to most PPs. This allows a user to drop in an arbitrary PP implementation and use it directly in BO. To do this, we describe black box versions of popular acquisition functions that can be used in our framework automatically, without model-specific derivation, and show how to optimize these functions. We also introduce a model, which we term the Bayesian Product of Experts, that integrates into ProBO and can be used to combine information from multiple models implemented with different PPs. We show empirical results using multiple PP implementations, and compare against standard BO methods.
Multimodal sentiment analysis is a core research area that studies speaker sentiment expressed from the language, visual, and acoustic modalities. The central challenge in multimodal learning involves inferring joint representations that can process and relate information from these modalities. However, existing work learns joint representations by requiring all modalities as input and as a result, the learned representations may be sensitive to noisy or missing modalities at test time. With the recent success of sequence to sequence (Seq2Seq) models in machine translation, there is an opportunity to explore new ways of learning joint representations that may not require all input modalities at test time. In this paper, we propose a method to learn robust joint representations by translating between modalities. Our method is based on the key insight that translation from a source to a target modality provides a method of learning joint representations using only the source modality as input. We augment modality translations with a cycle consistency loss to ensure that our joint representations retain maximal information from all modalities. Once our translation model is trained with paired multimodal data, we only need data from the source modality at test time for final sentiment prediction. This ensures that our model remains robust from perturbations or missing information in the other modalities. We train our model with a coupled translation-prediction objective and it achieves new state-of-the-art results on multimodal sentiment analysis datasets: CMU-MOSI, ICT-MMMO, and YouTube. Additional experiments show that our model learns increasingly discriminative joint representations with more input modalities while maintaining robustness to missing or perturbed modalities.
Our team of artists and machine learning researchers designed a creative algorithm that can generate authentic sculptural artworks. These artworks do not mimic any given forms and cannot be easily categorized into the dataset categories. Our approach extends DeepDream from images to 3D point clouds. The proposed algorithm, Amalgamated DeepDream (ADD), leverages the properties of point clouds to create objects with better quality than the naive extension. ADD presents promise for the creativity of machines, the kind of creativity that pushes artists to explore novel methods or materials and to create new genres instead of creating variations of existing forms or styles within one genre. For example, from Realism to Abstract Expressionism, or to Minimalism. Lastly, we present the sculptures that are 3D printed based on the point clouds created by ADD.
Generative Adversarial Networks (GAN) can achieve promising performance on learning complex data distributions on different types of data. In this paper, we first show a straightforward extension of existing GAN algorithm is not applicable to point clouds, because the constraint required for discriminators is undefined for set data. We propose a two fold modification to GAN algorithm for learning to generate point clouds (PC-GAN). First, we combine ideas from hierarchical Bayesian modeling and implicit generative models by learning a hierarchical and interpretable sampling process. A key component of our method is that we train a posterior inference network for the hidden variables. Second, instead of using only state-of-the-art Wasserstein GAN objective, we propose a sandwiching objective, which results in a tighter Wasserstein distance estimate than the commonly used dual form. Thereby, PC-GAN defines a generic framework that can incorporate many existing GAN algorithms. We validate our claims on ModelNet40 benchmark dataset. Using the distance between generated point clouds and true meshes as metric, we find that PC-GAN trained by the sandwiching objective achieves better results on test data than the existing methods. Moreover, as a byproduct, PC- GAN learns versatile latent representations of point clouds, which can achieve competitive performance with other unsupervised learning algorithms on object recognition task. Lastly, we also provide studies on generating unseen classes of objects and transforming image to point cloud, which demonstrates the compelling generalization capability and potentials of PC-GAN.
Multimodal machine learning is a core research area spanning the language, visual and acoustic modalities. The central challenge in multimodal learning involves learning representations that can process and relate information from multiple modalities. In this paper, we propose two methods for unsupervised learning of joint multimodal representations using sequence to sequence (Seq2Seq) methods: a \textit{Seq2Seq Modality Translation Model} and a \textit{Hierarchical Seq2Seq Modality Translation Model}. We also explore multiple different variations on the multimodal inputs and outputs of these seq2seq models. Our experiments on multimodal sentiment analysis using the CMU-MOSI dataset indicate that our methods learn informative multimodal representations that outperform the baselines and achieve improved performance on multimodal sentiment analysis, specifically in the Bimodal case where our model is able to improve F1 Score by twelve points. We also discuss future directions for multimodal Seq2Seq methods.