Alireza Moradzadeh

Peter St. John, Dejun Lin, Polina Binder et al.

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language models (pLM) training on hundreds of graphical processing units (GPUs). We introduce the BioNeMo Framework to facilitate the training of computational biology and chemistry AI models across hundreds of GPUs. Its modular design allows the integration of individual components, such as data loaders, into existing workflows and is open to community contributions. We detail technical features of the BioNeMo Framework through use cases such as pLM pre-training and fine-tuning. On 256 NVIDIA A100s, BioNeMo Framework trains a three billion parameter BERT-based pLM on over one trillion tokens in 4.2 days. The BioNeMo Framework is open-source and free for everyone to use.

Alireza Moradzadeh, Srimukh Prasad Veccham, Lukasz Wawrzyniak et al.

Kolmogorov-Arnold Networks (KANs) have recently emerged as a powerful alternative to traditional multilayer perceptrons. However, their reliance on predefined, bounded grids restricts their ability to approximate functions on unbounded domains. To address this, we present Unbounded Kolmogorov-Arnold Networks (UKANs), a method that removes the need for bounded grids in traditional Kolmogorov-Arnold Networks (KANs). The key innovation of this method is a coefficient-generator (CG) model that produces, on the fly, only the B-spline coefficients required locally on an unbounded symmetric grid. UKANs couple multilayer perceptrons with KANs by feeding the positional encoding of grid groups into the CG model, enabling function approximation on unbounded domains without requiring data normalization. To reduce the computational cost of both UKANs and KANs, we introduce a GPU-accelerated library that lowers B-spline evaluation complexity by a factor proportional to the grid size, enabling large-scale learning by leveraging efficient memory management, in line with recent software advances such as FlashAttention and FlashFFTConv. Performance benchmarking confirms the superior memory and computational efficiency of our accelerated KAN (warpKAN), and UKANs, showing a 3-30x speed-up and up to 1000x memory reduction compared to vanilla KANs. Experiments on regression, classification, and generative tasks demonstrate the effectiveness of UKANs to match or surpass KAN accuracy. Finally, we use both accelerated KAN and UKAN in a molecular property prediction task, establishing the feasibility of large-scale end-to-end training with our optimized implementation.