Yutong Hu

Yutong Hu, Yang Tan, Andi Han et al.

The advent of deep learning has introduced efficient approaches for de novo protein sequence design, significantly improving success rates and reducing development costs compared to computational or experimental methods. However, existing methods face challenges in generating proteins with diverse lengths and shapes while maintaining key structural features. To address these challenges, we introduce CPDiffusion-SS, a latent graph diffusion model that generates protein sequences based on coarse-grained secondary structural information. CPDiffusion-SS offers greater flexibility in producing a variety of novel amino acid sequences while preserving overall structural constraints, thus enhancing the reliability and diversity of generated proteins. Experimental analyses demonstrate the significant superiority of the proposed method in producing diverse and novel sequences, with CPDiffusion-SS surpassing popular baseline methods on open benchmarks across various quantitative measurements. Furthermore, we provide a series of case studies to highlight the biological significance of the generation performance by the proposed method. The source code is publicly available at https://github.com/riacd/CPDiffusion-SS

Yutong Hu, Quzhe Huang, Yansong Feng · pku

Event Temporal Relation Extraction (ETRE) aims to identify the temporal relationship between two events, which plays an important role in natural language understanding. Most previous works follow a single-label classification style, classifying an event pair into either a specific temporal relation (e.g., \textit{Before}, \textit{After}), or a special label \textit{Vague} when there may be multiple possible temporal relations between the pair. In our work, instead of directly making predictions on \textit{Vague}, we propose a multi-label classification solution for ETRE (METRE) to infer the possibility of each temporal relation independently, where we treat \textit{Vague} as the cases when there is more than one possible relation between two events. We design a speculation mechanism to explore the possible relations hidden behind \textit{Vague}, which enables the latent information to be used efficiently. Experiments on TB-Dense, MATRES and UDS-T show that our method can effectively utilize the \textit{Vague} instances to improve the recognition for specific temporal relations and outperforms most state-of-the-art methods.

Quzhe Huang, Yutong Hu, Shengqi Zhu et al.

Event temporal relation extraction~(ETRE) is usually formulated as a multi-label classification task, where each type of relation is simply treated as a one-hot label. This formulation ignores the meaning of relations and wipes out their intrinsic dependency. After examining the relation definitions in various ETRE tasks, we observe that all relations can be interpreted using the start and end time points of events. For example, relation \textit{Includes} could be interpreted as event 1 starting no later than event 2 and ending no earlier than event 2. In this paper, we propose a unified event temporal relation extraction framework, which transforms temporal relations into logical expressions of time points and completes the ETRE by predicting the relations between certain time point pairs. Experiments on TB-Dense and MATRES show significant improvements over a strong baseline and outperform the state-of-the-art model by 0.3\% on both datasets. By representing all relations in a unified framework, we can leverage the relations with sufficient data to assist the learning of other relations, thus achieving stable improvement in low-data scenarios. When the relation definitions are changed, our method can quickly adapt to the new ones by simply modifying the logic expressions that map time points to new event relations. The code is released at \url{https://github.com/AndrewZhe/A-Unified-Framework-for-ETRE}.

Yutong Hu, Quzhe Huang, Kangcheng Luo et al.

As the context length that large language models can handle continues to increase, these models demonstrate an enhanced ability to utilize distant information for tasks such as language modeling. This capability contrasts with human reading and writing habits, where it is uncommon to remember and use particularly distant information, except in cases of foreshadowing. In this paper, we aim to explore which kinds of words benefit more from long contexts in language models. By analyzing the changes in token probabilities with increasing context length, we find that content words (e.g., nouns, adjectives) and the initial tokens of words benefit the most. Frequent patterns in the context (N-grams) also significantly impact predictions. Additionally, the model's prior knowledge plays a crucial role in influencing predictions, especially for rare tokens. We also observe that language models become more confident with longer contexts, resulting in sharper probability distributions. This overconfidence may contribute to the increasing probabilities of tokens with distant contextual information. We hope that our analysis will help the community better understand long-text language modeling and contribute to the design of more reliable long-context models.

Yutong Hu, Quzhe Huang, Mingxu Tao et al.

Recent studies have shown that Large Language Models (LLMs) have the potential to process extremely long text. Many works only evaluate LLMs' long-text processing ability on the language modeling task, with perplexity (PPL) as the evaluation metric. However, in our study, we find that there is no correlation between PPL and LLMs' long-text understanding ability. Besides, PPL may only reflect the model's ability to model local information instead of catching long-range dependency. Therefore, only using PPL to prove the model could process long text is inappropriate. The local focus feature of PPL could also explain some existing phenomena, such as the great extrapolation ability of the position method ALiBi. When evaluating a model's ability in long text, we might pay more attention to PPL's limitation and avoid overly relying on it.