Nojun Park | Searcharxiv

arXiv2022

Homotopy-based training of NeuralODEs for accurate dynamics discovery

Neural Ordinary Differential Equations (NeuralODEs) present an attractive way to extract dynamical laws from time series data, as they bridge neural networks with the differential equation-based modeling paradigm of the physical sciences. However, these models often display long training times and suboptimal results, especially for longer duration data. While a common strategy in the literature imposes strong constraints to the NeuralODE architecture to inherently promote stable model dynamics, such methods are ill-suited for dynamics discovery as the unknown governing equation is not guaranteed to satisfy the assumed constraints. In this paper, we develop a new training method for NeuralODEs, based on synchronization and homotopy optimization, that does not require changes to the model architecture. We show that synchronizing the model dynamics and the training data tames the originally irregular loss landscape, which homotopy optimization can then leverage to enhance training. Through benchmark experiments, we demonstrate our method achieves competitive or better training loss while often requiring less than half the number of training epochs compared to other model-agnostic techniques. Furthermore, models trained with our method display better extrapolation capabilities, highlighting the effectiveness of our method.

cs.LG↗

arXiv2020

Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction

The characterization of drug-protein interactions is crucial in the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without trial-and-error by humans. However, because data labeling requires significant resources, the available protein data size is relatively small, which consequently decreases model performance. Here we propose two methods to construct a deep learning framework that exhibits superior performance with a small labeled dataset. At first, we use transfer learning in encoding protein sequences with a pretrained model, which trains general sequence representations in an unsupervised manner. Second, we use a Bayesian neural network to make a robust model by estimating the data uncertainty. As a result, our model performs better than the previous baselines for predicting drug-protein interactions. We also show that the quantified uncertainty from the Bayesian inference is related to the confidence and can be used for screening DPI data points.

cs.LG↗