Author name cluster

Fei Ni

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6 papers

1 author row

AAAI Conference 2025 Conference Paper

SWAMamba: A Sliding Window Attention Mamba Framework for Predicting Translation Elongation Rates

Xi Zeng
Fei Ni
Shaoqing Jiao
Dazhi Lu
Jianye Hao
Jiajie Peng

Translation elongation is essential for cellular proteostasis and is implicated in cancer and neurodegeneration. Accurately predicting the rate of ribosome elongation in each codon (also called ribosomal A site) on mRNA is important for understanding and modulating protein synthesis. However, predicting elongation rates is challenging due to the trade-off between capturing distal codon interactions and focusing on proximal codon effects at the A site. Approaches capturing distal codon interactions in the coding sequences (CDS) of mRNA fail to effectively differentiate critical regions (codons near the A site) due to insufficient effective mechanisms for focusing on these regions. Conversely, due to the limitations of models when handling long mRNA sequences, some methods simplify inputs by conditioning solely on proximal codons surrounding the A site, leading to the loss of important information from distal codons. To address this issue, we leverage Mamba's success in capturing long-range dependencies to enable the consideration of distant codons' impact on the A site. Additionally, we introduce a sliding window attention mechanism to emphasize the proximal codons around the A site during ribosome elongation. Building on these advancements, we present Sliding Window Attention Mamba (SWAMamba), a novel framework that simultaneously leverages both proximal and distal codon effects on the A site. We conduct comprehensive evaluations on ribosome data across four species and find that SWAMamba significantly outperformed current state-of-the-art methods in predicting translation elongation rates.

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NeurIPS Conference 2024 Conference Paper

CleanDiffuser: An Easy-to-use Modularized Library for Diffusion Models in Decision Making

Zibin Dong
Yifu Yuan
Jianye Hao
Fei Ni
Yi Ma
Pengyi Li
Yan Zheng

Leveraging the powerful generative capability of diffusion models (DMs) to build decision-making agents has achieved extensive success. However, there is still a demand for an easy-to-use and modularized open-source library that offers customized and efficient development for DM-based decision-making algorithms. In this work, we introduce CleanDiffuser, the first DM library specifically designed for decision-making algorithms. By revisiting the roles of DMs in the decision-making domain, we identify a set of essential sub-modules that constitute the core of CleanDiffuser, allowing for the implementation of various DM algorithms with simple and flexible building blocks. To demonstrate the reliability and flexibility of CleanDiffuser, we conduct comprehensive evaluations of various DM algorithms implemented with CleanDiffuser across an extensive range of tasks. The analytical experiments provide a wealth of valuable design choices and insights, reveal opportunities and challenges, and lay a solid groundwork for future research. CleanDiffuser will provide long-term support to the decision-making community, enhancing reproducibility and fostering the development of more robust solutions.

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NeurIPS Conference 2024 Conference Paper

DiffuserLite: Towards Real-time Diffusion Planning

Zibin Dong
Jianye Hao
Yifu Yuan
Fei Ni
Yitian Wang
Pengyi Li
Yan Zheng

Diffusion planning has been recognized as an effective decision-making paradigm in various domains. The capability of generating high-quality long-horizon trajectories makes it a promising research direction. However, existing diffusion planning methods suffer from low decision-making frequencies due to the expensive iterative sampling cost. To alleviate this, we introduce DiffuserLite, a super fast and lightweight diffusion planning framework, which employs a planning refinement process (PRP) to generate coarse-to-fine-grained trajectories, significantly reducing the modeling of redundant information and leading to notable increases in decision-making frequency. Our experimental results demonstrate that DiffuserLite achieves a decision-making frequency of $122. 2$Hz ($112. 7$x faster than predominant frameworks) and reaches state-of-the-art performance on D4RL, Robomimic, and FinRL benchmarks. In addition, DiffuserLite can also serve as a flexible plugin to increase the decision-making frequency of other diffusion planning algorithms, providing a structural design reference for future works. More details and visualizations are available at https: //diffuserlite. github. io/.

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NeurIPS Conference 2024 Conference Paper

PERIA: Perceive, Reason, Imagine, Act via Holistic Language and Vision Planning for Manipulation

Fei Ni
Jianye Hao
Shiguang Wu
Longxin Kou
Yifu Yuan
Zibin Dong
Jinyi Liu
Mingzhi Li

Long-horizon manipulation tasks with general instructions often implicitly encapsulate multiple sub-tasks, posing significant challenges in instruction following. While language planning is a common approach to decompose general instructions into stepwise sub-instructions, text-only guidance may lack expressiveness and lead to potential ambiguity. Considering that humans often imagine and visualize sub-instructions reasoning out before acting, the imagined subgoal images can provide more intuitive guidance and enhance the reliability of decomposition. Inspired by this, we propose PERIA ( PE rceive, R eason, I magine, A ct), a novel framework that integrates holistic language planning and vision planning for long-horizon manipulation tasks with complex instructions, leveraging both logical and intuitive aspects of task decomposition. Specifically, we first perform a lightweight multimodal alignment on the encoding side to empower the MLLM to perceive visual details and language instructions. The MLLM is then jointly instruction-tuned with a pretrained image-editing model to unlock capabilities of simultaneous reasoning of language instructions and generation of imagined subgoals. Furthermore, we introduce a consistency alignment loss to encourage coherent subgoal images and align with their corresponding instructions, mitigating potential hallucinations and semantic conflicts between the two planning manners. Comprehensive evaluations across three task domains demonstrate that PERIA, benefiting from holistic language and vision planning, significantly outperforms competitive baselines in both instruction following accuracy and task success rate on complex manipulation tasks.

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AAAI Conference 2023 Conference Paper

SplitNet: A Reinforcement Learning Based Sequence Splitting Method for the MinMax Multiple Travelling Salesman Problem

Hebin Liang
Yi Ma
Zilin Cao
Tianyang Liu
Fei Ni
Zhigang Li
Jianye Hao

MinMax Multiple Travelling Salesman Problem (mTSP) is an important class of combinatorial optimization problems with many practical applications, of which the goal is to minimize the longest tour of all vehicles. Due to its high computational complexity, existing methods for solving this problem cannot obtain a solution of satisfactory quality with fast speed, especially when the scale of the problem is large. In this paper, we propose a learning-based method named SplitNet to transform the single TSP solutions into the MinMax mTSP solutions of the same instances. Specifically, we generate single TSP solution sequences and split them into mTSP subsequences using an attention-based model trained by reinforcement learning. We also design a decision region for the splitting policy, which significantly reduces the policy action space on instances of various scales and thus improves the generalization ability of SplitNet. The experimental results show that SplitNet generalizes well and outperforms existing learning-based baselines and Google OR-Tools on widely-used random datasets of different scales and public datasets with fast solving speed.

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NeurIPS Conference 2022 Conference Paper

DOMINO: Decomposed Mutual Information Optimization for Generalized Context in Meta-Reinforcement Learning

Yao Mu
Yuzheng Zhuang
Fei Ni
Bin Wang
Jianyu Chen
Jianye Hao
Ping Luo

Adapting to the changes in transition dynamics is essential in robotic applications. By learning a conditional policy with a compact context, context-aware meta-reinforcement learning provides a flexible way to adjust behavior according to dynamics changes. However, in real-world applications, the agent may encounter complex dynamics changes. Multiple confounders can influence the transition dynamics, making it challenging to infer accurate context for decision-making. This paper addresses such a challenge by decomposed mutual information optimization (DOMINO) for context learning, which explicitly learns a disentangled context to maximize the mutual information between the context and historical trajectories while minimizing the state transition prediction error. Our theoretical analysis shows that DOMINO can overcome the underestimation of the mutual information caused by multi-confounded challenges via learning disentangled context and reduce the demand for the number of samples collected in various environments. Extensive experiments show that the context learned by DOMINO benefits both model-based and model-free reinforcement learning algorithms for dynamics generalization in terms of sample efficiency and performance in unseen environments.

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