Zeyuan Wang

Zeyuan Wang, Qiang Zhang, Keyan Ding et al.

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

Hongxin Zhang, Zeyuan Wang, Qiushi Lyu et al.

In this paper, we investigate the problem of embodied multi-agent cooperation, where decentralized agents must cooperate given only egocentric views of the world. To effectively plan in this setting, in contrast to learning world dynamics in a single-agent scenario, we must simulate world dynamics conditioned on an arbitrary number of agents' actions given only partial egocentric visual observations of the world. To address this issue of partial observability, we first train generative models to estimate the overall world state given partial egocentric observations. To enable accurate simulation of multiple sets of actions on this world state, we then propose to learn a compositional world model for multi-agent cooperation by factorizing the naturally composable joint actions of multiple agents and compositionally generating the video conditioned on the world state. By leveraging this compositional world model, in combination with Vision Language Models to infer the actions of other agents, we can use a tree search procedure to integrate these modules and facilitate online cooperative planning. We evaluate our methods on three challenging benchmarks with 2-4 agents. The results show our compositional world model is effective and the framework enables the embodied agents to cooperate efficiently with different agents across various tasks and an arbitrary number of agents, showing the promising future of our proposed methods. More videos can be found at https://umass-embodied-agi.github.io/COMBO/.

Hongzhe Bi, Hengkai Tan, Shenghao Xie et al.

While a general embodied agent must function as a unified system, current methods are built on isolated models for understanding, world modeling, and control. This fragmentation prevents unifying multimodal generative capabilities and hinders learning from large-scale, heterogeneous data. In this paper, we propose Motus, a unified latent action world model that leverages existing general pretrained models and rich, sharable motion information. Motus introduces a Mixture-of-Transformer (MoT) architecture to integrate three experts (i.e., understanding, video generation, and action) and adopts a UniDiffuser-style scheduler to enable flexible switching between different modeling modes (i.e., world models, vision-language-action models, inverse dynamics models, video generation models, and video-action joint prediction models). Motus further leverages the optical flow to learn latent actions and adopts a recipe with three-phase training pipeline and six-layer data pyramid, thereby extracting pixel-level "delta action" and enabling large-scale action pretraining. Experiments show that Motus achieves superior performance against state-of-the-art methods in both simulation (a +15% improvement over X-VLA and a +45% improvement over Pi0.5) and real-world scenarios(improved by +11~48%), demonstrating unified modeling of all functionalities and priors significantly benefits downstream robotic tasks.

Yuhao Wang, Keyan Ding, Kehua Feng et al.

Protein language models have emerged as powerful tools for sequence generation, offering substantial advantages in functional optimization and denovo design. However, these models also present significant risks of generating harmful protein sequences, such as those that enhance viral transmissibility or evade immune responses. These concerns underscore critical biosafety and ethical challenges. To address these issues, we propose a Knowledge-guided Preference Optimization (KPO) framework that integrates prior knowledge via a Protein Safety Knowledge Graph. This framework utilizes an efficient graph pruning strategy to identify preferred sequences and employs reinforcement learning to minimize the risk of generating harmful proteins. Experimental results demonstrate that KPO effectively reduces the likelihood of producing hazardous sequences while maintaining high functionality, offering a robust safety assurance framework for applying generative models in biotechnology.

Zeyuan Wang, Yifan Zhao, Jia Li et al.

Given base classes with sufficient labeled samples, the target of few-shot classification is to recognize unlabeled samples of novel classes with only a few labeled samples. Most existing methods only pay attention to the relationship between labeled and unlabeled samples of novel classes, which do not make full use of information within base classes. In this paper, we make two contributions to investigate the few-shot classification problem. First, we report a simple and effective baseline trained on base classes in the way of traditional supervised learning, which can achieve comparable results to the state of the art. Second, based on the baseline, we propose a cooperative bi-path metric for classification, which leverages the correlations between base classes and novel classes to further improve the accuracy. Experiments on two widely used benchmarks show that our method is a simple and effective framework, and a new state of the art is established in the few-shot classification field.

Zeyuan Wang, Josiah Poon, Simon Poon

In medical real-world study (RWS), how to fully utilize the fragmentary and scarce information in model training to generate the solid diagnosis results is a challenging task. In this work, we introduce a novel multi-instance neural network, AMI-Net+, to train and predict from the incomplete and extremely imbalanced data. It is more effective than the state-of-art method, AMI-Net. First, we also implement embedding, multi-head attention and gated attention-based multi-instance pooling to capture the relations of symptoms themselves and with the given disease. Besides, we propose var-ious improvements to AMI-Net, that the cross-entropy loss is replaced by focal loss and we propose a novel self-adaptive multi-instance pooling method on instance-level to obtain the bag representation. We validate the performance of AMI-Net+ on two real-world datasets, from two different medical domains. Results show that our approach outperforms other base-line models by a considerable margin.