BERTology of Molecular Property Prediction

Chemical language models (CLMs) have emerged as promising competitors to popular classical machine learning models for molecular property prediction (MPP) tasks. However, an increasing number of studies have reported inconsistent and contradictory results for the performance of CLMs across various MPP benchmark tasks. In this study, we conduct and analyze hundreds of meticulously controlled experiments to systematically investigate the effects of various factors, such as dataset size, model size, and standardization, on the pre-training and fine-tuning performance of CLMs for MPP. In the absence of well-established scaling laws for encoder-only masked language models, our aim is to provide comprehensive numerical evidence and a deeper understanding of the underlying mechanisms affecting the performance of CLMs for MPP tasks, some of which appear to be entirely overlooked in the literature.

Unification of popular artificial neural network activation functions

We present a unified representation of the most popular neural network activation functions. Adopting Mittag-Leffler functions of fractional calculus, we propose a flexible and compact functional form that is able to interpolate between various activation functions and mitigate common problems in training neural networks such as vanishing and exploding gradients. The presented gated representation extends the scope of fixed-shape activation functions to their adaptive counterparts whose shape can be learnt from the training data. The derivatives of the proposed functional form can also be expressed in terms of Mittag-Leffler functions making it a suitable candidate for gradient-based backpropagation algorithms. By training LeNet-5 neural network on MNIST and CIFAR-10 datasets, we demonstrate that adopting a unified gated representation of activation functions offers a promising and affordable alternative to individual built-in implementations of activation functions in conventional machine learning frameworks.