Graph Cross-Correlated Network for Recommendation

Collaborative filtering (CF) models have demonstrated remarkable performance in recommender systems, which represent users and items as embedding vectors. Recently, due to the powerful modeling capability of graph neural networks for user-item interaction graphs, graph-based CF models have gained increasing attention. They encode each user/item and its subgraph into a single super vector by combining graph embeddings after each graph convolution. However, each hop of the neighbor in the user-item subgraphs carries a specific semantic meaning. Encoding all subgraph information into single vectors and inferring user-item relations with dot products can weaken the semantic information between user and item subgraphs, thus leaving untapped potential. Exploiting this untapped potential provides insight into improving performance for existing recommendation models. To this end, we propose the Graph Cross-correlated Network for Recommendation (GCR), which serves as a general recommendation paradigm that explicitly considers correlations between user/item subgraphs. GCR first introduces the Plain Graph Representation (PGR) to extract information directly from each hop of neighbors into corresponding PGR vectors. Then, GCR develops Cross-Correlated Aggregation (CCA) to construct possible cross-correlated terms between PGR vectors of user/item subgraphs. Finally, GCR comprehensively incorporates the cross-correlated terms for recommendations. Experimental results show that GCR outperforms state-of-the-art models on both interaction prediction and click-through rate prediction tasks.

Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks?

Equivariant Graph Neural Networks (GNNs) that incorporate E(3) symmetry have achieved significant success in various scientific applications. As one of the most successful models, EGNN leverages a simple scalarization technique to perform equivariant message passing over only Cartesian vectors (i.e., 1st-degree steerable vectors), enjoying greater efficiency and efficacy compared to equivariant GNNs using higher-degree steerable vectors. This success suggests that higher-degree representations might be unnecessary. In this paper, we disprove this hypothesis by exploring the expressivity of equivariant GNNs on symmetric structures, including $k$-fold rotations and regular polyhedra. We theoretically demonstrate that equivariant GNNs will always degenerate to a zero function if the degree of the output representations is fixed to 1 or other specific values. Based on this theoretical insight, we propose HEGNN, a high-degree version of EGNN to increase the expressivity by incorporating high-degree steerable vectors while maintaining EGNN's efficiency through the scalarization trick. Our extensive experiments demonstrate that HEGNN not only aligns with our theoretical analyses on toy datasets consisting of symmetric structures, but also shows substantial improvements on more complicated datasets such as $N$-body and MD17. Our theoretical findings and empirical results potentially open up new possibilities for the research of equivariant GNNs.

Force-Guided Bridge Matching for Full-Atom Time-Coarsened Dynamics of Peptides

Molecular Dynamics (MD) simulations are irreplaceable and ubiquitous in fields of materials science, chemistry, pharmacology just to name a few. Conventional MD simulations are plagued by numerical stability as well as long equilibration time issues, which limits broader applications of MD simulations. Recently, a surge of deep learning approaches have been devised for time-coarsened dynamics, which learns the state transition mechanism over much larger time scales to overcome these limitations. However, only a few methods target the underlying Boltzmann distribution by resampling techniques, where proposals are rarely accepted as new states with low efficiency. In this work, we propose a force-guided bridge matching model, FBM, a novel framework that first incorporates physical priors into bridge matching for full-atom time-coarsened dynamics. With the guidance of our well-designed intermediate force field, FBM is feasible to target the Boltzmann-like distribution by direct inference without extra steps. Experiments on small peptides verify our superiority in terms of comprehensive metrics and demonstrate transferability to unseen peptide systems.

Towards Effective and Efficient Continual Pre-training of Large Language Models

Continual pre-training (CPT) has been an important approach for adapting language models to specific domains or tasks. To make the CPT approach more traceable, this paper presents a technical report for continually pre-training Llama-3 (8B), which significantly enhances the Chinese language ability and scientific reasoning ability of the backbone model. To enhance the new abilities while retaining the original abilities, we design specific data mixture and curriculum strategies by utilizing existing datasets and synthesizing high-quality datasets. Specifically, we synthesize multidisciplinary scientific question and answer (QA) pairs based on related web pages, and subsequently incorporate these synthetic data to improve the scientific reasoning ability of Llama-3. We refer to the model after CPT as Llama-3-SynE (Synthetic data Enhanced Llama-3). We also present the tuning experiments with a relatively small model -- TinyLlama, and employ the derived findings to train the backbone model. Extensive experiments on a number of evaluation benchmarks show that our approach can largely improve the performance of the backbone models, including both the general abilities (+8.81 on C-Eval and +6.31 on CMMLU) and the scientific reasoning abilities (+12.00 on MATH and +4.13 on SciEval), without hurting the original capacities. Our model, data, and codes are available at https://github.com/RUC-GSAI/Llama-3-SynE.

Subequivariant Reinforcement Learning in 3D Multi-Entity Physical Environments

Learning policies for multi-entity systems in 3D environments is far more complicated against single-entity scenarios, due to the exponential expansion of the global state space as the number of entities increases. One potential solution of alleviating the exponential complexity is dividing the global space into independent local views that are invariant to transformations including translations and rotations. To this end, this paper proposes Subequivariant Hierarchical Neural Networks (SHNN) to facilitate multi-entity policy learning. In particular, SHNN first dynamically decouples the global space into local entity-level graphs via task assignment. Second, it leverages subequivariant message passing over the local entity-level graphs to devise local reference frames, remarkably compressing the representation redundancy, particularly in gravity-affected environments. Furthermore, to overcome the limitations of existing benchmarks in capturing the subtleties of multi-entity systems under the Euclidean symmetry, we propose the Multi-entity Benchmark (MEBEN), a new suite of environments tailored for exploring a wide range of multi-entity reinforcement learning. Extensive experiments demonstrate significant advancements of SHNN on the proposed benchmarks compared to existing methods. Comprehensive ablations are conducted to verify the indispensability of task assignment and subequivariance.

YuLan: An Open-source Large Language Model

Large language models (LLMs) have become the foundation of many applications, leveraging their extensive capabilities in processing and understanding natural language. While many open-source LLMs have been released with technical reports, the lack of training details hinders further research and development. This paper presents the development of YuLan, a series of open-source LLMs with $12$ billion parameters. The base model of YuLan is pre-trained on approximately $1.7$T tokens derived from a diverse corpus, including massive English, Chinese, and multilingual texts. We design a three-stage pre-training method to enhance YuLan's overall capabilities. Subsequent phases of training incorporate instruction-tuning and human alignment, employing a substantial volume of high-quality synthesized data. To facilitate the learning of complex and long-tail knowledge, we devise a curriculum-learning framework throughout across these stages, which helps LLMs learn knowledge in an easy-to-hard manner. YuLan's training is finished on Jan, 2024 and has achieved performance on par with state-of-the-art LLMs across various English and Chinese benchmarks. This paper outlines a comprehensive technical roadmap for developing LLMs from scratch. Our model and codes are available at https://github.com/RUC-GSAI/YuLan-Chat.

Equivariant Spatio-Temporal Attentive Graph Networks to Simulate Physical Dynamics

Learning to represent and simulate the dynamics of physical systems is a crucial yet challenging task. Existing equivariant Graph Neural Network (GNN) based methods have encapsulated the symmetry of physics, \emph{e.g.}, translations, rotations, etc, leading to better generalization ability. Nevertheless, their frame-to-frame formulation of the task overlooks the non-Markov property mainly incurred by unobserved dynamics in the environment. In this paper, we reformulate dynamics simulation as a spatio-temporal prediction task, by employing the trajectory in the past period to recover the Non-Markovian interactions. We propose Equivariant Spatio-Temporal Attentive Graph Networks (ESTAG), an equivariant version of spatio-temporal GNNs, to fulfill our purpose. At its core, we design a novel Equivariant Discrete Fourier Transform (EDFT) to extract periodic patterns from the history frames, and then construct an Equivariant Spatial Module (ESM) to accomplish spatial message passing, and an Equivariant Temporal Module (ETM) with the forward attention and equivariant pooling mechanisms to aggregate temporal message. We evaluate our model on three real datasets corresponding to the molecular-, protein- and macro-level. Experimental results verify the effectiveness of ESTAG compared to typical spatio-temporal GNNs and equivariant GNNs.

Functional Protein Design with Local Domain Alignment

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation (PAAG), a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a nearly sixfold increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 8.7% in the immunoglobulin domain) in comparison to the existing model.

HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning

Understanding and leveraging the 3D structures of proteins is central to a variety of biological and drug discovery tasks. While deep learning has been applied successfully for structure-based protein function prediction tasks, current methods usually employ distinct training for each task. However, each of the tasks is of small size, and such a single-task strategy hinders the models' performance and generalization ability. As some labeled 3D protein datasets are biologically related, combining multi-source datasets for larger-scale multi-task learning is one way to overcome this problem. In this paper, we propose a neural network model to address multiple tasks jointly upon the input of 3D protein structures. In particular, we first construct a standard structure-based multi-task benchmark called Protein-MT, consisting of 6 biologically relevant tasks, including affinity prediction and property prediction, integrated from 4 public datasets. Then, we develop a novel graph neural network for multi-task learning, dubbed Heterogeneous Multichannel Equivariant Network (HeMeNet), which is E(3) equivariant and able to capture heterogeneous relationships between different atoms. Besides, HeMeNet can achieve task-specific learning via the task-aware readout mechanism. Extensive evaluations on our benchmark verify the effectiveness of multi-task learning, and our model generally surpasses state-of-the-art models.

Equivariant Local Reference Frames for Unsupervised Non-rigid Point Cloud Shape Correspondence

Unsupervised non-rigid point cloud shape correspondence underpins a multitude of 3D vision tasks, yet itself is non-trivial given the exponential complexity stemming from inter-point degree-of-freedom, i.e., pose transformations. Based on the assumption of local rigidity, one solution for reducing complexity is to decompose the overall shape into independent local regions using Local Reference Frames (LRFs) that are invariant to SE(3) transformations. However, the focus solely on local structure neglects global geometric contexts, resulting in less distinctive LRFs that lack crucial semantic information necessary for effective matching. Furthermore, such complexity introduces out-of-distribution geometric contexts during inference, thus complicating generalization. To this end, we introduce 1) EquiShape, a novel structure tailored to learn pair-wise LRFs with global structural cues for both spatial and semantic consistency, and 2) LRF-Refine, an optimization strategy generally applicable to LRF-based methods, aimed at addressing the generalization challenges. Specifically, for EquiShape, we employ cross-talk within separate equivariant graph neural networks (Cross-GVP) to build long-range dependencies to compensate for the lack of semantic information in local structure modeling, deducing pair-wise independent SE(3)-equivariant LRF vectors for each point. For LRF-Refine, the optimization adjusts LRFs within specific contexts and knowledge, enhancing the geometric and semantic generalizability of point features. Our overall framework surpasses the state-of-the-art methods by a large margin on three benchmarks. Code and models will be publicly available.