arXiv subjects

Bowen Jing

Publications and source records attributed to Bowen Jing.

40 records · Page 3Linked to original sources

arXiv2020

Protein model quality assessment using rotation-equivariant, hierarchical neural networks

Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate structural model among a large pool of candidates, a task addressed in model quality assessment. Here, we present a novel deep learning approach to assess the quality of a protein model. Our network builds on a point-based representation of the atomic structure and rotation-equivariant convolutions at different levels of structural resolution. These combined aspects allow the network to learn end-to-end from entire protein structures. Our method achieves state-of-the-art results in scoring protein models submitted to recent rounds of CASP, a blind prediction community experiment. Particularly striking is that our method does not use physics-inspired energy terms and does not rely on the availability of additional information (beyond the atomic structure of the individual protein model), such as sequence alignments of multiple proteins.

q-bio.QM↗

arXiv2020

Rotation-Invariant Gait Identification with Quaternion Convolutional Neural Networks

A desireable property of accelerometric gait-based identification systems is robustness to new device orientations presented by users during testing but unseen during the training phase. However, traditional Convolutional neural networks (CNNs) used in these systems compensate poorly for such transformations. In this paper, we target this problem by introducing Quaternion CNN, a network architecture which is intrinsically layer-wise equivariant and globally invariant under 3D rotations of an array of input vectors. We show empirically that this network indeed significantly outperforms a traditional CNN in a multi-user rotation-invariant gait classification setting .Lastly, we demonstrate how the kernels learned by this QCNN can also be visualized as basis-independent but origin- and chirality-dependent trajectory fragments in the euclidean space, thus yielding a novel mode of feature visualization and extraction.

cs.CV↗

arXiv2019

SGVAE: Sequential Graph Variational Autoencoder

Generative models of graphs are well-known, but many existing models are limited in scalability and expressivity. We present a novel sequential graphical variational autoencoder operating directly on graphical representations of data. In our model, the encoding and decoding of a graph as is framed as a sequential deconstruction and construction process, respectively, enabling the the learning of a latent space. Experiments on a cycle dataset show promise, but highlight the need for a relaxation of the distribution over node permutations.

cs.LG↗

arXiv2019

Modeling Sensorimotor Coordination as Multi-Agent Reinforcement Learning with Differentiable Communication

Multi-agent reinforcement learning has shown promise on a variety of cooperative tasks as a consequence of recent developments in differentiable inter-agent communication. However, most architectures are limited to pools of homogeneous agents, limiting their applicability. Here we propose a modular framework for learning complex tasks in which a traditional monolithic agent is framed as a collection of cooperating heterogeneous agents. We apply this approach to model sensorimotor coordination in the neocortex as a multi-agent reinforcement learning problem. Our results demonstrate proof-of-concept of the proposed architecture and open new avenues for learning complex tasks and for understanding functional localization in the brain and future intelligent systems.

cs.MA↗