Hot Topics #18 (Feb. 14, 2023)
DL for molecules, LLMs, Vision Transformers, and more.
Predicting reaction barriers of hydrogen atom transfer in proteins: Riedmiller et al.; Feb. 12, 2023
Abstract: Hydrogen atom transfer (HAT) reactions are important in many biological systems. As these reactions are hard to observe experimentally, it is of high interest to shed light on them using simulations. Here, we present a machine learning model based on graph neural networks for the prediction of activation energies of HAT reactions in proteins. It is trained on more than 17,000 energy barriers calculated using hybrid density functional theory. We built and evaluated the model in the context of HAT in collagen, but the same workflow can easily be applied to HAT reactions in other biological or synthetic polymers. We obtain for relevant reactions (small reaction distances) a model with good predictive power (R2 <0.9 and mean absolute error of <3 kcal/mol). As the inference speed is high, this model enables evaluations of many chemical situations in rapid succession. When combined with molecular dynamics in a kinetic Monte-Carlo scheme, the model paves the way toward reactive simulations.
CodeBERTScore: Evaluating Code Generation with Pretrained Models of Code: Zhou et al.; Feb. 10, 2023
Abstract: Since the rise of neural models of code that can generate long expressions and statements rather than a single next-token, one of the major problems has been reliably evaluating their generated output. In this paper, we propose CodeBERTScore: an automatic evaluation metric for code generation, which builds on BERTScore (Zhang et al., 2020). Instead of measuring exact token matching as BLEU, CodeBERTScore computes a soft similarity score between each token in the generated code and in the reference code, using the contextual encodings of large pretrained models. Further, instead of encoding only the generated tokens as in BERTScore, CodeBERTScore also encodes the programmatic context surrounding the generated code. We perform an extensive evaluation of CodeBERTScore across four programming languages. We find that CodeBERTScore achieves a higher correlation with human preference and with functional correctness than all existing metrics. That is, generated code that receives a higher score by CodeBERTScore is more likely to be preferred by humans, as well as to function correctly when executed. Finally, while CodeBERTScore can be used with a multilingual CodeBERT as its base model, we release five language-specific pretrained models to use with our publicly available code at this https URL . Our language-specific models have been downloaded more than 25,000 times from the Huggingface Hub.
SWARM Parallelism: Training Large Models Can Be Surprisingly Communication-Efficient: Ryabinim et al.; Jan. 27, 2023
Abstract: Many deep learning applications benefit from using large models with billions of parameters. Training these models is notoriously expensive due to the need for specialized HPC clusters. In this work, we consider alternative setups for training large models: using cheap "preemptible" instances or pooling existing resources from multiple regions. We analyze the performance of existing model-parallel algorithms in these conditions and find configurations where training larger models becomes less communication-intensive. Based on these findings, we propose SWARM parallelism, a model-parallel training algorithm designed for poorly connected, heterogeneous and unreliable devices. SWARM creates temporary randomized pipelines between nodes that are rebalanced in case of failure. We empirically validate our findings and compare SWARM parallelism with existing large-scale training approaches. Finally, we combine our insights with compression strategies to train a large Transformer language model with 1B shared parameters (approximately 13B before sharing) on preemptible T4 GPUs with less than 200Mb/s network.
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking: Corso et al.; Oct. 4, 2022
Abstract: Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime compared to traditional search-based methods but have yet to offer substantial improvements in accuracy. We instead frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses. To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Empirically, DiffDock obtains a 38% top-1 success rate (RMSD<2A) on PDBBind, significantly outperforming the previous state-of-the-art of traditional docking (23%) and deep learning (20%) methods. Moreover, while previous methods are not able to dock on computationally folded structures (maximum accuracy 10.4%), DiffDock maintains significantly higher precision (21.7%). Finally, DiffDock has fast inference times and provides confidence estimates with high selective accuracy.
Scaling Vision Transformers to 22 Billion Parameters: Dehghani et al.; Feb. 10, 2023
Abstract: The scaling of Transformers has driven breakthrough capabilities for language models. At present, the largest large language models (LLMs) contain upwards of 100B parameters. Vision Transformers (ViT) have introduced the same architecture to image and video modelling, but these have not yet been successfully scaled to nearly the same degree; the largest dense ViT contains 4B parameters (Chen et al., 2022). We present a recipe for highly efficient and stable training of a 22B-parameter ViT (ViT-22B) and perform a wide variety of experiments on the resulting model. When evaluated on downstream tasks (often with a lightweight linear model on frozen features), ViT-22B demonstrates increasing performance with scale. We further observe other interesting benefits of scale, including an improved tradeoff between fairness and performance, state-of-the-art alignment to human visual perception in terms of shape/texture bias, and improved robustness. ViT-22B demonstrates the potential for "LLM-like" scaling in vision, and provides key steps towards getting there.
Level Generation Through Large Language Models: Todd et al.; Feb. 11, 2023
Abstract: Large Language Models (LLMs) are powerful tools, capable of leveraging their training on natural language to write stories, generate code, and answer questions. But can they generate functional video game levels? Game levels, with their complex functional constraints and spatial relationships in more than one dimension, are very different from the kinds of data an LLM typically sees during training. Datasets of game levels are also hard to come by, potentially taxing the abilities of these data-hungry models. We investigate the use of LLMs to generate levels for the game Sokoban, finding that LLMs are indeed capable of doing so, and that their performance scales dramatically with dataset size. We also perform preliminary experiments on controlling LLM level generators and discuss promising areas for future work.
Token Merging: Your ViT But Faster: Bolya et al.; Oct. 17, 2022
Abstract: We introduce Token Merging (ToMe), a simple method to increase the throughput of existing ViT models without needing to train. ToMe gradually combines similar tokens in a transformer using a general and light-weight matching algorithm that is as fast as pruning while being more accurate. Off-the-shelf, ToMe can 2x the throughput of state-of-the-art ViT-L @ 512 and ViT-H @ 518 models on images and 2.2x the throughput of ViT-L on video with only a 0.2-0.3% accuracy drop in each case. ToMe can also easily be applied during training, improving in practice training speed up to 2x for MAE fine-tuning on video. Training with ToMe further minimizes accuracy drop, leading to 2x the throughput of ViT-B on audio for only a 0.4% mAP drop. Qualitatively, we find that ToMe merges object parts into one token, even over multiple frames of video. Overall, ToMe's accuracy and speed are competitive with state-of-the-art on images, video, and audio.
ANARCI; Antibody Numbering and Antigen Receptor ClassIfication
ProteinGAN; Generative network architecture that may be used to produce de-novo protein sequences.
fpocket; The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.
