Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in models like the series of ESM and AlphaFold2. Despite these developments, the study and modeling of multi-chain proteins remain largely uncharted, though they are vital for understanding biological functions. Recognizing the importance of these interactions, we introduce APM (All-Atom Protein Generative Model), a model specifically designed for modeling multi-chain proteins. By integrating atom-level information and leveraging data on multi-chain proteins, APM is capable of precisely modeling inter-chain interactions and designing protein complexes with binding capabilities from scratch. It also performs folding and inverse-folding tasks for multi-chain proteins. Moreover, APM demonstrates versatility in downstream applications: it achieves enhanced performance through supervised fine-tuning (SFT) while also supporting zero-shot sampling in certain tasks, achieving state-of-the-art results. We released our code at https://github.com/bytedance/apm.

Code comment generation which aims to automatically generate natural language descriptions for source code, is a crucial task in the field of automatic software development. Traditional comment generation methods use manually-crafted templates or information retrieval (IR) techniques to generate summaries for source code. In recent years, neural network-based methods which leveraged acclaimed encoder-decoder deep learning framework to learn comment generation patterns from a large-scale parallel code corpus, have achieved impressive results. However, these emerging methods only take code-related information as input. Software reuse is common in the process of software development, meaning that comments of similar code snippets are helpful for comment generation. Inspired by the IR-based and template-based approaches, in this paper, we propose a neural comment generation approach where we use the existing comments of similar code snippets as exemplars to guide comment generation. Specifically, given a piece of code, we first use an IR technique to retrieve a similar code snippet and treat its comment as an exemplar. Then we design a novel seq2seq neural network that takes the given code, its AST, its similar code, and its exemplar as input, and leverages the information from the exemplar to assist in the target comment generation based on the semantic similarity between the source code and the similar code. We evaluate our approach on a large-scale Java corpus, which contains about 2M samples, and experimental results demonstrate that our model outperforms the state-of-the-art methods by a substantial margin.

Reinforcement learning agents usually learn from scratch, which requires a large number of interactions with the environment. This is quite different from the learning process of human. When faced with a new task, human naturally have the common sense and use the prior knowledge to derive an initial policy and guide the learning process afterwards. Although the prior knowledge may be not fully applicable to the new task, the learning process is significantly sped up since the initial policy ensures a quick-start of learning and intermediate guidance allows to avoid unnecessary exploration. Taking this inspiration, we propose knowledge guided policy network (KoGuN), a novel framework that combines human prior suboptimal knowledge with reinforcement learning. Our framework consists of a fuzzy rule controller to represent human knowledge and a refine module to fine-tune suboptimal prior knowledge. The proposed framework is end-to-end and can be combined with existing policy-based reinforcement learning algorithm. We conduct experiments on both discrete and continuous control tasks. The empirical results show that our approach, which combines human suboptimal knowledge and RL, achieves significant improvement on learning efficiency of flat RL algorithms, even with very low-performance human prior knowledge.