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Protein structure prediction has been a grand challenge for over 50 years, owing to its broad scientific and application interests. There are two primary types of modeling algorithms, template-free modeling and template-based modeling. The latter one is suitable for easy prediction tasks and is widely adopted in computer-aided drug discoveries for drug design and screening. Although it has been several decades since its first edition, the current template-based modeling approach suffers from two critical problems: 1) there are many missing regions in the template-query sequence alignment, and 2) the accuracy of the distance pairs from different regions of the template varies, and this information is not well introduced into the modeling. To solve these two problems, we propose a structural optimization process based on template modeling, introducing two neural network models to predict the distance information of the missing regions and the accuracy of the distance pairs of different regions in the template modeling structure. The predicted distances and residue pairwise-specific deviations are incorporated into the potential energy function for structural optimization, which significantly improves the qualities of the original template modeling decoys.
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Ultrasound elasticity images which enable the visualization of quantitative maps of tissue stiffness can be reconstructed by solving an inverse problem. Classical model-based approaches for ultrasound elastography use deterministic finite element methods (FEMs) to incorporate the governing physical laws resulting in poor performance in noisy conditions. Moreover, these approaches utilize fixed regularizers for various tissue patterns while appropriate data-adaptive priors might be required for capturing the complex spatial elasticity distribution. In this regard, we propose a joint model-based and learning-based framework for estimating the elasticity distribution by solving a regularized optimization problem. We present an integrated objective function composed of a statistical physics-based forward model and a data-driven regularizer to leverage deep neural networks for learning the underlying elasticity prior. This constrained optimization problem is solved using the gradient descent (GD) method and the gradient of regularizer is simply replaced by the residual of the trained denoiser network for having an explicit objective function with reduced computation time.
We refine the OrbNet model to accurately predict energy, forces, and other response properties for molecules using a graph neural-network architecture based on features from low-cost approximated quantum operators in the symmetry-adapted atomic orbital basis. The model is end-to-end differentiable due to the derivation of analytic gradients for all electronic structure terms, and is shown to be transferable across chemical space due to the use of domain-specific features. The learning efficiency is improved by incorporating physically motivated constraints on the electronic structure through multi-task learning. The model outperforms existing methods on energy prediction tasks for the QM9 dataset and for molecular geometry optimizations on conformer datasets, at a computational cost that is thousand-fold or more reduced compared to conventional quantum-chemistry calculations (such as density functional theory) that offer similar accuracy.
In this paper, we are interested in building a domain knowledge based deep learning framework to solve the chiller plants energy optimization problems. Compared to the hotspot applications of deep learning (e.g. image classification and NLP), it is difficult to collect enormous data for deep network training in real-world physical systems. Most existing methods reduce the complex systems into linear model to facilitate the training on small samples. To tackle the small sample size problem, this paper considers domain knowledge in the structure and loss design of deep network to build a nonlinear model with lower redundancy function space. Specifically, the energy consumption estimation of most chillers can be physically viewed as an input-output monotonic problem. Thus, we can design a Neural Network with monotonic constraints to mimic the physical behavior of the system. We verify the proposed method in a cooling system of a data center, experimental results show the superiority of our framework in energy optimization compared to the existing ones.
Recently, click-through rate (CTR) prediction models have evolved from shallow methods to deep neural networks. Most deep CTR models follow an Embedding&MLP paradigm, that is, first mapping discrete id features, e.g. user visited items, into low dimensional vectors with an embedding module, then learn a multi-layer perception (MLP) to fit the target. In this way, embedding module performs as the representative learning and plays a key role in the model performance. However, in many real-world applications, deep CTR model often suffers from poor generalization performance, which is mostly due to the learning of embedding parameters. In this paper, we model user behavior using an interest delay model, study carefully the embedding mechanism, and obtain two important results: (i) We theoretically prove that small aggregation radius of embedding vectors of items which belongs to a same user interest domain will result in good generalization performance of deep CTR model. (ii) Following our theoretical analysis, we design a new embedding structure named res-embedding. In res-embedding module, embedding vector of each item is the sum of two components: (i) a central embedding vector calculated from an item-based interest graph (ii) a residual embedding vector with its scale to be relatively small. Empirical evaluation on several public datasets demonstrates the effectiveness of the proposed res-embedding structure, which brings significant improvement on the model performance.
Approaches based on refinement operators have been successfully applied to class expression learning on RDF knowledge graphs. These approaches often need to explore a large number of concepts to find adequate hypotheses. This need arguably stems from current approaches relying on myopic heuristic functions to guide their search through an infinite concept space. In turn, deep reinforcement learning provides effective means to address myopia by estimating how much discounted cumulated future reward states promise. In this work, we leverage deep reinforcement learning to accelerate the learning of concepts in $mathcal{ALC}$ by proposing DRILL -- a novel class expression learning approach that uses a convolutional deep Q-learning model to steer its search. By virtue of its architecture, DRILL is able to compute the expected discounted cumulated future reward of more than $10^3$ class expressions in a second on standard hardware. We evaluate DRILL on four benchmark datasets against state-of-the-art approaches. Our results suggest that DRILL converges to goal states at least 2.7$times$ faster than state-of-the-art models on all benchmark datasets. We provide an open-source implementation of our approach, including training and evaluation scripts as well as pre-trained models.
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