Liang Zeng

Lanqing Li, Liang Zeng, Ziqi Gao et al.

The last decade has witnessed a prosperous development of computational methods and dataset curation for AI-aided drug discovery (AIDD). However, real-world pharmaceutical datasets often exhibit highly imbalanced distribution, which is overlooked by the current literature but may severely compromise the fairness and generalization of machine learning applications. Motivated by this observation, we introduce ImDrug, a comprehensive benchmark with an open-source Python library which consists of 4 imbalance settings, 11 AI-ready datasets, 54 learning tasks and 16 baseline algorithms tailored for imbalanced learning. It provides an accessible and customizable testbed for problems and solutions spanning a broad spectrum of the drug discovery pipeline such as molecular modeling, drug-target interaction and retrosynthesis. We conduct extensive empirical studies with novel evaluation metrics, to demonstrate that the existing algorithms fall short of solving medicinal and pharmaceutical challenges in the data imbalance scenario. We believe that ImDrug opens up avenues for future research and development, on real-world challenges at the intersection of AIDD and deep imbalanced learning.

Liang Zeng, Lanqing Li, Ziqi Gao et al.

Graph contrastive learning (GCL) has attracted a surge of attention due to its superior performance for learning node/graph representations without labels. However, in practice, the underlying class distribution of unlabeled nodes for the given graph is usually imbalanced. This highly imbalanced class distribution inevitably deteriorates the quality of learned node representations in GCL. Indeed, we empirically find that most state-of-the-art GCL methods cannot obtain discriminative representations and exhibit poor performance on imbalanced node classification. Motivated by this observation, we propose a principled GCL framework on Imbalanced node classification (ImGCL), which automatically and adaptively balances the representations learned from GCL without labels. Specifically, we first introduce the online clustering based progressively balanced sampling (PBS) method with theoretical rationale, which balances the training sets based on pseudo-labels obtained from learned representations in GCL. We then develop the node centrality based PBS method to better preserve the intrinsic structure of graphs, by upweighting the important nodes of the given graph. Extensive experiments on multiple imbalanced graph datasets and imbalanced settings demonstrate the effectiveness of our proposed framework, which significantly improves the performance of the recent state-of-the-art GCL methods. Further experimental ablations and analyses show that the ImGCL framework consistently improves the representation quality of nodes in under-represented (tail) classes.

Liang Zeng, Attila Lengyel, Nergis Tömen et al.

In this work, we leverage estimated depth to boost self-supervised contrastive learning for segmentation of urban scenes, where unlabeled videos are readily available for training self-supervised depth estimation. We argue that the semantics of a coherent group of pixels in 3D space is self-contained and invariant to the contexts in which they appear. We group coherent, semantically related pixels into coherent depth regions given their estimated depth and use copy-paste to synthetically vary their contexts. In this way, cross-context correspondences are built in contrastive learning and a context-invariant representation is learned. For unsupervised semantic segmentation of urban scenes, our method surpasses the previous state-of-the-art baseline by +7.14% in mIoU on Cityscapes and +6.65% on KITTI. For fine-tuning on Cityscapes and KITTI segmentation, our method is competitive with existing models, yet, we do not need to pre-train on ImageNet or COCO, and we are also more computationally efficient. Our code is available on https://github.com/LeungTsang/CPCDR

He Wang, Liang Zeng

Automated algorithm discovery in scientific computing faces fundamental challenges: vast design spaces with expensive evaluations, domain-specific physical constraints requiring expert knowledge, and the necessity for interpretable solutions that scientists can validate and understand. We present the Evo-MCTS (Evolutionary Monte Carlo Tree Search) framework, integrating large language models (LLMs) with tree-structured evolutionary search for interpretable algorithm discovery. Evo-MCTS combines reflective code synthesis leveraging LLM domain knowledge, multi-scale evolutionary operations on structured code representations, and interpretable algorithmic pathways emerging from tree-guided exploration. When applied to gravitational wave detection-a challenging domain with continuous parameter spaces and strict physical constraints-Evo-MCTS achieves 20.2% improvement over domain-specific methods and 59.1% over LLM-based optimization frameworks. This improvement arises from its ability to consistently converge toward interpretable algorithmic structures that integrate multiple functional components. Our domain-agnostic architecture establishes a generalizable methodology for automated algorithm discovery in scientific computing, where algorithmic transparency and physical validity are as essential as performance optimization.

Liang Zeng, Lanqing Li, Jian Li

How to effectively represent molecules is a long-standing challenge for molecular property prediction and drug discovery. This paper studies this problem and proposes to incorporate chemical domain knowledge, specifically related to chemical reactions, for learning effective molecular representations. However, the inherent cross-modality property between chemical reactions and molecules presents a significant challenge to address. To this end, we introduce a novel method, namely MolKD, which Distills cross-modal Knowledge in chemical reactions to assist Molecular property prediction. Specifically, the reaction-to-molecule distillation model within MolKD transfers cross-modal knowledge from a pre-trained teacher network learning with one modality (i.e., reactions) into a student network learning with another modality (i.e., molecules). Moreover, MolKD learns effective molecular representations by incorporating reaction yields to measure transformation efficiency of the reactant-product pair when pre-training on reactions. Extensive experiments demonstrate that MolKD significantly outperforms various competitive baseline models, e.g., 2.1% absolute AUC-ROC gain on Tox21. Further investigations demonstrate that pre-trained molecular representations in MolKD can distinguish chemically reasonable molecular similarities, which enables molecular property prediction with high robustness and interpretability.

Yuchen Fang, Yanjun Qin, Haiyong Luo et al.

Traffic forecasting is crucial for public safety and resource optimization, yet is very challenging due to three aspects: i) current existing works mostly exploit intricate temporal patterns (e.g., the short-term thunderstorm and long-term daily trends) within a single method, which fail to accurately capture spatio-temporal dependencies under different schemas; ii) the under-exploration of the graph positional encoding limit the extraction of spatial information in the commonly used full graph attention network; iii) the quadratic complexity of the full graph attention introduces heavy computational needs. To achieve the effective traffic flow forecasting, we propose an efficient spectral graph attention network with disentangled traffic sequences. Specifically, the discrete wavelet transform is leveraged to obtain the low- and high-frequency components of traffic sequences, and a dual-channel encoder is elaborately designed to accurately capture the spatio-temporal dependencies under long- and short-term schemas of the low- and high-frequency components. Moreover, a novel wavelet-based graph positional encoding and a query sampling strategy are introduced in our spectral graph attention to effectively guide message passing and efficiently calculate the attention. Extensive experiments on four real-world datasets show the superiority of our model, i.e., the higher traffic forecasting precision with lower computational cost.

Liang Zeng, Lei Wang, Hui Niu et al.

Price movement forecasting, aimed at predicting financial asset trends based on current market information, has achieved promising advancements through machine learning (ML) methods. Most existing ML methods, however, struggle with the extremely low signal-to-noise ratio and stochastic nature of financial data, often mistaking noises for real trading signals without careful selection of potentially profitable samples. To address this issue, we propose LARA, a novel price movement forecasting framework with two main components: Locality-Aware Attention (LA-Attention) and Iterative Refinement Labeling (RA-Labeling). (1) LA-Attention, enhanced by metric learning techniques, automatically extracts the potentially profitable samples through masked attention scheme and task-specific distance metrics. (2) RA-Labeling further iteratively refines the noisy labels of potentially profitable samples, and combines the learned predictors robust to the unseen and noisy samples. In a set of experiments on three real-world financial markets: stocks, cryptocurrencies, and ETFs, LARA significantly outperforms several machine learning based methods on the Qlib quantitative investment platform. Extensive ablation studies confirm LARA's superior ability in capturing more reliable trading opportunities.