In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available in huggingface.

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.

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.

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.

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.

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.

Shuqi Lu, Di He, Chenyan Xiong, Guolin Ke, Waleed Malik, Zhicheng Dou, Paul Bennett, Tie-Yan Liu, Arnold Overwijk. Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing. 2021.

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}.

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.

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}.

For a target task where the labeled data are unavailable, domain adaptation can transfer a learner from a different source domain. Previous deep domain adaptation methods mainly learn a global domain shift, i.e., align the global source and target distributions without considering the relationships between two subdomains within the same category of different domains, leading to unsatisfying transfer learning performance without capturing the fine-grained information. Recently, more and more researchers pay attention to subdomain adaptation that focuses on accurately aligning the distributions of the relevant subdomains. However, most of them are adversarial methods that contain several loss functions and converge slowly. Based on this, we present a deep subdomain adaptation network (DSAN) that learns a transfer network by aligning the relevant subdomain distributions of domain-specific layer activations across different domains based on a local maximum mean discrepancy (LMMD). Our DSAN is very simple but effective, which does not need adversarial training and converges fast. The adaptation can be achieved easily with most feedforward network models by extending them with LMMD loss, which can be trained efficiently via backpropagation. Experiments demonstrate that DSAN can achieve remarkable results on both object recognition tasks and digit classification tasks. Our code will be available at https://github.com/easezyc/deep-transfer-learning.

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 drastically-reduced 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 Multi-segment 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.

Online prediction has become one of the most essential tasks in many real-world applications. Two main characteristics of typical online prediction tasks include tabular input space and online data generation. Specifically, tabular input space indicates the existence of both sparse categorical features and dense numerical ones, while online data generation implies continuous task-generated data with potentially dynamic distribution. Consequently, effective learning with tabular input space as well as fast adaption to online data generation become two vital challenges for obtaining the online prediction model. Although Gradient Boosting Decision Tree (GBDT) and Neural Network (NN) have been widely used in practice, either of them yields their own weaknesses. Particularly, GBDT can hardly be adapted to dynamic online data generation, and it tends to be ineffective when facing sparse categorical features; NN, on the other hand, is quite difficult to achieve satisfactory performance when facing dense numerical features. In this paper, we propose a new learning framework, DeepGBM, which integrates the advantages of the both NN and GBDT by using two corresponding NN components: (1) CatNN, focusing on handling sparse categorical features. (2) GBDT2NN, focusing on dense numerical features with distilled knowledge from GBDT. Powered by these two components, DeepGBM can leverage both categorical and numerical features while retaining the ability of efficient online update. Comprehensive experiments on a variety of publicly available datasets have demonstrated that DeepGBM can outperform other well-recognized baselines in various online prediction tasks.

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.

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.