Yao Ma

Kangyu Zheng, Yingzhou Lu, Zaixi Zhang et al.

Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning. While existing works have typically focused on comparing models within a single algorithmic category, cross-algorithm comparisons remain scarce. In this paper, to fill the gap, we establish a benchmark to evaluate the performance of sixteen models across these different algorithmic foundations by assessing the pharmaceutical properties of the generated molecules and their docking affinities with specified target proteins. We highlight the unique advantages of each algorithmic approach and offer recommendations for the design of future SBDD models. We emphasize that 1D/2D ligand-centric drug design methods can be used in SBDD by treating the docking function as a black-box oracle, which is typically neglected. The empirical results show that 1D/2D methods achieve competitive performance compared with 3D-based methods that use the 3D structure of the target protein explicitly. Also, AutoGrow4, a 2D molecular graph-based genetic algorithm, dominates SBDD in terms of optimization ability. The relevant code is available in https://github.com/zkysfls/2024-sbdd-benchmark.

Xuwei Tan, Yao Ma, Xueru Zhang

Detecting fraud in financial transactions typically relies on tabular models that demand heavy feature engineering to handle high-dimensional data and offer limited interpretability, making it difficult for humans to understand predictions. Large Language Models (LLMs), in contrast, can produce human-readable explanations and facilitate feature analysis, potentially reducing the manual workload of fraud analysts and informing system refinements. However, they perform poorly when applied directly to tabular fraud detection due to the difficulty of reasoning over many features, the extreme class imbalance, and the absence of contextual information. To bridge this gap, we introduce FinFRE-RAG, a two-stage approach that applies importance-guided feature reduction to serialize a compact subset of numeric/categorical attributes into natural language and performs retrieval-augmented in-context learning over label-aware, instance-level exemplars. Across four public fraud datasets and three families of open-weight LLMs, FinFRE-RAG substantially improves F1/MCC over direct prompting and is competitive with strong tabular baselines in several settings. Although these LLMs still lag behind specialized classifiers, they narrow the performance gap and provide interpretable rationales, highlighting their value as assistive tools in fraud analysis.

Qian Ma, Hongliang Chi, Hengrui Zhang et al.

The rise of self-supervised learning, which operates without the need for labeled data, has garnered significant interest within the graph learning community. This enthusiasm has led to the development of numerous Graph Contrastive Learning (GCL) techniques, all aiming to create a versatile graph encoder that leverages the wealth of unlabeled data for various downstream tasks. However, the current evaluation standards for GCL approaches are flawed due to the need for extensive hyper-parameter tuning during pre-training and the reliance on a single downstream task for assessment. These flaws can skew the evaluation away from the intended goals, potentially leading to misleading conclusions. In our paper, we thoroughly examine these shortcomings and offer fresh perspectives on how GCL methods are affected by hyper-parameter choices and the choice of downstream tasks for their evaluation. Additionally, we introduce an enhanced evaluation framework designed to more accurately gauge the effectiveness, consistency, and overall capability of GCL methods.