Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has been sampled in nature, it accounts for a tiny fraction of the possible protein universe. If we could tap into this pool of unexplored protein structures, we could search for novel proteins with useful properties that we could apply to tackle the environmental and medical challenges facing humanity. This is the purpose of protein design. Sequence design is an important aspect of protein design, and many successful methods to do this have been developed. Recently, deep-learning methods that frame it as a classification problem have emerged as a powerful approach. Beyond their reported improvement in performance, their primary advantage over physics-based methods is that the computational burden is shifted from the user to the developers, thereby increasing accessibility to the design method. Despite this trend, the tools for assessment and comparison of such models remain quite generic. The goal of this paper is to both address the timely problem of evaluation and to shine a spotlight, within the Machine Learning community, on specific assessment criteria that will accelerate impact. We present a carefully curated benchmark set of proteins and propose a number of standard tests to assess the performance of deep learning based methods. Our robust benchmark provides biological insight into the behaviour of design methods, which is essential for evaluating their performance and utility. We compare five existing models with two novel models for sequence prediction. Finally, we test the designs produced by these models with AlphaFold2, a state-of-the-art structure-prediction algorithm, to determine if they are likely to fold into the intended 3D shapes.
相關內容
Hidden Markov models (HMMs) and their extensions have proven to be powerful tools for classification of observations that stem from systems with temporal dependence as they take into account that observations close in time are likely generated from the same state (i.e.\ class). When information on the classes of the observations is available in advanced, supervised methods can be applied. In this paper, we provide details for the implementation of four models for classification in a supervised learning context: HMMs, hidden semi-Markov models (HSMMs), autoregressive-HMMs, and autoregressive-HSMMs. Using simulations, we study the classification performance under various degrees of model misspecification to characterize when it would be important to extend a basic HMM to an HSMM. As an application of these techniques we use the models to classify accelerometer data from Merino sheep to distinguish between four different behaviors of interest. In particular in the field of movement ecology, collection of fine-scale animal movement data over time to identify behavioral states has become ubiquitous, necessitating models that can account for the dependence structure in the data. We demonstrate that when the aim is to conduct classification, various degrees of model misspecification of the proposed model may not impede good classification performance unless there is high overlap between the state-dependent distributions, that is, unless the observation distributions of the different states are difficult to differentiate.
Exabytes of data are generated daily by humans, leading to the growing need for new efforts in dealing with the grand challenges for multi-label learning brought by big data. For example, extreme multi-label classification is an active and rapidly growing research area that deals with classification tasks with an extremely large number of classes or labels; utilizing massive data with limited supervision to build a multi-label classification model becomes valuable for practical applications, etc. Besides these, there are tremendous efforts on how to harvest the strong learning capability of deep learning to better capture the label dependencies in multi-label learning, which is the key for deep learning to address real-world classification tasks. However, it is noted that there has been a lack of systemic studies that focus explicitly on analyzing the emerging trends and new challenges of multi-label learning in the era of big data. It is imperative to call for a comprehensive survey to fulfill this mission and delineate future research directions and new applications.
Heterogeneous tabular data are the most commonly used form of data and are essential for numerous critical and computationally demanding applications. On homogeneous data sets, deep neural networks have repeatedly shown excellent performance and have therefore been widely adopted. However, their application to modeling tabular data (inference or generation) remains highly challenging. This work provides an overview of state-of-the-art deep learning methods for tabular data. We start by categorizing them into three groups: data transformations, specialized architectures, and regularization models. We then provide a comprehensive overview of the main approaches in each group. A discussion of deep learning approaches for generating tabular data is complemented by strategies for explaining deep models on tabular data. Our primary contribution is to address the main research streams and existing methodologies in this area, while highlighting relevant challenges and open research questions. To the best of our knowledge, this is the first in-depth look at deep learning approaches for tabular data. This work can serve as a valuable starting point and guide for researchers and practitioners interested in deep learning with tabular data.
In the last decade or so, we have witnessed deep learning reinvigorating the machine learning field. It has solved many problems in the domains of computer vision, speech recognition, natural language processing, and various other tasks with state-of-the-art performance. The data is generally represented in the Euclidean space in these domains. Various other domains conform to non-Euclidean space, for which graph is an ideal representation. Graphs are suitable for representing the dependencies and interrelationships between various entities. Traditionally, handcrafted features for graphs are incapable of providing the necessary inference for various tasks from this complex data representation. Recently, there is an emergence of employing various advances in deep learning to graph data-based tasks. This article provides a comprehensive survey of graph neural networks (GNNs) in each learning setting: supervised, unsupervised, semi-supervised, and self-supervised learning. Taxonomy of each graph based learning setting is provided with logical divisions of methods falling in the given learning setting. The approaches for each learning task are analyzed from both theoretical as well as empirical standpoints. Further, we provide general architecture guidelines for building GNNs. Various applications and benchmark datasets are also provided, along with open challenges still plaguing the general applicability of GNNs.
This paper studies the single image super-resolution problem using adder neural networks (AdderNet). Compared with convolutional neural networks, AdderNet utilizing additions to calculate the output features thus avoid massive energy consumptions of conventional multiplications. However, it is very hard to directly inherit the existing success of AdderNet on large-scale image classification to the image super-resolution task due to the different calculation paradigm. Specifically, the adder operation cannot easily learn the identity mapping, which is essential for image processing tasks. In addition, the functionality of high-pass filters cannot be ensured by AdderNet. To this end, we thoroughly analyze the relationship between an adder operation and the identity mapping and insert shortcuts to enhance the performance of SR models using adder networks. Then, we develop a learnable power activation for adjusting the feature distribution and refining details. Experiments conducted on several benchmark models and datasets demonstrate that, our image super-resolution models using AdderNet can achieve comparable performance and visual quality to that of their CNN baselines with an about 2$\times$ reduction on the energy consumption.
Point cloud is point sets defined in 3D metric space. Point cloud has become one of the most significant data format for 3D representation. Its gaining increased popularity as a result of increased availability of acquisition devices, such as LiDAR, as well as increased application in areas such as robotics, autonomous driving, augmented and virtual reality. Deep learning is now the most powerful tool for data processing in computer vision, becoming the most preferred technique for tasks such as classification, segmentation, and detection. While deep learning techniques are mainly applied to data with a structured grid, point cloud, on the other hand, is unstructured. The unstructuredness of point clouds makes use of deep learning for its processing directly very challenging. Earlier approaches overcome this challenge by preprocessing the point cloud into a structured grid format at the cost of increased computational cost or lost of depth information. Recently, however, many state-of-the-arts deep learning techniques that directly operate on point cloud are being developed. This paper contains a survey of the recent state-of-the-art deep learning techniques that mainly focused on point cloud data. We first briefly discussed the major challenges faced when using deep learning directly on point cloud, we also briefly discussed earlier approaches which overcome the challenges by preprocessing the point cloud into a structured grid. We then give the review of the various state-of-the-art deep learning approaches that directly process point cloud in its unstructured form. We introduced the popular 3D point cloud benchmark datasets. And we also further discussed the application of deep learning in popular 3D vision tasks including classification, segmentation and detection.
We study the impact of neural networks in text classification. Our focus is on training deep neural networks with proper weight initialization and greedy layer-wise pretraining. Results are compared with 1-layer neural networks and Support Vector Machines. We work with a dataset of labeled messages from the Twitter microblogging service and aim to predict weather conditions. A feature extraction procedure specific for the task is proposed, which applies dimensionality reduction using Latent Semantic Analysis. Our results show that neural networks outperform Support Vector Machines with Gaussian kernels, noticing performance gains from introducing additional hidden layers with nonlinearities. The impact of using Nesterov's Accelerated Gradient in backpropagation is also studied. We conclude that deep neural networks are a reasonable approach for text classification and propose further ideas to improve performance.
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 learns 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 arbitrary depth. Although the primitive GNNs 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.
Machine-learning models have demonstrated great success in learning complex patterns that enable them to make predictions about unobserved data. In addition to using models for prediction, the ability to interpret what a model has learned is receiving an increasing amount of attention. However, this increased focus has led to considerable confusion about the notion of interpretability. In particular, it is unclear how the wide array of proposed interpretation methods are related, and what common concepts can be used to evaluate them. We aim to address these concerns by defining interpretability in the context of machine learning and introducing the Predictive, Descriptive, Relevant (PDR) framework for discussing interpretations. The PDR framework provides three overarching desiderata for evaluation: predictive accuracy, descriptive accuracy and relevancy, with relevancy judged relative to a human audience. Moreover, to help manage the deluge of interpretation methods, we introduce a categorization of existing techniques into model-based and post-hoc categories, with sub-groups including sparsity, modularity and simulatability. To demonstrate how practitioners can use the PDR framework to evaluate and understand interpretations, we provide numerous real-world examples. These examples highlight the often under-appreciated role played by human audiences in discussions of interpretability. Finally, based on our framework, we discuss limitations of existing methods and directions for future work. We hope that this work will provide a common vocabulary that will make it easier for both practitioners and researchers to discuss and choose from the full range of interpretation methods.
The field of natural language processing has seen impressive progress in recent years, with neural network models replacing many of the traditional systems. A plethora of new models have been proposed, many of which are thought to be opaque compared to their feature-rich counterparts. This has led researchers to analyze, interpret, and evaluate neural networks in novel and more fine-grained ways. In this survey paper, we review analysis methods in neural language processing, categorize them according to prominent research trends, highlight existing limitations, and point to potential directions for future work.
小貼士
登錄享
相關主題
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191