Cong Fu

Xuan Zhang, Limei Wang, Jacob Helwig et al. · cambridge, mit

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science.

Yuxuan Zhu, Cong Fu, Yabo Ni et al.

Temporal distribution shift (TDS) erodes the long-term accuracy of recommender systems, yet industrial practice still relies on periodic incremental training, which struggles to capture both stable and transient patterns. Existing approaches such as invariant learning and self-supervised learning offer partial solutions but often suffer from unstable temporal generalization, representation collapse, or inefficient data utilization. To address these limitations, we propose ELBO$_\text{TDS}$, a probabilistic framework that integrates seamlessly into industry-scale incremental learning pipelines. First, we identify key shifting factors through statistical analysis of real-world production data and design a simple yet effective data augmentation strategy that resamples these time-varying factors to extend the training support. Second, to harness the benefits of this extended distribution while preventing representation collapse, we model the temporal recommendation scenario using a causal graph and derive a self-supervised variational objective, ELBO$_\text{TDS}$, grounded in the causal structure. Extensive experiments supported by both theoretical and empirical analysis demonstrate that our method achieves superior temporal generalization, yielding a 2.33\% uplift in GMV per user and has been successfully deployed in Shopee Product Search. Code is available at https://github.com/FuCongResearchSquad/ELBO4TDS.

Yu Liang, Zhongjin Zhang, Yuxuan Zhu et al.

Semantic ID (SID)-based recommendation is a promising paradigm for scaling sequential recommender systems, but existing methods largely follow a semantic-centric pipeline: item embeddings are learned from foundation models and discretized using generic quantization schemes. This design is misaligned with generative recommendation objectives: semantic embeddings are weakly coupled with collaborative prediction, and generic quantization is inefficient at reducing sequential uncertainty for autoregressive modeling. To address these, we propose ReSID, a recommendation-native, principled SID framework that rethinks representation learning and quantization from the perspective of information preservation and sequential predictability, without relying on LLMs. ReSID consists of two components: (i) Field-Aware Masked Auto-Encoding (FAMAE), which learns predictive-sufficient item representations from structured features, and (ii) Globally Aligned Orthogonal Quantization (GAOQ), which produces compact and predictable SID sequences by jointly reducing semantic ambiguity and prefix-conditional uncertainty. Theoretical analysis and extensive experiments across ten datasets show the effectiveness of ReSID. ReSID consistently outperforms strong sequential and SID-based generative baselines by an average of over 10%, while reducing tokenization cost by up to 122x. Code is available at https://github.com/FuCongResearchSquad/ReSID.

Keqiang Yan, Cong Fu, Xiaofeng Qian et al.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Meng Liu, Cong Fu, Xuan Zhang et al.

Molecular property prediction is gaining increasing attention due to its diverse applications. One task of particular interests and importance is to predict quantum chemical properties without 3D equilibrium structures. This is practically favorable since obtaining 3D equilibrium structures requires extremely expensive calculations. In this work, we design a deep graph neural network to predict quantum properties by directly learning from 2D molecular graphs. In addition, we propose a 3D graph neural network to learn from low-cost conformer sets, which can be obtained with open-source tools using an affordable budget. We employ our methods to participate in the 2021 KDD Cup on OGB Large-Scale Challenge (OGB-LSC), which aims to predict the HOMO-LUMO energy gap of molecules. Final evaluation results reveal that we are one of the winners with a mean absolute error of 0.1235 on the holdout test set. Our implementation is available as part of the MoleculeX package (https://github.com/divelab/MoleculeX).

Meng Liu, Youzhi Luo, Limei Wang et al.

Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning. In the research community, implementing and benchmarking various advanced tasks are still painful and time-consuming with existing libraries. To facilitate graph deep learning research, we introduce DIG: Dive into Graphs, a turnkey library that provides a unified testbed for higher level, research-oriented graph deep learning tasks. Currently, we consider graph generation, self-supervised learning on graphs, explainability of graph neural networks, and deep learning on 3D graphs. For each direction, we provide unified implementations of data interfaces, common algorithms, and evaluation metrics. Altogether, DIG is an extensible, open-source, and turnkey library for researchers to develop new methods and effortlessly compare with common baselines using widely used datasets and evaluation metrics. Source code is available at https://github.com/divelab/DIG.

Cong Fu, Tong Chen, Meng Qu et al.

In recent years, there has been a surge of interests in interpretable graph reasoning methods. However, these models often suffer from limited performance when working on sparse and incomplete graphs, due to the lack of evidential paths that can reach target entities. Here we study open knowledge graph reasoning---a task that aims to reason for missing facts over a graph augmented by a background text corpus. A key challenge of the task is to filter out "irrelevant" facts extracted from corpus, in order to maintain an effective search space during path inference. We propose a novel reinforcement learning framework to train two collaborative agents jointly, i.e., a multi-hop graph reasoner and a fact extractor. The fact extraction agent generates fact triples from corpora to enrich the graph on the fly; while the reasoning agent provides feedback to the fact extractor and guides it towards promoting facts that are helpful for the interpretable reasoning. Experiments on two public datasets demonstrate the effectiveness of the proposed approach. Source code and datasets used in this paper can be downloaded at https://github.com/shanzhenren/CPL

Cong Fu, Changxu Wang, Deng Cai

Approximate Nearest Neighbor Search (ANNS) in high dimensional space is essential in database and information retrieval. Recently, there has been a surge of interest in exploring efficient graph-based indices for the ANNS problem. Among them, Navigating Spreading-out Graph (NSG) provides fine theoretical analysis and achieves state-of-the-art performance. However, we find there are several limitations with NSG: 1) NSG has no theoretical guarantee on nearest neighbor search when the query is not indexed in the database; 2) NSG is too sparse which harms the search performance. In addition, NSG suffers from high indexing complexity. To address the above problems, we propose the Satellite System Graphs (SSG) and a practical variant NSSG. Specifically, we propose a novel pruning strategy to produce SSGs from the complete graph. SSGs define a new family of MSNETs in which the out-edges of each node are distributed evenly in all directions. Each node in the graph builds effective connections to its neighborhood omnidirectionally, whereupon we derive SSG's excellent theoretical properties for both indexed and unindexed queries. We can adaptively adjust the sparsity of an SSG with a hyper-parameter to optimize the search performance. Further, NSSG is proposed to reduce the indexing complexity of the SSG for large-scale applications. Both theoretical and extensive experimental analyses are provided to demonstrate the strengths of the proposed approach over the existing representative algorithms. Our code has been released at https://github.com/ZJULearning/SSG.

Wenxiao Wang, Cong Fu, Jishun Guo et al.

Neural network compression empowers the effective yet unwieldy deep convolutional neural networks (CNN) to be deployed in resource-constrained scenarios. Most state-of-the-art approaches prune the model in filter-level according to the "importance" of filters. Despite their success, we notice they suffer from at least two of the following problems: 1) The redundancy among filters is not considered because the importance is evaluated independently. 2) Cross-layer filter comparison is unachievable since the importance is defined locally within each layer. Consequently, we must manually specify layer-wise pruning ratios. 3) They are prone to generate sub-optimal solutions because they neglect the inequality between reducing parameters and reducing computational cost. Reducing the same number of parameters in different positions in the network may reduce different computational cost. To address the above problems, we develop a novel algorithm named as COP (correlation-based pruning), which can detect the redundant filters efficiently. We enable the cross-layer filter comparison through global normalization. We add parameter-quantity and computational-cost regularization terms to the importance, which enables the users to customize the compression according to their preference (smaller or faster). Extensive experiments have shown COP outperforms the others significantly. The code is released at https://github.com/ZJULearning/COP.

Cong Fu, Chao Xiang, Changxu Wang et al.

Approximate nearest neighbor search (ANNS) is a fundamental problem in databases and data mining. A scalable ANNS algorithm should be both memory-efficient and fast. Some early graph-based approaches have shown attractive theoretical guarantees on search time complexity, but they all suffer from the problem of high indexing time complexity. Recently, some graph-based methods have been proposed to reduce indexing complexity by approximating the traditional graphs; these methods have achieved revolutionary performance on million-scale datasets. Yet, they still can not scale to billion-node databases. In this paper, to further improve the search-efficiency and scalability of graph-based methods, we start by introducing four aspects: (1) ensuring the connectivity of the graph; (2) lowering the average out-degree of the graph for fast traversal; (3) shortening the search path; and (4) reducing the index size. Then, we propose a novel graph structure called Monotonic Relative Neighborhood Graph (MRNG) which guarantees very low search complexity (close to logarithmic time). To further lower the indexing complexity and make it practical for billion-node ANNS problems, we propose a novel graph structure named Navigating Spreading-out Graph (NSG) by approximating the MRNG. The NSG takes the four aspects into account simultaneously. Extensive experiments show that NSG outperforms all the existing algorithms significantly. In addition, NSG shows superior performance in the E-commercial search scenario of Taobao (Alibaba Group) and has been integrated into their search engine at billion-node scale.

Cong Fu, Deng Cai

Approximate nearest neighbor (ANN) search is a fundamental problem in many areas of data mining, machine learning and computer vision. The performance of traditional hierarchical structure (tree) based methods decreases as the dimensionality of data grows, while hashing based methods usually lack efficiency in practice. Recently, the graph based methods have drawn considerable attention. The main idea is that \emph{a neighbor of a neighbor is also likely to be a neighbor}, which we refer as \emph{NN-expansion}. These methods construct a $k$-nearest neighbor ($k$NN) graph offline. And at online search stage, these methods find candidate neighbors of a query point in some way (\eg, random selection), and then check the neighbors of these candidate neighbors for closer ones iteratively. Despite some promising results, there are mainly two problems with these approaches: 1) These approaches tend to converge to local optima. 2) Constructing a $k$NN graph is time consuming. We find that these two problems can be nicely solved when we provide a good initialization for NN-expansion. In this paper, we propose EFANNA, an extremely fast approximate nearest neighbor search algorithm based on $k$NN Graph. Efanna nicely combines the advantages of hierarchical structure based methods and nearest-neighbor-graph based methods. Extensive experiments have shown that EFANNA outperforms the state-of-art algorithms both on approximate nearest neighbor search and approximate nearest neighbor graph construction. To the best of our knowledge, EFANNA is the fastest algorithm so far both on approximate nearest neighbor graph construction and approximate nearest neighbor search. A library EFANNA based on this research is released on Github.