arXiv subjects

Cong Fu

Publications and source records attributed to Cong Fu.

At least 37 records · Page 2Linked to original sources

arXiv2025

Maximum Inner Product is Query-Scaled Nearest Neighbor

Maximum Inner Product Search (MIPS) for high-dimensional vectors is pivotal across databases, information retrieval, and artificial intelligence. Existing methods either reduce MIPS to Nearest Neighbor Search (NNS) while suffering from harmful vector space transformations, or attempt to tackle MIPS directly but struggle to mitigate redundant computations due to the absence of the triangle inequality. This paper presents a novel theoretical framework that equates MIPS with NNS without requiring space transformation, thereby allowing us to leverage advanced graph-based indices for NNS and efficient edge pruning strategies, significantly reducing unnecessary computations. Despite a strong baseline set by our theoretical analysis, we identify and address two persistent challenges to further refine our method: the introduction of the Proximity Graph with Spherical Pathway (PSP), designed to mitigate the issue of MIPS solutions clustering around large-norm vectors, and the implementation of Adaptive Early Termination (AET), which efficiently curtails the excessive exploration once an accuracy bottleneck is reached. Extensive experiments reveal the superiority of our method over existing state-of-the-art techniques in search efficiency, scalability, and practical applicability. Compared with state-of-the-art graph based methods, it achieves an average 35% speed-up in query processing and a 3x reduction in index size. Notably, our approach has been validated and deployed in the search engines of Shopee, a well-known online shopping platform. Our code and an industrial-scale dataset for offline evaluation will also be released to address the absence of e-commerce data in public benchmarks.

cs.DB↗

arXiv2025

Stitching Inner Product and Euclidean Metrics for Topology-aware Maximum Inner Product Search

Maximum Inner Product Search (MIPS) is a fundamental challenge in machine learning and information retrieval, particularly in high-dimensional data applications. Existing approaches to MIPS either rely solely on Inner Product (IP) similarity, which faces issues with local optima and redundant computations, or reduce the MIPS problem to the Nearest Neighbor Search under the Euclidean metric via space projection, leading to topology destruction and information loss. Despite the divergence of the two paradigms, we argue that there is no inherent binary opposition between IP and Euclidean metrics. By stitching IP and Euclidean in the design of indexing and search algorithms, we can significantly enhance MIPS performance. Specifically, this paper explores the theoretical and empirical connections between these two metrics from the MIPS perspective. Our investigation, grounded in graph-based search, reveals that different indexing and search strategies offer distinct advantages for MIPS, depending on the underlying data topology. Building on these insights, we introduce a novel graph-based index called Metric-Amphibious Graph (MAG) and a corresponding search algorithm, Adaptive Navigation with Metric Switch (ANMS). To facilitate parameter tuning for optimal performance, we identify three statistical indicators that capture essential data topology properties and correlate strongly with parameter tuning. Extensive experiments on 12 real-world datasets demonstrate that MAG outperforms existing state-of-the-art methods, achieving up to 4x search speedup while maintaining adaptability and scalability.

cs.DB↗

arXiv2025

A Benchmark for Quantum Chemistry Relaxations via Machine Learning Interatomic Potentials

Computational quantum chemistry plays a critical role in drug discovery, chemical synthesis, and materials science. While first-principles methods, such as density functional theory (DFT), provide high accuracy in modeling electronic structures and predicting molecular properties, they are computationally expensive. Machine learning interatomic potentials (MLIPs) have emerged as promising surrogate models that aim to achieve DFT-level accuracy while enabling efficient large-scale atomistic simulations. The development of accurate and transferable MLIPs requires large-scale, high-quality datasets with both energy and force labels. Critically, MLIPs must generalize not only to stable geometries but also to intermediate, non-equilibrium conformations encountered during atomistic simulations. In this work, we introduce PubChemQCR, a large-scale dataset of molecular relaxation trajectories curated from the raw geometry optimization outputs of the PubChemQC project. PubChemQCR is the largest publicly available dataset of DFT-based relaxation trajectories for small organic molecules, comprising approximately 3.5 million trajectories and over 300 million molecular conformations computed at various levels of theory. Each conformation is labeled with both total energy and atomic forces, making the dataset suitable for training and evaluating MLIPs. To provide baselines for future developments, we benchmark nine representative MLIP models on the dataset. Our resources are publicly available at https://huggingface.co/divelab

q-bio.QM↗

arXiv2025

Fast Approximate Nearest Neighbor Search With The Navigating Spreading-out Graph

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.

cs.LG↗

arXiv2025

Embed Progressive Implicit Preference in Unified Space for Deep Collaborative Filtering

Embedding-based collaborative filtering, often coupled with nearest neighbor search, is widely deployed in large-scale recommender systems for personalized content selection. Modern systems leverage multiple implicit feedback signals (e.g., clicks, add to cart, purchases) to model user preferences comprehensively. However, prevailing approaches adopt a feedback-wise modeling paradigm, which (1) fails to capture the structured progression of user engagement entailed among different feedback and (2) embeds feedback-specific information into disjoint spaces, making representations incommensurable, increasing system complexity, and leading to suboptimal retrieval performance. A promising alternative is Ordinal Logistic Regression (OLR), which explicitly models discrete ordered relations. However, existing OLR-based recommendation models mainly focus on explicit feedback (e.g., movie ratings) and struggle with implicit, correlated feedback, where ordering is vague and non-linear. Moreover, standard OLR lacks flexibility in handling feedback-dependent covariates, resulting in suboptimal performance in real-world systems. To address these limitations, we propose Generalized Neural Ordinal Logistic Regression (GNOLR), which encodes multiple feature-feedback dependencies into a unified, structured embedding space and enforces feedback-specific dependency learning through a nested optimization framework. Thus, GNOLR enhances predictive accuracy, captures the progression of user engagement, and simplifies the retrieval process. We establish a theoretical comparison with existing paradigms, demonstrating how GNOLR avoids disjoint spaces while maintaining effectiveness. Extensive experiments on ten real-world datasets show that GNOLR significantly outperforms state-of-the-art methods in efficiency and adaptability.

cs.IR↗

arXiv2025

MedCT: A Clinical Terminology Graph for Generative AI Applications in Healthcare

We introduce the world's first clinical terminology for the Chinese healthcare community, namely MedCT, accompanied by a clinical foundation model MedBERT and an entity linking model MedLink. The MedCT system enables standardized and programmable representation of Chinese clinical data, successively stimulating the development of new medicines, treatment pathways, and better patient outcomes for the populous Chinese community. Moreover, the MedCT knowledge graph provides a principled mechanism to minimize the hallucination problem of large language models (LLMs), therefore achieving significant levels of accuracy and safety in LLM-based clinical applications. By leveraging the LLMs' emergent capabilities of generativeness and expressiveness, we were able to rapidly built a production-quality terminology system and deployed to real-world clinical field within three months, while classical terminologies like SNOMED CT have gone through more than twenty years development. Our experiments show that the MedCT system achieves state-of-the-art (SOTA) performance in semantic matching and entity linking tasks, not only for Chinese but also for English. We also conducted a longitudinal field experiment by applying MedCT and LLMs in a representative spectrum of clinical tasks, including electronic health record (EHR) auto-generation and medical document search for diagnostic decision making. Our study shows a multitude of values of MedCT for clinical workflows and patient outcomes, especially in the new genre of clinical LLM applications. We present our approach in sufficient engineering detail, such that implementing a clinical terminology for other non-English societies should be readily reproducible. We openly release our terminology, models and algorithms, along with real-world clinical datasets for the development.

cs.CL↗

arXiv2024

Residual Multi-Task Learner for Applied Ranking

Modern e-commerce platforms rely heavily on modeling diverse user feedback to provide personalized services. Consequently, multi-task learning has become an integral part of their ranking systems. However, existing multi-task learning methods encounter two main challenges: some lack explicit modeling of task relationships, resulting in inferior performance, while others have limited applicability due to being computationally intensive, having scalability issues, or relying on strong assumptions. To address these limitations and better fit our real-world scenario, pre-rank in Shopee Search, we introduce in this paper ResFlow, a lightweight multi-task learning framework that enables efficient cross-task information sharing via residual connections between corresponding layers of task networks. Extensive experiments on datasets from various scenarios and modalities demonstrate its superior performance and adaptability over state-of-the-art methods. The online A/B tests in Shopee Search showcase its practical value in large-scale industrial applications, evidenced by a 1.29% increase in OPU (order-per-user) without additional system latency. ResFlow is now fully deployed in the pre-rank module of Shopee Search. To facilitate efficient online deployment, we propose a novel offline metric Weighted Recall@K, which aligns well with our online metric OPU, addressing the longstanding online-offline metric misalignment issue. Besides, we propose to fuse scores from the multiple tasks additively when ranking items, which outperforms traditional multiplicative fusion. The code is released at https://github.com/BrunoTruthAlliance/ResFlow

cs.IR↗

arXiv2024

SoftTiger: A Clinical Foundation Model for Healthcare Workflows

We introduce SoftTiger, a clinical large language model (CLaM) designed as a foundation model for healthcare workflows. The narrative and unstructured nature of clinical notes is a major obstacle for healthcare intelligentization. We address a critical problem of structuring clinical notes into clinical data, according to international interoperability standards. We collect and annotate data for three subtasks, namely, international patient summary, clinical impression and medical encounter. We then supervised fine-tuned a state-of-the-art LLM using public and credentialed clinical data. The training is orchestrated in a way that the target model can first support basic clinical tasks such as abbreviation expansion and temporal information extraction, and then learn to perform more complex downstream clinical tasks. Moreover, we address several modeling challenges in the healthcare context, e.g., extra long context window. Our blind pairwise evaluation shows that SoftTiger outperforms other popular open-source models and GPT-3.5, comparable to Gemini-pro, with a mild gap from GPT-4. We believe that LLMs may become a step-stone towards healthcare digitalization and democratization. Therefore, we publicly release SoftTiger models at scales of 13 billion and 70 billion parameters, as well as datasets and code for our innovative scalable evaluation, hopefully, making a significant contribution to the healthcare industry.

cs.CL↗

arXiv2024

Fragment and Geometry Aware Tokenization of Molecules for Structure-Based Drug Design Using Language Models

Structure-based drug design (SBDD) is crucial for developing specific and effective therapeutics against protein targets but remains challenging due to complex protein-ligand interactions and vast chemical space. Although language models (LMs) have excelled in natural language processing, their application in SBDD is underexplored. To bridge this gap, we introduce a method, known as Frag2Seq, to apply LMs to SBDD by generating molecules in a fragment-based manner in which fragments correspond to functional modules. We transform 3D molecules into fragment-informed sequences using SE(3)-equivariant molecule and fragment local frames, extracting SE(3)-invariant sequences that preserve geometric information of 3D fragments. Furthermore, we incorporate protein pocket embeddings obtained from a pre-trained inverse folding model into the LMs via cross-attention to capture protein-ligand interaction, enabling effective target-aware molecule generation. Benefiting from employing LMs with fragment-based generation and effective protein context encoding, our model achieves the best performance on binding vina score and chemical properties such as QED and Lipinski, which shows our model's efficacy in generating drug-like ligands with higher binding affinity against target proteins. Moreover, our method also exhibits higher sampling efficiency compared to atom-based autoregressive and diffusion baselines with at most ~300x speedup.

q-bio.BM↗

arXiv2024

Narrow Linewidth Laser Based on Extended Topological Interface States in One-Dimensional Photonic Crystals

Recent advances in topological one-dimensional photonic crystal concepts have enabled the development of robust light-emitting devices by incorporating a topological interface state (TIS) at the cavity center. In this study, we theoretically and experimentally demonstrate a one-dimensional TIS-extended photonic crystal (1D-TISE-PC) structure. By integrating a linearly dispersive zero-index one-dimensional photonic crystal structure with a four-phase shift sampled grating, photons propagate along the cavity without phase differences, enhancing the robustness to material variations and extending the TIS. Our findings indicate that extending the TIS promotes a more uniform photon distribution along the laser cavity and mitigates the spatial hole burning (SHB) effect. We fabricated and characterized a 1550 nm sidewall 1D-TISE-PC semiconductor laser, achieving stable single-mode operation across a wide current range from 60 to 420 mA, with a side-mode suppression ratio of 50 dB. The 1D-TISE-PC structure exhibited a linewidth narrowing effect to approximately 150 kHz Lorentzian linewidth. Utilizing reconstruction equivalent-chirp technology for the 4PS sampled grating enabled precise wavelength control in 1D-TISE-PC laser arrays, achieving a wavelength spacing of 0.796 nm +- 0.003 nm. We show that the TIS still exists in the TISE cavity and topological protection is preserved. Its mode extension characteristics mitigate the SHB so narrows the linewidth. We argue that the design simplicity and improvement of the fabrication tolerance make this architecture suitable for high-power and narrow-linewidth semiconductor lasers development.

physics.optics↗

arXiv2024

SineNet: Learning Temporal Dynamics in Time-Dependent Partial Differential Equations

We consider using deep neural networks to solve time-dependent partial differential equations (PDEs), where multi-scale processing is crucial for modeling complex, time-evolving dynamics. While the U-Net architecture with skip connections is commonly used by prior studies to enable multi-scale processing, our analysis shows that the need for features to evolve across layers results in temporally misaligned features in skip connections, which limits the model's performance. To address this limitation, we propose SineNet, consisting of multiple sequentially connected U-shaped network blocks, referred to as waves. In SineNet, high-resolution features are evolved progressively through multiple stages, thereby reducing the amount of misalignment within each stage. We furthermore analyze the role of skip connections in enabling both parallel and sequential processing of multi-scale information. Our method is rigorously tested on multiple PDE datasets, including the Navier-Stokes equations and shallow water equations, showcasing the advantages of our proposed approach over conventional U-Nets with a comparable parameter budget. We further demonstrate that increasing the number of waves in SineNet while maintaining the same number of parameters leads to a monotonically improved performance. The results highlight the effectiveness of SineNet and the potential of our approach in advancing the state-of-the-art in neural PDE solver design. Our code is available as part of AIRS (https://github.com/divelab/AIRS).

cs.LG↗

arXiv2024

Complete and Efficient Graph Transformers for Crystal Material Property Prediction

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).

cs.LG↗

arXiv2023

TigerBot: An Open Multilingual Multitask LLM

We release and introduce the TigerBot family of large language models (LLMs), consisting of base and chat models, sized from 7, 13, 70 and 180 billion parameters. We develop our models embarking from Llama-2 and BLOOM, and push the boundary further in data, training algorithm, infrastructure, and application tools. Our models yield meaningful performance gain over SOTA open-source models, e.g., Llama-2, specifically 6% gain in English and 20% gain in Chinese. TigerBot model family also achieves leading performance in major academic and industrial benchmarks and leaderboards. We believe that TigerBot represents just a snapshot of lightning-fast progression in LLM open-source community. Therefore, we are thrilled to give back by publicly releasing our models and reporting our approach behind, with additional emphases on building SOTA LLMs in a democratized way and making LLMs of use in real-world applications.

cs.CL↗

arXiv2023

A Latent Diffusion Model for Protein Structure Generation

Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery. However, it remains a challenging computational task due to the large modeling space of protein structures. In this study, we propose a latent diffusion model that can reduce the complexity of protein modeling while flexibly capturing the distribution of natural protein structures in a condensed latent space. Specifically, we propose an equivariant protein autoencoder that embeds proteins into a latent space and then uses an equivariant diffusion model to learn the distribution of the latent protein representations. Experimental results demonstrate that our method can effectively generate novel protein backbone structures with high designability and efficiency. The code will be made publicly available at https://github.com/divelab/AIRS/tree/main/OpenProt/LatentDiff

q-bio.BM↗

arXiv2023

Group Equivariant Fourier Neural Operators for Partial Differential Equations

We consider solving partial differential equations (PDEs) with Fourier neural operators (FNOs), which operate in the frequency domain. Since the laws of physics do not depend on the coordinate system used to describe them, it is desirable to encode such symmetries in the neural operator architecture for better performance and easier learning. While encoding symmetries in the physical domain using group theory has been studied extensively, how to capture symmetries in the frequency domain is under-explored. In this work, we extend group convolutions to the frequency domain and design Fourier layers that are equivariant to rotations, translations, and reflections by leveraging the equivariance property of the Fourier transform. The resulting $G$-FNO architecture generalizes well across input resolutions and performs well in settings with varying levels of symmetry. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

cs.LG↗

arXiv2022

Lattice Convolutional Networks for Learning Ground States of Quantum Many-Body Systems

Deep learning methods have been shown to be effective in representing ground-state wave functions of quantum many-body systems. Existing methods use convolutional neural networks (CNNs) for square lattices due to their image-like structures. For non-square lattices, existing method uses graph neural network (GNN) in which structure information is not precisely captured, thereby requiring additional hand-crafted sublattice encoding. In this work, we propose lattice convolutions in which a set of proposed operations are used to convert non-square lattices into grid-like augmented lattices on which regular convolution can be applied. Based on the proposed lattice convolutions, we design lattice convolutional networks (LCN) that use self-gating and attention mechanisms. Experimental results show that our method achieves performance on par or better than existing methods on spin 1/2 $J_1$-$J_2$ Heisenberg model over the square, honeycomb, triangular, and kagome lattices while without using hand-crafted encoding.

quant-ph↗

arXiv2021

DIG: A Turnkey Library for Diving into Graph Deep Learning Research

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.

cs.LG↗

arXiv2021

Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks

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).

cs.LG↗