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Guolin Ke

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15 papers

2 author rows

ICML Conference 2025 Conference Paper

Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling

Shuqi Lu
Xiaohong Ji
Bohang Zhang
Lin Yao 0003
Siyuan Liu
Zhifeng Gao
Linfeng Zhang 0002
Guolin Ke

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1)grid-based space discretization; (2)grid sampling/merging; and (3)efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

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ICLR Conference 2025 Conference Paper

SciLitLLM: How to Adapt LLMs for Scientific Literature Understanding

Sihang Li 0002
Jin Huang 0001
Jiaxi Zhuang
Yaorui Shi
Xiaochen Cai
Mingjun Xu
Xiang Wang 0010
Linfeng Zhang 0002

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks. In this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for less-represented scientific domains. (3) SciLitLLM achieves promising performance in scientific literature understanding benchmarks.

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TMLR Journal 2024 Journal Article

3D Molecular Generation via Virtual Dynamics

Shuqi Lu
Lin Yao
Xi Chen
Hang Zheng
Di He
Guolin Ke

Structure-based drug design, a critical aspect of drug discovery, aims to identify high-affinity molecules for target protein pockets. Traditional virtual screening methods, which involve exhaustive searches within large molecular databases, are inefficient and limited in discovering novel molecules. The pocket-based 3D molecular generation model offers a promising alternative by directly generating molecules with 3D structures and binding positions in the pocket. In this paper, we present VD-Gen, a novel pocket-based 3D molecular generation pipeline. VD-Gen features a series of carefully designed stages to generate fine-grained 3D molecules with binding positions in the pocket cavity end-to-end. Rather than directly generating or sampling atoms with 3D positions in the pocket, VD-Gen randomly initializes multiple virtual particles within the pocket and learns to iteratively move them to approximate the distribution of molecular atoms in 3D space. After the iterative movement, a 3D molecule is extracted and further refined through additional iterative movement, yielding a high-quality 3D molecule with a confidence score. Comprehensive experimental results on pocket-based molecular generation demonstrate that VD-Gen can generate novel 3D molecules that fill the target pocket cavity with high binding affinities, significantly outperforming previous baselines.

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NeurIPS Conference 2024 Conference Paper

Exploring Molecular Pretraining Model at Scale

Xiaohong Ji
Zhen Wang
Zhifeng Gao
Hang Zheng
Linfeng Zhang
Guolin Ke
Weinan E

In recent years, pretraining models have made significant advancements in the fields of natural language processing (NLP), computer vision (CV), and life sciences. The significant advancements in NLP and CV are predominantly driven by the expansion of model parameters and data size, a phenomenon now recognized as the scaling laws. However, research exploring scaling law in molecular pretraining model remains unexplored. In this work, we present an innovative molecular pretraining model that leverages a two-track transformer to effectively integrate features at the atomic level, graph level, and geometry structure level. Along with this, we systematically investigate the scaling law within molecular pretraining models, examining the power-law correlations between validation loss and model size, dataset size, and computational resources. Consequently, we successfully scale the model to 1. 1 billion parameters through pretraining on 800 million conformations, making it the largest molecular pretraining model to date. Extensive experiments show the consistent improvement on the downstream tasks as the model size grows up. The model with 1. 1 billion parameters also outperform over existing methods, achieving an average 27\% improvement on the QM9 and 14\% on COMPAS-1D dataset.

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NeurIPS Conference 2024 Conference Paper

S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search

Gengmo Zhou
Zhen Wang
Feng Yu
Guolin Ke
Zhewei Wei
Zhifeng Gao

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due to its efficacy in conducting extensive database screenings without relying on specific protein-binding site information. Obtaining binding affinity data for complexes is highly expensive, resulting in a limited amount of available data that covers a relatively small chemical space. Moreover, these datasets contain a significant amount of inconsistent noise. It is challenging to identify an inductive bias that consistently maintains the integrity of molecular activity during data augmentation. To tackle these challenges, we propose S-MolSearch, the first framework to our knowledge, that leverages molecular 3D information and affinity information in semi-supervised contrastive learning for ligand-based virtual screening. % S-MolSearch processes both labeled and unlabeled data, trains molecular structural encoders, and generates soft labels for unlabeled data, drawing on the principles of inverse optimal transport. Drawing on the principles of inverse optimal transport, S-MolSearch efficiently processes both labeled and unlabeled data, training molecular structural encoders while generating soft labels for the unlabeled data. This design allows S-MolSearch to adaptively utilize unlabeled data within the learning process. Empirically, S-MolSearch demonstrates superior performance on widely-used benchmarks LIT-PCBA and DUD-E. It surpasses both structure-based and ligand-based virtual screening methods for AUROC, BEDROC and EF.

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ICLR Conference 2023 Conference Paper

Uni-Mol: A Universal 3D Molecular Representation Learning Framework

Gengmo Zhou
Zhifeng Gao
Qiankun Ding
Hang Zheng
Hongteng Xu
Zhewei Wei
Linfeng Zhang 0002
Guolin Ke

Molecular representation learning (MRL) has gained tremendous attention due to its critical role in learning from limited supervised data for applications like drug design. In most MRL methods, molecules are treated as 1D sequential tokens or 2D topology graphs, limiting their ability to incorporate 3D information for downstream tasks and, in particular, making it almost impossible for 3D geometry prediction/generation. In this paper, we propose a universal 3D MRL framework, called Uni-Mol, that significantly enlarges the representation ability and application scope of MRL schemes. Uni-Mol contains two pretrained models with the same SE(3) Transformer architecture: a molecular model pretrained by 209M molecular conformations; a pocket model pretrained by 3M candidate protein pocket data. Besides, Uni-Mol contains several finetuning strategies to apply the pretrained models to various downstream tasks. By properly incorporating 3D information, Uni-Mol outperforms SOTA in 14/15 molecular property prediction tasks. Moreover, Uni-Mol achieves superior performance in 3D spatial tasks, including protein-ligand binding pose prediction, molecular conformation generation, etc. The code, model, and data are made publicly available at https://github.com/dptech-corp/Uni-Mol.

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NeurIPS Conference 2022 Conference Paper

Quantized Training of Gradient Boosting Decision Trees

Yu Shi
Guolin Ke
Zhuoming Chen
Shuxin Zheng
Tie-Yan Liu

Recent years have witnessed significant success in Gradient Boosting Decision Trees (GBDT) for a wide range of machine learning applications. Generally, a consensus about GBDT's training algorithms is gradients and statistics are computed based on high-precision floating points. In this paper, we investigate an essentially important question which has been largely ignored by the previous literature - how many bits are needed for representing gradients in training GBDT? To solve this mystery, we propose to quantize all the high-precision gradients in a very simple yet effective way in the GBDT's training algorithm. Surprisingly, both our theoretical analysis and empirical studies show that the necessary precisions of gradients without hurting any performance can be quite low, e. g. , 2 or 3 bits. With low-precision gradients, most arithmetic operations in GBDT training can be replaced by integer operations of 8, 16, or 32 bits. Promisingly, these findings may pave the way for much more efficient training of GBDT from several aspects: (1) speeding up the computation of gradient statistics in histograms; (2) compressing the communication cost of high-precision statistical information during distributed training; (3) the inspiration of utilization and development of hardware architectures which well support low-precision computation for GBDT training. Benchmarked on CPUs, GPUs, and distributed clusters, we observe up to 2$\times$ speedup of our simple quantization strategy compared with SOTA GBDT systems on extensive datasets, demonstrating the effectiveness and potential of the low-precision training of GBDT. The code will be released to the official repository of LightGBM.

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NeurIPS Conference 2021 Conference Paper

Do Transformers Really Perform Badly for Graph Representation?

Chengxuan Ying
Tianle Cai
Shengjie Luo
Shuxin Zheng
Guolin Ke
Di He
Yanming Shen
Tie-Yan Liu

The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer. The code and models of Graphormer will be made publicly available at \url{https: //github. com/Microsoft/Graphormer}.

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ICML Conference 2021 Conference Paper

How could Neural Networks understand Programs?

Dinglan Peng
Shuxin Zheng
Yatao Li
Guolin Ke
Di He 0001
Tie-Yan Liu

Semantic understanding of programs is a fundamental problem for programming language processing (PLP). Recent works that learn representations of code based on pre-training techniques in NLP have pushed the frontiers in this direction. However, the semantics of PL and NL have essential differences. These being ignored, we believe it is difficult to build a model to better understand programs, by either directly applying off-the-shelf NLP pre-training techniques to the source code, or adding features to the model by the heuristic. In fact, the semantics of a program can be rigorously defined by formal semantics in PL theory. For example, the operational semantics, describes the meaning of a valid program as updating the environment (i. e. , the memory address-value function) through fundamental operations, such as memory I/O and conditional branching. Inspired by this, we propose a novel program semantics learning paradigm, that the model should learn from information composed of (1) the representations which align well with the fundamental operations in operational semantics, and (2) the information of environment transition, which is indispensable for program understanding. To validate our proposal, we present a hierarchical Transformer-based pre-training model called OSCAR to better facilitate the understanding of programs. OSCAR learns from intermediate representation (IR) and an encoded representation derived from static analysis, which are used for representing the fundamental operations and approximating the environment transitions respectively. OSCAR empirically shows the outstanding capability of program semantics understanding on many practical software engineering tasks. Code and models are released at: \url{https: //github. com/pdlan/OSCAR}.

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ICLR Conference 2021 Conference Paper

Rethinking Positional Encoding in Language Pre-training

Guolin Ke
Di He 0001
Tie-Yan Liu

In this work, we investigate the positional encoding methods used in language pre-training (e.g., BERT) and identify several problems in the existing formulations. First, we show that in the absolute positional encoding, the addition operation applied on positional embeddings and word embeddings brings mixed correlations between the two heterogeneous information resources. It may bring unnecessary randomness in the attention and further limit the expressiveness of the model. Second, we question whether treating the position of the symbol \texttt{[CLS]} the same as other words is a reasonable design, considering its special role (the representation of the entire sentence) in the downstream tasks. Motivated from above analysis, we propose a new positional encoding method called \textbf{T}ransformer with \textbf{U}ntied \textbf{P}ositional \textbf{E}ncoding (TUPE). In the self-attention module, TUPE computes the word contextual correlation and positional correlation separately with different parameterizations and then adds them together. This design removes the mixed and noisy correlations over heterogeneous embeddings and offers more expressiveness by using different projection matrices. Furthermore, TUPE unties the \texttt{[CLS]} symbol from other positions, making it easier to capture information from all positions. Extensive experiments and ablation studies on GLUE benchmark demonstrate the effectiveness of the proposed method. Codes and models are released at \url{https://github.com/guolinke/TUPE}.

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NeurIPS Conference 2021 Conference Paper

Stable, Fast and Accurate: Kernelized Attention with Relative Positional Encoding

Shengjie Luo
Shanda Li
Tianle Cai
Di He
Dinglan Peng
Shuxin Zheng
Guolin Ke
Liwei Wang

The attention module, which is a crucial component in Transformer, cannot scale efficiently to long sequences due to its quadratic complexity. Many works focus on approximating the dot-then-exponentiate softmax function in the original attention, leading to sub-quadratic or even linear-complexity Transformer architectures. However, we show that these methods cannot be applied to more powerful attention modules that go beyond the dot-then-exponentiate style, e. g. , Transformers with relative positional encoding (RPE). Since in many state-of-the-art models, relative positional encoding is used as default, designing efficient Transformers that can incorporate RPE is appealing. In this paper, we propose a novel way to accelerate attention calculation for Transformers with RPE on top of the kernelized attention. Based upon the observation that relative positional encoding forms a Toeplitz matrix, we mathematically show that kernelized attention with RPE can be calculated efficiently using Fast Fourier Transform (FFT). With FFT, our method achieves $\mathcal{O}(n\log n)$ time complexity. Interestingly, we further demonstrate that properly using relative positional encoding can mitigate the training instability problem of vanilla kernelized attention. On a wide range of tasks, we empirically show that our models can be trained from scratch without any optimization issues. The learned model performs better than many efficient Transformer variants and is faster than standard Transformer in the long-sequence regime.

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ICLR Conference 2021 Conference Paper

Taking Notes on the Fly Helps Language Pre-Training

Qiyu Wu 0001
Chen Xing
Yatao Li
Guolin Ke
Di He 0001
Tie-Yan Liu

How to make unsupervised language pre-training more efficient and less resource-intensive is an important research direction in NLP. In this paper, we focus on improving the efficiency of language pre-training methods through providing better data utilization. It is well-known that in language data corpus, words follow a heavy-tail distribution. A large proportion of words appear only very few times and the embeddings of rare words are usually poorly optimized. We argue that such embeddings carry inadequate semantic signals, which could make the data utilization inefficient and slow down the pre-training of the entire model. To mitigate this problem, we propose Taking Notes on the Fly (TNF), which takes notes for rare words on the fly during pre-training to help the model understand them when they occur next time. Specifically, TNF maintains a note dictionary and saves a rare word's contextual information in it as notes when the rare word occurs in a sentence. When the same rare word occurs again during training, the note information saved beforehand can be employed to enhance the semantics of the current sentence. By doing so, TNF provides a better data utilization since cross-sentence information is employed to cover the inadequate semantics caused by rare words in the sentences. We implement TNF on both BERT and ELECTRA to check its efficiency and effectiveness. Experimental results show that TNF's training time is 60% less than its backbone pre-training models when reaching the same performance. When trained with same number of iterations, TNF outperforms its backbone methods on most of downstream tasks and the average GLUE score. Code is attached in the supplementary material.

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AAAI Conference 2020 Conference Paper

Light Multi-Segment Activation for Model Compression

Zhenhui Xu
Guolin Ke
Jia Zhang
Jiang Bian
Tie-Yan Liu

Model compression has become necessary when applying neural networks (NN) into many real application tasks that can accept slightly-reduced model accuracy but with strict tolerance to model complexity. Recently, Knowledge Distillation, which distills the knowledge from well-trained and highly complex teacher model into a compact student model, has been widely used for model compression. However, under the strict requirement on the resource cost, it is quite challenging to make student model achieve comparable performance with the teacher one, essentially due to the drasticallyreduced expressiveness ability of the compact student model. Inspired by the nature of the expressiveness ability in NN, we propose to use multi-segment activation, which can signiﬁcantly improve the expressiveness ability with very little cost, in the compact student model. Speciﬁcally, we propose a highly efﬁcient multi-segment activation, called Light Multisegment Activation (LMA), which can rapidly produce multiple linear regions with very few parameters by leveraging the statistical information. With using LMA, the compact student model is capable of achieving much better performance effectively and efﬁciently, than the ReLU-equipped one with same model complexity. Furthermore, the proposed method is compatible with other model compression techniques, such as quantization, which means they can be used jointly for better compression performance. Experiments on state-of-the-art NN architectures over the real-world tasks demonstrate the effectiveness and extensibility of the LMA.

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NeurIPS Conference 2017 Conference Paper

LightGBM: A Highly Efficient Gradient Boosting Decision Tree

Guolin Ke
Qi Meng
Thomas Finley
Taifeng Wang
Wei Chen
Weidong Ma
Qiwei Ye
Tie-Yan Liu

Gradient Boosting Decision Tree (GBDT) is a popular machine learning algorithm, and has quite a few effective implementations such as XGBoost and pGBRT. Although many engineering optimizations have been adopted in these implementations, the efficiency and scalability are still unsatisfactory when the feature dimension is high and data size is large. A major reason is that for each feature, they need to scan all the data instances to estimate the information gain of all possible split points, which is very time consuming. To tackle this problem, we propose two novel techniques: \emph{Gradient-based One-Side Sampling} (GOSS) and \emph{Exclusive Feature Bundling} (EFB). With GOSS, we exclude a significant proportion of data instances with small gradients, and only use the rest to estimate the information gain. We prove that, since the data instances with larger gradients play a more important role in the computation of information gain, GOSS can obtain quite accurate estimation of the information gain with a much smaller data size. With EFB, we bundle mutually exclusive features (i. e. , they rarely take nonzero values simultaneously), to reduce the number of features. We prove that finding the optimal bundling of exclusive features is NP-hard, but a greedy algorithm can achieve quite good approximation ratio (and thus can effectively reduce the number of features without hurting the accuracy of split point determination by much). We call our new GBDT implementation with GOSS and EFB \emph{LightGBM}. Our experiments on multiple public datasets show that, LightGBM speeds up the training process of conventional GBDT by up to over 20 times while achieving almost the same accuracy.

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NeurIPS Conference 2016 Conference Paper

A Communication-Efficient Parallel Algorithm for Decision Tree

Qi Meng
Guolin Ke
Taifeng Wang
Wei Chen
Qiwei Ye
Zhi-Ming Ma
Tie-Yan Liu

Decision tree (and its extensions such as Gradient Boosting Decision Trees and Random Forest) is a widely used machine learning algorithm, due to its practical effectiveness and model interpretability. With the emergence of big data, there is an increasing need to parallelize the training process of decision tree. However, most existing attempts along this line suffer from high communication costs. In this paper, we propose a new algorithm, called \emph{Parallel Voting Decision Tree (PV-Tree)}, to tackle this challenge. After partitioning the training data onto a number of (e. g. , $M$) machines, this algorithm performs both local voting and global voting in each iteration. For local voting, the top-$k$ attributes are selected from each machine according to its local data. Then, the indices of these top attributes are aggregated by a server, and the globally top-$2k$ attributes are determined by a majority voting among these local candidates. Finally, the full-grained histograms of the globally top-$2k$ attributes are collected from local machines in order to identify the best (most informative) attribute and its split point. PV-Tree can achieve a very low communication cost (independent of the total number of attributes) and thus can scale out very well. Furthermore, theoretical analysis shows that this algorithm can learn a near optimal decision tree, since it can find the best attribute with a large probability. Our experiments on real-world datasets show that PV-Tree significantly outperforms the existing parallel decision tree algorithms in the tradeoff between accuracy and efficiency.

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