Junyi An

Junyi An, Xinyu Lu, Yun-Fei Shi et al.

We introduce Suiren-1.0, a family of molecular foundation models for the accurate modeling of diverse organic systems. Suiren-1.0 comprising three specialized variants (Suiren-Base, Suiren-Dimer, and Suiren-ConfAvg) is integrated within an algorithmic framework that bridges the gap between 3D conformational geometry and 2D statistical ensemble spaces. We first pre-train Suiren-Base (1.8B parameters) on a 70M-sample Density Functional Theory dataset using spatial self-supervision and SE(3)-equivariant architectures, achieving robust performance in quantum property prediction. Suiren-Dimer extends this capability through continued pre-training on 13.5M intermolecular interaction samples. To enable efficient downstream application, we propose Conformation Compression Distillation (CCD), a diffusion-based framework that distills complex 3D structural representations into 2D conformation-averaged representations. This yields the lightweight Suiren-ConfAvg, which generates high-fidelity representations from SMILES or molecular graphs. Our extensive evaluations demonstrate that Suiren-1.0 establishes state-of-the-art results across a range of tasks. All models and benchmarks are open-sourced.

Yinghao Ai, Yukai Zhou, Ruoxi Jiang et al.

Spatiotemporal forecasting is critical for real-world applications like traffic management, yet capturing reliable interactions remains challenging under noisy and non-stationary conditions. Existing methods primarily rely on historical spatial priors, often failing to account for evolving temporal correlations and suffering from systematic errors. In this work, we propose a nested forecasting framework that couples future macro-level regional trends with micro-level historical observations, enabling top-down guidance from abstract future representations for fine-grained forecasting. Specifically, we employ a spectral clustering-based approach to construct semantically coherent regions, providing both theoretical and empirical evidence that this representation effectively filters systematic noise while preserving essential trends. Building on this, we develop a progressive coarse-to-fine predictor to integrate these representative features into the inference process. This enables the model to leverage trend predictions to anticipate dynamic anomalies, such as periodic offsets, in advance. Furthermore, extensive experiments on multiple high-dimensional datasets demonstrate that our method consistently outperforms state-of-the-art baselines, validating the effectiveness of future macro-guided nested forecasting.

Junyi An, Chao Qu, Yun-Fei Shi et al.

Graph neural networks (GNNs) have shown considerable promise in computational chemistry. However, the limited availability of molecular data raises concerns regarding GNNs' ability to effectively capture the fundamental principles of physics and chemistry, which constrains their generalization capabilities. To address this challenge, we introduce a novel self-supervised approach termed Equivariant Masked Position Prediction (EMPP), grounded in intramolecular potential and force theory. Unlike conventional attribute masking techniques, EMPP formulates a nuanced position prediction task that is more well-defined and enhances the learning of quantum mechanical features. EMPP also bypasses the approximation of the Gaussian mixture distribution commonly used in denoising methods, allowing for more accurate acquisition of physical properties. Experimental results indicate that EMPP significantly enhances performance of advanced molecular architectures, surpassing state-of-the-art self-supervised approaches. Our code is released in https://github.com/ajy112/EMPP

Zhijian Zhou, Junyi An, Zongkai Liu et al.

Generating physically realistic 3D molecular structures remains a core challenge in molecular generative modeling. While diffusion models equipped with equivariant neural networks have made progress in capturing molecular geometries, they often struggle to produce equilibrium structures that adhere to physical principles such as force field consistency. To bridge this gap, we propose Reinforcement Learning with Physical Feedback (RLPF), a novel framework that extends Denoising Diffusion Policy Optimization to 3D molecular generation. RLPF formulates the task as a Markov decision process and applies proximal policy optimization to fine-tune equivariant diffusion models. Crucially, RLPF introduces reward functions derived from force-field evaluations, providing direct physical feedback to guide the generation toward energetically stable and physically meaningful structures. Experiments on the QM9 and GEOM-drug datasets demonstrate that RLPF significantly improves molecular stability compared to existing methods. These results highlight the value of incorporating physics-based feedback into generative modeling. The code is available at: https://github.com/ZhijianZhou/RLPF/tree/verl_diffusion.

Junyi An, Chao Qu, Yun-Fei Shi et al.

Recent 3D molecular generation methods primarily use asynchronous auto-regressive or synchronous diffusion models. While auto-regressive models build molecules sequentially, they're limited by a short horizon and a discrepancy between training and inference. Conversely, synchronous diffusion models denoise all atoms at once, offering a molecule-level horizon but failing to capture the causal relationships inherent in hierarchical molecular structures. We introduce Equivariant Asynchronous Diffusion (EAD) to overcome these limitations. EAD is a novel diffusion model that combines the strengths of both approaches: it uses an asynchronous denoising schedule to better capture molecular hierarchy while maintaining a molecule-level horizon. Since these relationships are often complex, we propose a dynamic scheduling mechanism to adaptively determine the denoising timestep. Experimental results show that EAD achieves state-of-the-art performance in 3D molecular generation.

Junyi An, Xinyu Lu, Chao Qu et al.

Equivariant Graph Neural Networks (GNNs) have significantly advanced the modeling of 3D molecular structure by leveraging group representations. However, their message passing, heavily relying on Clebsch-Gordan tensor product convolutions, suffers from restricted expressiveness due to the limited non-linearity and low degree of group representations. To overcome this, we introduce the Equivariant Spherical Transformer (EST), a novel plug-and-play framework that applies a Transformer-like architecture to the Fourier spatial domain of group representations. EST achieves higher expressiveness than conventional models while preserving the crucial equivariant inductive bias through a uniform sampling strategy of spherical Fourier transforms. As demonstrated by our experiments on challenging benchmarks like OC20 and QM9, EST-based models achieve state-of-the-art performance. For the complex molecular systems within OC20, small models empowered by EST can outperform some larger models and those using additional data. In addition to demonstrating such strong expressiveness,we provide both theoretical and experimental validation of EST's equivariance as well, paving the way for new research in this area.

Zhou Wu, Junyi An, Baile Xu et al.

Recently, the superior performance of Transformers has made them a more robust and scalable solution for sequence modeling than traditional recurrent neural networks (RNNs). However, the effectiveness of Transformer in capturing long-term dependencies is primarily attributed to their comprehensive pair-modeling process rather than inherent inductive biases toward sequence semantics. In this study, we explore the capabilities of pure RNNs and reassess their long-term learning mechanisms. Inspired by the physics energy transition models that track energy changes over time, we propose a effective recurrent structure called the``Physics-inspired Energy Transition Neural Network" (PETNN). We demonstrate that PETNN's memory mechanism effectively stores information over long-term dependencies. Experimental results indicate that PETNN outperforms transformer-based methods across various sequence tasks. Furthermore, owing to its recurrent nature, PETNN exhibits significantly lower complexity. Our study presents an optimal foundational recurrent architecture and highlights the potential for developing effective recurrent neural networks in fields currently dominated by Transformer.

Liang Pan, Tong Wu, Zhongang Cai et al.

As real-scanned point clouds are mostly partial due to occlusions and viewpoints, reconstructing complete 3D shapes based on incomplete observations becomes a fundamental problem for computer vision. With a single incomplete point cloud, it becomes the partial point cloud completion problem. Given multiple different observations, 3D reconstruction can be addressed by performing partial-to-partial point cloud registration. Recently, a large-scale Multi-View Partial (MVP) point cloud dataset has been released, which consists of over 100,000 high-quality virtual-scanned partial point clouds. Based on the MVP dataset, this paper reports methods and results in the Multi-View Partial Point Cloud Challenge 2021 on Completion and Registration. In total, 128 participants registered for the competition, and 31 teams made valid submissions. The top-ranked solutions will be analyzed, and then we will discuss future research directions.

Hua Yan, Feng Han, Junyi An et al.

Subtext is a kind of deep semantics which can be acquired after one or more rounds of expression transformation. As a popular way of expressing one's intentions, it is well worth studying. In this paper, we try to make computers understand whether there is a subtext by means of machine learning. We build a Chinese dataset whose source data comes from the popular social media (e.g. Weibo, Netease Music, Zhihu, and Bilibili). In addition, we also build a baseline model called SASICM to deal with subtext recognition. The F1 score of SASICMg, whose pretrained model is GloVe, is as high as 64.37%, which is 3.97% higher than that of BERT based model, 12.7% higher than that of traditional methods on average, including support vector machine, logistic regression classifier, maximum entropy classifier, naive bayes classifier and decision tree and 2.39% higher than that of the state-of-the-art, including MARIN and BTM. The F1 score of SASICMBERT, whose pretrained model is BERT, is 65.12%, which is 0.75% higher than that of SASICMg. The accuracy rates of SASICMg and SASICMBERT are 71.16% and 70.76%, respectively, which can compete with those of other methods which are mentioned before.

Junyi An, Fengshan Liu, Jian Zhao et al.

Convolutional neural network (CNN) is a class of artificial neural networks widely used in computer vision tasks. Most CNNs achieve excellent performance by stacking certain types of basic units. In addition to increasing the depth and width of the network, designing more effective basic units has become an important research topic. Inspired by the elastic collision model in physics, we present a general structure which can be integrated into the existing CNNs to improve their performance. We term it the "Inter-layer Collision" (IC) structure. Compared to the traditional convolution structure, the IC structure introduces nonlinearity and feature recalibration in the linear convolution operation, which can capture more fine-grained features. In addition, a new training method, namely weak logit distillation (WLD), is proposed to speed up the training of IC networks by extracting knowledge from pre-trained basic models. In the ImageNet experiment, we integrate the IC structure into ResNet-50 and reduce the top-1 error from 22.38% to 21.75%, which also catches up the top-1 error of ResNet-100 (21.75%) with nearly half of FLOPs.

Junyi An, Fengshan Liu, Jian Zhao et al.

As a popular machine learning method, neural networks can be used to solve many complex tasks. Their strong generalization ability comes from the representation ability of the basic neuron model. The most popular neuron is the MP neuron, which uses a linear transformation and a non-linear activation function to process the input successively. Inspired by the elastic collision model in physics, we propose a new neuron model that can represent more complex distributions. We term it Inter-layer collision (IC) neuron. The IC neuron divides the input space into multiple subspaces used to represent different linear transformations. This operation enhanced non-linear representation ability and emphasizes some useful input features for the given task. We build the IC networks by integrating the IC neurons into the fully-connected (FC), convolutional, and recurrent structures. The IC networks outperform the traditional networks in a wide range of experiments. We believe that the IC neuron can be a basic unit to build network structures.

Junyi An, Fengshan Liu, Jian Zhao et al.

Neural networks have been widely used, and most networks achieve excellent performance by stacking certain types of basic units. Compared to increasing the depth and width of the network, designing more effective basic units has become an important research topic. Inspired by the elastic collision model in physics, we present a universal structure that could be integrated into the existing network structures to speed up the training process and increase their generalization abilities. We term this structure the "Inter-layer Collision" (IC) structure. We built two kinds of basic computational units (IC layer and IC block) that compose the convolutional neural networks (CNNs) by combining the IC structure with the convolution operation. Compared to traditional convolutions, both of the proposed computational units have a stronger non-linear representation ability and can filter features useful for a given task. Using these computational units to build networks, we bring significant improvements in performance for existing state-of-the-art CNNs. On the imagenet experiment, we integrate the IC block into ResNet-50 and reduce the top-1 error from 22.85% to 21.49%, which also exceeds the top-1 error of ResNet-100 (21.75%).