To accelerate the process of materials design, materials science has increasingly used data driven techniques to extract information from collected data. Specially, machine learning (ML) algorithms, which span the ML discipline, have demonstrated ability to predict various properties of materials with the level of accuracy similar to explicit calculation of quantum mechanical theories, but with significantly reduced run time and computational resources. Within ML, graph neural networks have emerged as an important algorithm within the field of machine learning, since they are capable of predicting accurately a wide range of important physical, chemical and electronic properties due to their higher learning ability based on the graph representation of material and molecular descriptors through the aggregation of information embedded within the graph. In parallel with the development of state of the art classical machine learning applications, the fusion of quantum computing and machine learning have created a new paradigm where classical machine learning model can be augmented with quantum layers which are able to encode high dimensional data more efficiently. Leveraging the structure of existing algorithms, we developed a unique and novel gradient free hybrid quantum classical convoluted graph neural network (HyQCGNN) to predict formation energies of perovskite materials. The performance of our hybrid statistical model is competitive with the results obtained purely from a classical convoluted graph neural network, and other classical machine learning algorithms, such as XGBoost. Consequently, our study suggests a new pathway to explore how quantum feature encoding and parametric quantum circuits can yield drastic improvements of complex ML algorithm like graph neural network.
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Software engineering is a domain characterized by intricate decision-making processes, often relying on nuanced intuition and consultation. Recent advancements in deep learning have started to revolutionize software engineering practices through elaborate designs implemented at various stages of software development. In this paper, we present an innovative paradigm that leverages large language models (LLMs) throughout the entire software development process, streamlining and unifying key processes through natural language communication, thereby eliminating the need for specialized models at each phase. At the core of this paradigm lies ChatDev, a virtual chat-powered software development company that mirrors the established waterfall model, meticulously dividing the development process into four distinct chronological stages: designing, coding, testing, and documenting. Each stage engages a team of agents, such as programmers, code reviewers, and test engineers, fostering collaborative dialogue and facilitating a seamless workflow. The chat chain acts as a facilitator, breaking down each stage into atomic subtasks. This enables dual roles, allowing for proposing and validating solutions through context-aware communication, leading to efficient resolution of specific subtasks. The instrumental analysis of ChatDev highlights its remarkable efficacy in software generation, enabling the completion of the entire software development process in under seven minutes at a cost of less than one dollar. It not only identifies and alleviates potential vulnerabilities but also rectifies potential hallucinations while maintaining commendable efficiency and cost-effectiveness. The potential of ChatDev unveils fresh possibilities for integrating LLMs into the realm of software development.
The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.
Molecular design and synthesis planning are two critical steps in the process of molecular discovery that we propose to formulate as a single shared task of conditional synthetic pathway generation. We report an amortized approach to generate synthetic pathways as a Markov decision process conditioned on a target molecular embedding. This approach allows us to conduct synthesis planning in a bottom-up manner and design synthesizable molecules by decoding from optimized conditional codes, demonstrating the potential to solve both problems of design and synthesis simultaneously. The approach leverages neural networks to probabilistically model the synthetic trees, one reaction step at a time, according to reactivity rules encoded in a discrete action space of reaction templates. We train these networks on hundreds of thousands of artificial pathways generated from a pool of purchasable compounds and a list of expert-curated templates. We validate our method with (a) the recovery of molecules using conditional generation, (b) the identification of synthesizable structural analogs, and (c) the optimization of molecular structures given oracle functions relevant to drug discovery.
Contrastive learning models have achieved great success in unsupervised visual representation learning, which maximize the similarities between feature representations of different views of the same image, while minimize the similarities between feature representations of views of different images. In text summarization, the output summary is a shorter form of the input document and they have similar meanings. In this paper, we propose a contrastive learning model for supervised abstractive text summarization, where we view a document, its gold summary and its model generated summaries as different views of the same mean representation and maximize the similarities between them during training. We improve over a strong sequence-to-sequence text generation model (i.e., BART) on three different summarization datasets. Human evaluation also shows that our model achieves better faithfulness ratings compared to its counterpart without contrastive objectives.
Recent contrastive representation learning methods rely on estimating mutual information (MI) between multiple views of an underlying context. E.g., we can derive multiple views of a given image by applying data augmentation, or we can split a sequence into views comprising the past and future of some step in the sequence. Contrastive lower bounds on MI are easy to optimize, but have a strong underestimation bias when estimating large amounts of MI. We propose decomposing the full MI estimation problem into a sum of smaller estimation problems by splitting one of the views into progressively more informed subviews and by applying the chain rule on MI between the decomposed views. This expression contains a sum of unconditional and conditional MI terms, each measuring modest chunks of the total MI, which facilitates approximation via contrastive bounds. To maximize the sum, we formulate a contrastive lower bound on the conditional MI which can be approximated efficiently. We refer to our general approach as Decomposed Estimation of Mutual Information (DEMI). We show that DEMI can capture a larger amount of MI than standard non-decomposed contrastive bounds in a synthetic setting, and learns better representations in a vision domain and for dialogue generation.
Mining graph data has become a popular research topic in computer science and has been widely studied in both academia and industry given the increasing amount of network data in the recent years. However, the huge amount of network data has posed great challenges for efficient analysis. This motivates the advent of graph representation which maps the graph into a low-dimension vector space, keeping original graph structure and supporting graph inference. The investigation on efficient representation of a graph has profound theoretical significance and important realistic meaning, we therefore introduce some basic ideas in graph representation/network embedding as well as some representative models in this chapter.
Embedding entities and relations into a continuous multi-dimensional vector space have become the dominant method for knowledge graph embedding in representation learning. However, most existing models ignore to represent hierarchical knowledge, such as the similarities and dissimilarities of entities in one domain. We proposed to learn a Domain Representations over existing knowledge graph embedding models, such that entities that have similar attributes are organized into the same domain. Such hierarchical knowledge of domains can give further evidence in link prediction. Experimental results show that domain embeddings give a significant improvement over the most recent state-of-art baseline knowledge graph embedding models.
Benefit from the quick development of deep learning techniques, salient object detection has achieved remarkable progresses recently. However, there still exists following two major challenges that hinder its application in embedded devices, low resolution output and heavy model weight. To this end, this paper presents an accurate yet compact deep network for efficient salient object detection. More specifically, given a coarse saliency prediction in the deepest layer, we first employ residual learning to learn side-output residual features for saliency refinement, which can be achieved with very limited convolutional parameters while keep accuracy. Secondly, we further propose reverse attention to guide such side-output residual learning in a top-down manner. By erasing the current predicted salient regions from side-output features, the network can eventually explore the missing object parts and details which results in high resolution and accuracy. Experiments on six benchmark datasets demonstrate that the proposed approach compares favorably against state-of-the-art methods, and with advantages in terms of simplicity, efficiency (45 FPS) and model size (81 MB).
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
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