Large Language Models (LLMs) have become pivotal tools for automating code generation in software development. However, these models face significant challenges in producing version-aware code for rapidly evolving languages like Rust, where frequent Application Programming Interfaces (API) changes across versions lead to compatibility issues and correctness errors. Existing benchmarks lack systematic evaluation of how models navigate API transitions, relying on labor-intensive manual curation and offering limited version-specific insights. To address this gap, we present RustEvo, a novel framework for constructing dynamic benchmarks that evaluate the ability of LLMs to adapt to evolving Rust APIs. RustEvo automates dataset creation by synthesizing 588 API changes (380 from Rust standard libraries, 208 from 15 third-party crates) into programming tasks mirroring real-world challenges. These tasks cover four API evolution categories: Stabilizations, Signature Changes, Behavioral Changes, and Deprecations, reflecting their actual distribution in the Rust ecosystem. Experiments on state-of-the-art (SOTA) LLMs reveal significant performance variations: models achieve a 65.8% average success rate on stabilized APIs but only 38.0% on behavioral changes, highlighting difficulties in detecting semantic shifts without signature alterations. Knowledge cutoff dates strongly influence performance, with models scoring 56.1% on before-cutoff APIs versus 32.5% on after-cutoff tasks. Retrieval-Augmented Generation (RAG) mitigates this gap, improving success rates by 13.5% on average for APIs released after model training. Our findings underscore the necessity of our evolution-aware benchmarks to advance the adaptability of LLMs in fast-paced software ecosystems. The framework and the benchmarks are publicly released at https://github.com/SYSUSELab/RustEvo.

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains plateau, focusing primarily on increasing model sizes rather than optimizing the efficient compute frontier that balances performance and compute budgets. Our investigation is grounded in a massive dataset consisting of 939 million protein sequences. We trained over 300 models ranging from 3.5 million to 10.7 billion parameters on 5 to 200 billion unique tokens, to investigate the relations between model sizes, training token numbers, and objectives. First, we observed the effect of diminishing returns for the Causal Language Model (CLM) and that of overfitting for the Masked Language Model~(MLM) when repeating the commonly used Uniref database. To address this, we included metagenomic protein sequences in the training set to increase the diversity and avoid the plateau or overfitting effects. Second, we obtained the scaling laws of CLM and MLM on Transformer, tailored to the specific characteristics of protein sequence data. Third, we observe a transfer scaling phenomenon from CLM to MLM, further demonstrating the effectiveness of transfer through scaling behaviors based on estimated Effectively Transferred Tokens. Finally, to validate our scaling laws, we compare the large-scale versions of ESM-2 and PROGEN2 on downstream tasks, encompassing evaluations of protein generation as well as structure- and function-related tasks, all within less or equivalent pre-training compute budgets.

Federated learning heavily relies on distributed gradient descent techniques. In the situation where gradient information is not available, the gradients need to be estimated from zeroth-order information, which typically involves computing finite-differences along isotropic random directions. This method suffers from high estimation errors, as the geometric features of the objective landscape may be overlooked during the isotropic sampling. In this work, we propose a non-isotropic sampling method to improve the gradient estimation procedure. Gradients in our method are estimated in a subspace spanned by historical trajectories of solutions, aiming to encourage the exploration of promising regions and hence improve the convergence. The proposed method uses a covariance matrix for sampling which is a convex combination of two parts. The first part is a thin projection matrix containing the basis of the subspace which is designed to improve the exploitation ability. The second part is the historical trajectories. We implement this method in zeroth-order federated settings, and show that the convergence rate aligns with existing ones while introducing no significant overheads in communication or local computation. The effectiveness of our proposal is verified on several numerical experiments in comparison to several commonly-used zeroth-order federated optimization algorithms.

Semantic code search, retrieving code that matches a given natural language query, is an important task to improve productivity in software engineering. Existing code search datasets are problematic: either using unrealistic queries, or with mismatched codes, and typically using one-to-one query-code pairing, which fails to reflect the reality that a query might have multiple valid code matches. This paper introduces CoSQA+, pairing high-quality queries (reused from CoSQA) with multiple suitable codes. We collect code candidates from diverse sources and form candidate pairs by pairing queries with these codes. Utilizing the power of large language models (LLMs), we automate pair annotation, filtering, and code generation for queries without suitable matches. Through extensive experiments, CoSQA+ has demonstrated superior quality over CoSQA. Models trained on CoSQA+ exhibit improved performance. Furthermore, we propose a new metric Mean Multi-choice Reciprocal Rank (MMRR), to assess one-to-N code search performance. We provide the code and data at https://github.com/DeepSoftwareAnalytics/CoSQA_Plus.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

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 xTrimoGene$^\alpha$ (or xTrimoGene for short), 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. xTrimoGene model is now available for use as a service via the following link: https://api.biomap.com/xTrimoGene/apply.

Distributed training techniques have been widely deployed in large-scale deep neural networks (DNNs) training on dense-GPU clusters. However, on public cloud clusters, due to the moderate inter-connection bandwidth between instances, traditional state-of-the-art distributed training systems cannot scale well in training large-scale models. In this paper, we propose a new computing and communication efficient top-k sparsification communication library for distributed training. To further improve the system scalability, we optimize I/O by proposing a simple yet efficient multi-level data caching mechanism and optimize the update operation by introducing a novel parallel tensor operator. Experimental results on a 16-node Tencent Cloud cluster (each node with 8 Nvidia Tesla V100 GPUs) show that our system achieves 25%-40% faster than existing state-of-the-art systems on CNNs and Transformer. We finally break the record on DAWNBench on training ResNet-50 to 93% top-5 accuracy on ImageNet.