The study of compounds with antioxidant capabilities is of great interest to the scientific community, as it has implications in several areas, from Agricultural Sciences to Biological Sciences, including Food Engineering, Medicine and Pharmacy. In applications related to human health, it is known that antioxidant activity can delay or inhibit oxidative damage to cells, reducing damage caused by free radicals, helping in the treatment, or even preventing or postponing the onset of various diseases. Among the compounds that have antioxidant properties, there are several classes of Phenolic Compounds, which include several compounds with different chemical structures. In this work, based on the molecular branching of compounds and their intramolecular charge distributions, and using Molecular Topology, we propose a significant topological-mathematical model to evaluate the potential of candidate compounds to have an antioxidant function.
Molecule generation with desired properties has grown immensely in popularity by disruptively changing the way scientists design molecular structures and providing support for chemical and materials design. However, despite the promising outcome, previous machine learning-based deep generative models suffer from a reliance on complex, task-specific fine-tuning, limited dimensional latent spaces, or the quality of expert rules. In this work, we propose MolGen, a pre-trained molecular language model that effectively learns and shares knowledge across multiple generation tasks and domains. Specifically, we pre-train MolGen with the chemical language SELFIES on more than 100 million unlabelled molecules. We further propose multi-task molecular prefix tuning across several molecular generation tasks and different molecular domains (synthetic & natural products) with a self-feedback mechanism. Extensive experiments show that MolGen can obtain superior performances on well-known molecular generation benchmark datasets. The further analysis illustrates that MolGen can accurately capture the distribution of molecules, implicitly learn their structural characteristics, and efficiently explore the chemical space with the guidance of multi-task molecular prefix tuning. Codes, datasets, and the pre-trained model will be available in //github.com/zjunlp/MolGen.
Recent progress in empirical and certified robustness promises to deliver reliable and deployable Deep Neural Networks (DNNs). Despite that success, most existing evaluations of DNN robustness have been done on images sampled from the same distribution on which the model was trained. However, in the real world, DNNs may be deployed in dynamic environments that exhibit significant distribution shifts. In this work, we take a first step towards thoroughly investigating the interplay between empirical and certified adversarial robustness on one hand and domain generalization on another. To do so, we train robust models on multiple domains and evaluate their accuracy and robustness on an unseen domain. We observe that: (1) both empirical and certified robustness generalize to unseen domains, and (2) the level of generalizability does not correlate well with input visual similarity, measured by the FID between source and target domains. We also extend our study to cover a real-world medical application, in which adversarial augmentation significantly boosts the generalization of robustness with minimal effect on clean data accuracy.
Despite the great development of document summarization techniques nowadays, factual inconsistencies between the generated summaries and the original text still occur from time to time. This paper proposes a prefix-tuning-based approach that uses a set of trainable continuous prefix prompt together with discrete prompts to aid model generation, which makes a significant impact on both CNN/Daily Mail and XSum summaries generated using GPT-2. The improvements on fact preservation in the generated summaries indicates the effectiveness of adopting this prefix-tuning-based method in knowledge-enhanced document summarization, and also shows a great potential on other natural language processing tasks.
Most classification models treat all misclassifications equally. However, different classes may be related, and these hierarchical relationships must be considered in some classification problems. These problems can be addressed by using hierarchical information during training. Unfortunately, this information is not available for all datasets. Many classification-based metric learning methods use class representatives in embedding space to represent different classes. The relationships among the learned class representatives can then be used to estimate class hierarchical structures. If we have a predefined class hierarchy, the learned class representatives can be assessed to determine whether the metric learning model learned semantic distances that match our prior knowledge. In this work, we train a softmax classifier and three metric learning models with several training options on benchmark and real-world datasets. In addition to the standard classification accuracy, we evaluate the hierarchical inference performance by inspecting learned class representatives and the hierarchy-informed performance, i.e., the classification performance, and the metric learning performance by considering predefined hierarchical structures. Furthermore, we investigate how the considered measures are affected by various models and training options. When our proposed ProxyDR model is trained without using predefined hierarchical structures, the hierarchical inference performance is significantly better than that of the popular NormFace model. Additionally, our model enhances some hierarchy-informed performance measures under the same training options. We also found that convolutional neural networks (CNNs) with random weights correspond to the predefined hierarchies better than random chance.
Diffusion models are a class of deep generative models that have shown impressive results on various tasks with dense theoretical founding. Although diffusion models have achieved impressive quality and diversity of sample synthesis than other state-of-the-art models, they still suffer from costly sampling procedure and sub-optimal likelihood estimation. Recent studies have shown great enthusiasm on improving the performance of diffusion model. In this article, we present a first comprehensive review of existing variants of the diffusion models. Specifically, we provide a first taxonomy of diffusion models and categorize them variants to three types, namely sampling-acceleration enhancement, likelihood-maximization enhancement and data-generalization enhancement. We also introduce in detail other five generative models (i.e., variational autoencoders, generative adversarial networks, normalizing flow, autoregressive models, and energy-based models), and clarify the connections between diffusion models and these generative models. Then we make a thorough investigation into the applications of diffusion models, including computer vision, natural language processing, waveform signal processing, multi-modal modeling, molecular graph generation, time series modeling, and adversarial purification. Furthermore, we propose new perspectives pertaining to the development of this generative model.
Recent years have witnessed the resurgence of knowledge engineering which is featured by the fast growth of knowledge graphs. However, most of existing knowledge graphs are represented with pure symbols, which hurts the machine's capability to understand the real world. The multi-modalization of knowledge graphs is an inevitable key step towards the realization of human-level machine intelligence. The results of this endeavor are Multi-modal Knowledge Graphs (MMKGs). In this survey on MMKGs constructed by texts and images, we first give definitions of MMKGs, followed with the preliminaries on multi-modal tasks and techniques. We then systematically review the challenges, progresses and opportunities on the construction and application of MMKGs respectively, with detailed analyses of the strength and weakness of different solutions. We finalize this survey with open research problems relevant to MMKGs.
Deep learning models on graphs have achieved remarkable performance in various graph analysis tasks, e.g., node classification, link prediction and graph clustering. However, they expose uncertainty and unreliability against the well-designed inputs, i.e., adversarial examples. Accordingly, various studies have emerged for both attack and defense addressed in different graph analysis tasks, leading to the arms race in graph adversarial learning. For instance, the attacker has poisoning and evasion attack, and the defense group correspondingly has preprocessing- and adversarial- based methods. Despite the booming works, there still lacks a unified problem definition and a comprehensive review. To bridge this gap, we investigate and summarize the existing works on graph adversarial learning tasks systemically. Specifically, we survey and unify the existing works w.r.t. attack and defense in graph analysis tasks, and give proper definitions and taxonomies at the same time. Besides, we emphasize the importance of related evaluation metrics, and investigate and summarize them comprehensively. Hopefully, our works can serve as a reference for the relevant researchers, thus providing assistance for their studies. More details of our works are available at //github.com/gitgiter/Graph-Adversarial-Learning.
Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require that a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with an arbitrary depth. Although the primitive graph neural networks have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on graph convolutional network (GCN) and gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research.
Text Classification is an important and classical problem in natural language processing. There have been a number of studies that applied convolutional neural networks (convolution on regular grid, e.g., sequence) to classification. However, only a limited number of studies have explored the more flexible graph convolutional neural networks (e.g., convolution on non-grid, e.g., arbitrary graph) for the task. In this work, we propose to use graph convolutional networks for text classification. We build a single text graph for a corpus based on word co-occurrence and document word relations, then learn a Text Graph Convolutional Network (Text GCN) for the corpus. Our Text GCN is initialized with one-hot representation for word and document, it then jointly learns the embeddings for both words and documents, as supervised by the known class labels for documents. Our experimental results on multiple benchmark datasets demonstrate that a vanilla Text GCN without any external word embeddings or knowledge outperforms state-of-the-art methods for text classification. On the other hand, Text GCN also learns predictive word and document embeddings. In addition, experimental results show that the improvement of Text GCN over state-of-the-art comparison methods become more prominent as we lower the percentage of training data, suggesting the robustness of Text GCN to less training data in text classification.
A variety of deep neural networks have been applied in medical image segmentation and achieve good performance. Unlike natural images, medical images of the same imaging modality are characterized by the same pattern, which indicates that same normal organs or tissues locate at similar positions in the images. Thus, in this paper we try to incorporate the prior knowledge of medical images into the structure of neural networks such that the prior knowledge can be utilized for accurate segmentation. Based on this idea, we propose a novel deep network called knowledge-based fully convolutional network (KFCN) for medical image segmentation. The segmentation function and corresponding error is analyzed. We show the existence of an asymptotically stable region for KFCN which traditional FCN doesn't possess. Experiments validate our knowledge assumption about the incorporation of prior knowledge into the convolution kernels of KFCN and show that KFCN can achieve a reasonable segmentation and a satisfactory accuracy.