Siyuan Zhou

Zheming Xing, Siyuan Zhou, Ruinan Wang et al.

Accurate prediction of synthetic lethality (SL) is important for guiding the development of cancer drugs and therapies. SL prediction faces significant challenges in the effective fusion of heterogeneous multi-source data. Existing multimodal methods often suffer from "modality laziness" due to disparate convergence speeds, which hinders the exploitation of complementary information. This is also one reason why most existing SL prediction models cannot perform well on both pan-cancer and single-cancer SL pair prediction. In this study, we propose SynLeaF, a dual-stage multimodal fusion framework for SL prediction across pan- and single-cancer contexts. The framework employs a VAE-based cross-encoder with a product of experts mechanism to fuse four omics data types (gene expression, mutation, methylation, and CNV), while simultaneously utilizing a relational graph convolutional network to capture structured gene representations from biomedical knowledge graphs. To mitigate modality laziness, SynLeaF introduces a dual-stage training mechanism employing featurelevel knowledge distillation with adaptive uni-modal teacher and ensemble strategies. In extensive experiments across eight specific cancer types and a pancancer dataset, SynLeaF achieves superior performance in 17 out of 19 scenarios. Ablation studies and gradient analyses further validate the critical contributions of the proposed fusion and distillation mechanisms to model robustness and generalization. To facilitate community use, a web server is available at https://synleaf.bioinformatics-lilab.cn.

Siyuan Zhou, Yilun Du, Yuncong Yang et al.

The ability to simulate the effects of future actions on the world is a crucial ability of intelligent embodied agents, enabling agents to anticipate the effects of their actions and make plans accordingly. While a large body of existing work has explored how to construct such world models using video models, they are often myopic in nature, without any memory of a scene not captured by currently observed images, preventing agents from making consistent long-horizon plans in complex environments where many parts of the scene are partially observed. We introduce a new persistent embodied world model with an explicit memory of previously generated content, enabling much more consistent long-horizon simulation. During generation time, our video diffusion model predicts RGB-D video of the future observations of the agent. This generation is then aggregated into a persistent 3D map of the environment. By conditioning the video model on this 3D spatial map, we illustrate how this enables video world models to faithfully simulate both seen and unseen parts of the world. Finally, we illustrate the efficacy of such a world model in downstream embodied applications, enabling effective planning and policy learning.

Zhiao Huang, Yuanming Hu, Tao Du et al.

Simulated virtual environments serve as one of the main driving forces behind developing and evaluating skill learning algorithms. However, existing environments typically only simulate rigid body physics. Additionally, the simulation process usually does not provide gradients that might be useful for planning and control optimizations. We introduce a new differentiable physics benchmark called PasticineLab, which includes a diverse collection of soft body manipulation tasks. In each task, the agent uses manipulators to deform the plasticine into the desired configuration. The underlying physics engine supports differentiable elastic and plastic deformation using the DiffTaichi system, posing many under-explored challenges to robotic agents. We evaluate several existing reinforcement learning (RL) methods and gradient-based methods on this benchmark. Experimental results suggest that 1) RL-based approaches struggle to solve most of the tasks efficiently; 2) gradient-based approaches, by optimizing open-loop control sequences with the built-in differentiable physics engine, can rapidly find a solution within tens of iterations, but still fall short on multi-stage tasks that require long-term planning. We expect that PlasticineLab will encourage the development of novel algorithms that combine differentiable physics and RL for more complex physics-based skill learning tasks.

Chuang Gan, Siyuan Zhou, Jeremy Schwartz et al.

We introduce a visually-guided and physics-driven task-and-motion planning benchmark, which we call the ThreeDWorld Transport Challenge. In this challenge, an embodied agent equipped with two 9-DOF articulated arms is spawned randomly in a simulated physical home environment. The agent is required to find a small set of objects scattered around the house, pick them up, and transport them to a desired final location. We also position containers around the house that can be used as tools to assist with transporting objects efficiently. To complete the task, an embodied agent must plan a sequence of actions to change the state of a large number of objects in the face of realistic physical constraints. We build this benchmark challenge using the ThreeDWorld simulation: a virtual 3D environment where all objects respond to physics, and where can be controlled using fully physics-driven navigation and interaction API. We evaluate several existing agents on this benchmark. Experimental results suggest that: 1) a pure RL model struggles on this challenge; 2) hierarchical planning-based agents can transport some objects but still far from solving this task. We anticipate that this benchmark will empower researchers to develop more intelligent physics-driven robots for the physical world.