Cryo-electron microscopy (cryo-EM) has become a major experimental technology to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize. Although cryo-EM has been drastically improved to generate high-resolution three-dimensional (3D) maps that contain detailed structural information about macromolecules, the computational methods for using the data to automatically build structure models are lagging far behind. Traditional cryo-EM model building approach is template-based homology modeling. Manual de novo modeling is very time-consuming when no template model could be found in the database. In recent years, de novo cryo-EM modeling using machine learning (ML) and deep learning (DL) has ranked among the top-performing methods in macromolecular structure modeling. Deep-learning-based de novo cryo-EM modeling is an important application of artificial intelligence, with impressive results and great potential for the next generation of molecular biomedicine. Accordingly, we systematically review the representative ML/DL-based de novo cryo-EM modeling methods. And their significances are discussed from both practical and methodological viewpoints. We also briefly describe the background of cryo-EM data processing workflow. Overall, this review provides an introductory guide to modern research on artificial intelligence (AI) for de novo molecular structure modeling and future directions in this emerging field.

This paper introduces a new metamodel-based knowledge representation that significantly improves autonomous learning and adaptation. While interest in hybrid machine learning / symbolic AI systems leveraging, for example, reasoning and knowledge graphs, is gaining popularity, we find there remains a need for both a clear definition of knowledge and a metamodel to guide the creation and manipulation of knowledge. Some of the benefits of the metamodel we introduce in this paper include a solution to the symbol grounding problem, cumulative learning, and federated learning. We have applied the metamodel to problems ranging from time series analysis, computer vision, and natural language understanding and have found that the metamodel enables a wide variety of learning mechanisms ranging from machine learning, to graph network analysis and learning by reasoning engines to interoperate in a highly synergistic way. Our metamodel-based projects have consistently exhibited unprecedented accuracy, performance, and ability to generalize. This paper is inspired by the state-of-the-art approaches to AGI, recent AGI-aspiring work, the granular computing community, as well as Alfred Korzybski's general semantics. One surprising consequence of the metamodel is that it not only enables a new level of autonomous learning and optimal functioning for machine intelligences, but may also shed light on a path to better understanding how to improve human cognition.

In recent years, there has been an ever increasing amount of multivariate time series (MTS) data in various domains, typically generated by a large family of sensors such as wearable devices. This has led to the development of novel learning methods on MTS data, with deep learning models dominating the most recent advancements. Prior literature has primarily focused on designing new network architectures for modeling temporal dependencies within MTS. However, a less studied challenge is associated with high dimensionality of MTS data. In this paper, we propose a novel neural component, namely Neural Feature Se-lector (NFS), as an end-2-end solution for feature selection in MTS data. Specifically, NFS is based on decomposed convolution design and includes two modules: firstly each feature stream within MTS is processed by a temporal CNN independently; then an aggregating CNN combines the processed streams to produce input for other downstream networks. We evaluated the proposed NFS model on four real-world MTS datasets and found that it achieves comparable results with state-of-the-art methods while providing the benefit of feature selection. Our paper also highlights the robustness and effectiveness of feature selection with NFS compared to using recent autoencoder-based methods.

Neural networks (NNs) lack measures of "reliability" estimation that would enable reasoning over their predictions. Despite the vital importance, especially in areas of human well-being and health, state-of-the-art uncertainty estimation techniques are computationally expensive when applied to resource-constrained devices. We propose an efficient framework for predictive uncertainty estimation in NNs deployed on embedded edge systems with no need for fine-tuning or re-training strategies. To meet the energy and latency requirements of these embedded platforms the framework is built from the ground up to provide predictive uncertainty based only on one forward pass and a negligible amount of additional matrix multiplications with theoretically proven correctness. Our aim is to enable already trained deep learning models to generate uncertainty estimates on resource-limited devices at inference time focusing on classification tasks. This framework is founded on theoretical developments casting dropout training as approximate inference in Bayesian NNs. Our layerwise distribution approximation to the convolution layer cascades through the network, providing uncertainty estimates in one single run which ensures minimal overhead, especially compared with uncertainty techniques that require multiple forwards passes and an equal linear rise in energy and latency requirements making them unsuitable in practice. We demonstrate that it yields better performance and flexibility over previous work based on multilayer perceptrons to obtain uncertainty estimates. Our evaluation with mobile applications datasets shows that our approach not only obtains robust and accurate uncertainty estimations but also outperforms state-of-the-art methods in terms of systems performance, reducing energy consumption (up to 28x), keeping the memory overhead at a minimum while still improving accuracy (up to 16%).

This work aims at intensifying text-independent speaker identification performance in real application situations such as noisy and emotional talking conditions. This is achieved by incorporating two different modules: a Computational Auditory Scene Analysis CASA based pre-processing module for noise reduction and cascaded Gaussian Mixture Model Convolutional Neural Network GMM-CNN classifier for speaker identification followed by emotion recognition. This research proposes and evaluates a novel algorithm to improve the accuracy of speaker identification in emotional and highly-noise susceptible conditions. Experiments demonstrate that the proposed model yields promising results in comparison with other classifiers when Speech Under Simulated and Actual Stress SUSAS database, Emirati Speech Database ESD, the Ryerson Audio-Visual Database of Emotional Speech and Song RAVDESS database and the Fluent Speech Commands database are used in a noisy environment.

This paper introduces a new deep learning approach to approximately solve the Covering Salesman Problem (CSP). In this approach, given the city locations of a CSP as input, a deep neural network model is designed to directly output the solution. It is trained using the deep reinforcement learning without supervision. Specifically, in the model, we apply the Multi-head Attention to capture the structural patterns, and design a dynamic embedding to handle the dynamic patterns of the problem. Once the model is trained, it can generalize to various types of CSP tasks (different sizes and topologies) with no need of re-training. Through controlled experiments, the proposed approach shows desirable time complexity: it runs more than 20 times faster than the traditional heuristic solvers with a tiny gap of optimality. Moreover, it significantly outperforms the current state-of-the-art deep learning approaches for combinatorial optimization in the aspect of both training and inference. In comparison with traditional solvers, this approach is highly desirable for most of the challenging tasks in practice that are usually large-scale and require quick decisions.

Current deep learning (DL) systems rely on a centralized computing paradigm which limits the amount of available training data, increases system latency, and adds privacy and security constraints. On-device learning, enabled by decentralized and distributed training of DL models over peer-to-peer wirelessly connected edge devices, not only alleviate the above limitations but also enable next-gen applications that need DL models to continuously interact and learn from their environment. However, this necessitates the development of novel training algorithms that train DL models over time-varying and directed peer-to-peer graph structures while minimizing the amount of communication between the devices and also being resilient to non-IID data distributions. In this work we propose, Sparse-Push, a communication efficient decentralized distributed training algorithm that supports training over peer-to-peer, directed, and time-varying graph topologies. The proposed algorithm enables 466x reduction in communication with only 1% degradation in performance when training various DL models such as ResNet-20 and VGG11 over the CIFAR-10 dataset. Further, we demonstrate how communication compression can lead to significant performance degradation in-case of non-IID datasets, and propose Skew-Compensated Sparse Push algorithm that recovers this performance drop while maintaining similar levels of communication compression.

Platforms that support online commentary, from social networks to news sites, are increasingly leveraging machine learning to assist their moderation efforts. But this process does not typically provide feedback to the author that would help them contribute according to the community guidelines. This is prohibitively time-consuming for human moderators to do, and computational approaches are still nascent. This work focuses on models that can help suggest rephrasings of toxic comments in a more civil manner. Inspired by recent progress in unpaired sequence-to-sequence tasks, a self-supervised learning model is introduced, called CAE-T5. CAE-T5 employs a pre-trained text-to-text transformer, which is fine tuned with a denoising and cyclic auto-encoder loss. Experimenting with the largest toxicity detection dataset to date (Civil Comments) our model generates sentences that are more fluent and better at preserving the initial content compared to earlier text style transfer systems which we compare with using several scoring systems and human evaluation.

Estimation of spatially-varying parameters for computationally expensive forward models governed by partial differential equations is addressed. A novel multiscale Bayesian inference approach is introduced based on deep probabilistic generative models. Such generative models provide a flexible representation by inferring on each scale a low-dimensional latent encoding while allowing hierarchical parameter generation from coarse- to fine-scales. Combining the multiscale generative model with Markov Chain Monte Carlo (MCMC), inference across scales is achieved enabling us to efficiently obtain posterior parameter samples at various scales. The estimation of coarse-scale parameters using a low-dimensional latent embedding captures global and notable parameter features using an inexpensive but inaccurate solver. MCMC sampling of the fine-scale parameters is enabled by utilizing the posterior information in the immediate coarser-scale. In this way, the global features are identified in the coarse-scale with inference of low-dimensional variables and inexpensive forward computation, and the local features are refined and corrected in the fine-scale. The developed method is demonstrated with two types of permeability estimation for flow in heterogeneous media. One is a Gaussian random field (GRF) with uncertain length scales, and the other is channelized permeability with the two regions defined by different GRFs. The obtained results indicate that the method allows high-dimensional parameter estimation while exhibiting stability, efficiency and accuracy.

Prior work has focused on evaluating the ability of neural networks to reason about novel combinations from known components, an intrinsic property of human cognition. In this work, we aim to study systematic generalization in predicting future state trajectories of a dynamical system, conditioned on past states' trajectory (dependent variables), past and future actions (control variables). In our context, systematic generalization implies that a good model should perform well on all new combinations of future actions after being trained on all of them, but only on a limited set of their combinations. For models to generalize out-of-distribution to unseen action combinations, they should reason about the states and their dependency relation with the applied actions. We conduct a rigorous study of useful inductive biases that learn to predict the trajectories up to large horizons well, and capture true dependency relations between the states and the controls through our synthetic setup, and simulated data from electric motors.