arXiv subjects

Oscar Chang

Publications and source records attributed to Oscar Chang.

21 records · Page 2Linked to original sources

arXiv2018

PepCVAE: Semi-Supervised Targeted Design of Antimicrobial Peptide Sequences

Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model learns a rich latent space of the biological peptide context by taking advantage of abundant, unlabeled peptide sequences. The model further learns a disentangled antimicrobial attribute space by using the feedback from a jointly trained AMP classifier that uses limited labeled instances. The disentangled representation allows for controllable generation of AMPs. Extensive analysis of the PepCVAE-generated sequences reveals superior performance of our model in comparison to a plain VAE, as PepCVAE generates novel AMP sequences with higher long-range diversity, while being closer to the training distribution of biological peptides. These features are highly desired in next-generation antimicrobial design.

q-bio.QM↗

arXiv2018

Neural Network Quine

Self-replication is a key aspect of biological life that has been largely overlooked in Artificial Intelligence systems. Here we describe how to build and train self-replicating neural networks. The network replicates itself by learning to output its own weights. The network is designed using a loss function that can be optimized with either gradient-based or non-gradient-based methods. We also describe a method we call regeneration to train the network without explicit optimization, by injecting the network with predictions of its own parameters. The best solution for a self-replicating network was found by alternating between regeneration and optimization steps. Finally, we describe a design for a self-replicating neural network that can solve an auxiliary task such as MNIST image classification. We observe that there is a trade-off between the network's ability to classify images and its ability to replicate, but training is biased towards increasing its specialization at image classification at the expense of replication. This is analogous to the trade-off between reproduction and other tasks observed in nature. We suggest that a self-replication mechanism for artificial intelligence is useful because it introduces the possibility of continual improvement through natural selection.

cs.AI↗

arXiv2018

Gradient Normalization & Depth Based Decay For Deep Learning

In this paper we introduce a novel method of gradient normalization and decay with respect to depth. Our method leverages the simple concept of normalizing all gradients in a deep neural network, and then decaying said gradients with respect to their depth in the network. Our proposed normalization and decay techniques can be used in conjunction with most current state of the art optimizers and are a very simple addition to any network. This method, although simple, showed improvements in convergence time on state of the art networks such as DenseNet and ResNet on image classification tasks, as well as on an LSTM for natural language processing tasks.

cs.LG↗