Honggang Wen

Zongru Li, Xingsheng Chen, Honggang Wen et al.

Molecular property prediction integrates quantum chemistry, cheminformatics, and deep learning to connect molecular structure with physicochemical and biological behavior. This survey traces four complementary paradigms, including Quantum, Descriptor Machine Learning, Geometric Deep Learning, and Foundation Models, and outlines a unified taxonomy linking molecular representations, model architectures, and interdisciplinary applications. Benchmark analyses integrate evidence from both widely used datasets and datasets reflecting industry perspectives, encompassing quantum, physicochemical, physiological, and biophysical domains. The survey examines current standards in data curation, splitting strategies, and evaluation protocols, highlighting challenges including inconsistent stereochemistry, heterogeneous assay sources, and reproducibility limitations under random or poorly defined splits. These observations motivate the modernization of benchmark design toward more transparent, time- and scaffold-aware methodologies. We further propose three forward-looking directions: (i) physics-aware learning embedding quantum consistency, (ii) uncertainty-calibrated foundation models for trustworthy inference, and (iii) realistic multimodal benchmark ecosystems integrating computational and experimental data. Repository: https://github.com/Zongru-Li/Survey-and-Benchmarks-of-DL-for-Molecular-Property-Prediction-in-the-Foundation-Model-Era.

Qianru Zhang, Honggang Wen, Ming Li et al.

Time series forecasting requires architectures that simultaneously achieve three competing objectives: (1) strict temporal causality for reliable predictions, (2) sub-quadratic complexity for practical scalability, and (3) multi-scale pattern recognition for accurate long-horizon forecasting. We introduce AutoHFormer, a hierarchical autoregressive transformer that addresses these challenges through three key innovations: 1) Hierarchical Temporal Modeling: Our architecture decomposes predictions into segment-level blocks processed in parallel, followed by intra-segment sequential refinement. This dual-scale approach maintains temporal coherence while enabling efficient computation. 2) Dynamic Windowed Attention: The attention mechanism employs learnable causal windows with exponential decay, reducing complexity while preserving precise temporal relationships. This design avoids both the anti-causal violations of standard transformers and the sequential bottlenecks of RNN hybrids. 3) Adaptive Temporal Encoding: a novel position encoding system is adopted to capture time patterns at multiple scales. It combines fixed oscillating patterns for short-term variations with learnable decay rates for long-term trends. Comprehensive experiments demonstrate that AutoHFormer 10.76X faster training and 6.06X memory reduction compared to PatchTST on PEMS08, while maintaining consistent accuracy across 96-720 step horizons in most of cases. These breakthroughs establish new benchmarks for efficient and precise time series modeling. Implementations of our method and all baselines in hierarchical autoregressive mechanism are available at https://github.com/lizzyhku/Autotime.

Regina Zhang, Zongru Li, Honggang Wen et al.

Forecasting systems in science must be accurate, physically consistent, and certifiably reliable. Most existing models address prediction, constraint enforcement, and verification separately, limiting scalability and interpretability. We introduce GeoCert, a geometric AI framework that unifies forecasting, physical reasoning, and formal verification within a single differentiable computation. GeoCert formulates forecasting as evolution along a hyperbolic manifold, where negative curvature induces contraction dynamics, intrinsic robustness, and logarithmic-time certification. A hierarchical constraint architecture separates universal physical laws from domain-specific dynamics, enabling certified generalization across energy, climate, finance, and transportation systems. GeoCert achieves state-of-the-art accuracy while reducing computational cost by 97.5% and maintaining better certification rates. By embedding verification into the geometry of learning, GeoCert transforms forecasting from empirical approximation to formally verified inference, offering a scalable foundation for trustworthy, reproducible, and physically grounded scientific AI.

Qianru Zhang, Yuting Sun, Honggang Wen et al.

Frequency-domain analysis has emerged as a powerful paradigm for time series analysis, offering unique advantages over traditional time-domain approaches while introducing new theoretical and practical challenges. This survey provides a comprehensive examination of spectral methods from classical Fourier analysis to modern neural operators, systematically summarizing three open challenges in current research: (1) causal structure preservation during spectral transformations, (2) uncertainty quantification in learned frequency representations, and (3) topology-aware analysis for non-Euclidean data structures. Through rigorous reviewing of over 100 studies, we develop a unified taxonomy that bridges conventional spectral techniques with cutting-edge machine learning approaches, while establishing standardized benchmarks for performance evaluation. Our work identifies key knowledge gaps in the field, particularly in geometric deep learning and quantum-enhanced spectral analysis. The survey offers practitioners a systematic framework for method selection and implementation, while charting promising directions for future research in this rapidly evolving domain.