Advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions at the single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M records for humans with each record measuring 20,000 genes. This highlights the need for unsupervised representation learning to fully ingest these data, yet classical transformer architectures are prohibitive to train on such data in terms of both computation and memory. To address this challenge, we propose a novel asymmetric encoder-decoder transformer for scRNA-seq data, called xTrimoGeneα (or xTrimoGene for short)4, which leverages the sparse characteristic of the data to scale up the pre-training. This scalable design of xTrimoGene reduces FLOPs by one to two orders of magnitude compared to classical transformers while maintaining high accuracy, enabling us to train the largest transformer models over the largest scRNA-seq dataset today. Our experiments also show that the performance of xTrimoGene improves as we scale up the model sizes, and it also leads to SOTA performance over various downstream tasks, such as cell type annotation, perturb-seq effect prediction, and drug combination prediction.

Large language models (LLMs) can learn to perform a wide range of natural language tasks from just a handful of in-context examples. However, for generating strings from highly structured languages (e.g., semantic parsing to complex domainspecific languages), it is challenging for the LLM to generalize from just a few exemplars. We propose grammar prompting, a simple approach to enable LLMs to use external knowledge and domain-specific constraints, expressed through a grammar in Backus-Naur Form (BNF), during in-context learning. Grammar prompting augments each demonstration example with a specialized grammar that is minimally sufficient for generating the particular output example, where the specialized grammar is a subset of the full DSL grammar. For inference, the LLM first predicts a BNF grammar given a test input, and then generates the output according to the rules of the grammar. Experiments demonstrate that grammar prompting can enable LLMs to perform competitively on a diverse set of DSL generation tasks, including semantic parsing (SMCalFlow, Overnight, GeoQuery), PDDL planning, and SMILES-based molecule generation.

The advent of high-capacity pre-trained models has revolutionized problem-solving in computer vision, shifting the focus from training task-specific models to adapting pre-trained models. Consequently, effectively adapting large pre-trained models to downstream tasks in an efficient manner has become a prominent research area. Existing solutions primarily concentrate on designing lightweight adapters and their interaction with pre-trained models, with the goal of minimizing the number of parameters requiring updates. In this study, we propose a novel Adapter ReComposing (ARC) strategy that addresses efficient pre-trained model adaptation from a fresh perspective. Our approach considers the reusability of adaptation parameters and introduces a parameter-sharing scheme. Specifically, we leverage symmetric down-/up-projections to construct bottleneck operations, which are shared across layers.