20 accepted papers
Accurate prediction of nuclear magnetic resonance (NMR) chemical shifts is fundamental to spectral analysis and molecular structure elucidation, yet existing machine learning methods rely on limited, labor-intensive atom-assigned datasets. We propose a semi-supervised framework that learns NMR chemi…
Autoregressive (AR) models are promising for image generation, yet continuous-token AR variants often trail latent diffusion and masked-generation models. The core issue is heterogeneous variance in VAE latents, which is amplified during AR decoding, especially under classifier-free guidance (CFG),…
Recent advances in few-step diffusion models have demonstrated their efficiency and effectiveness by shortcutting the probabilistic paths of diffusion models, especially in training one-step diffusion models from scratch (a.k.a. shortcut models). However, their theoretical derivation and practical i…
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 co…
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,…
Recent breakthroughs in Large Language Models (LLMs) have revolutionized scientific literature analysis. However, existing benchmarks fail to adequately evaluate the proficiency of LLMs in this domain, particularly in scenarios requiring higher-level abilities beyond mere memorization and the handli…
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…
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…
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 screening…
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…
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 in…
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…
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.…
Dense retrieval requires high-quality text sequence embeddings to support effective search in the representation space. Autoencoder-based language models are appealing in dense retrieval as they train the encoder to output high-quality embedding that can reconstruct the input texts. However, in this…
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 bri…
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 Tr…
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…
High-resolution digital images are usually downscaled to fit various display screens or save the cost of storage and bandwidth, meanwhile the post-upscaling is adpoted to recover the original resolutions or the details in the zoom-in images. However, typical image downscaling is a non-injective mapp…
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 th…
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…