Guirong Xue

Huinan Xu, Xuyang Feng, Junhong Chen et al.

Current genomic foundation models (GFMs) rely on extensive neural computation to implicitly approximate conserved biological motifs from single-nucleotide inputs. We propose Gengram, a conditional memory module that introduces an explicit and highly efficient lookup primitive for multi-base motifs via a genomic-specific hashing scheme, establishing genomic "syntax". Integrated into the backbone of state-of-the-art GFMs, Gengram achieves substantial gains (up to 14%) across several functional genomics tasks. The module demonstrates robust architectural generalization, while further inspection of Gengram's latent space reveals the emergence of meaningful representations that align closely with fundamental biological knowledge. By establishing structured motif memory as a modeling primitive, Gengram simultaneously boosts empirical performance and mechanistic interpretability, providing a scalable and biology-aligned pathway for the next generation of GFMs. The code is available at https://github.com/zhejianglab/Genos, and the model checkpoint is available at https://huggingface.co/ZhejiangLab/Gengram.

Xiaosheng Zhao, Yang Huang, Guirong Xue et al.

In recent years, large language models (LLMs) have transformed natural language understanding through vast datasets and large-scale parameterization. Inspired by this success, we present SpecCLIP, a foundation model framework that extends LLM-inspired methodologies to stellar spectral analysis. Stellar spectra, akin to structured language, encode rich physical and chemical information about stars. By training foundation models on large-scale spectral datasets, our goal is to learn robust and informative embeddings that support diverse downstream applications. As a proof of concept, SpecCLIP involves pre-training on two spectral types--LAMOST low-resolution and Gaia XP--followed by contrastive alignment using the CLIP (Contrastive Language-Image Pre-training) framework, adapted to associate spectra from different instruments. This alignment is complemented by auxiliary decoders that preserve spectrum-specific information and enable translation (prediction) between spectral types, with the former achieved by maximizing mutual information between embeddings and input spectra. The result is a cross-spectrum framework enabling intrinsic calibration and flexible applications across instruments. We demonstrate that fine-tuning these models on moderate-sized labeled datasets improves adaptability to tasks such as stellar-parameter estimation and chemical-abundance determination. SpecCLIP also enhances the accuracy and precision of parameter estimates benchmarked against external survey data. Additionally, its similarity search and cross-spectrum prediction capabilities offer potential for anomaly detection. Our results suggest that contrastively trained foundation models enriched with spectrum-aware decoders can advance precision stellar spectroscopy.

Shiyu Shen, Bin Pan, Guirong Xue

City-scale traffic volume prediction plays a pivotal role in intelligent transportation systems, yet remains a challenge due to the inherent incompleteness and bias in observational data. Although deep learning-based methods have shown considerable promise, most existing approaches produce deterministic point estimates, thereby neglecting the uncertainty arising from unobserved traffic flows. Furthermore, current models are typically trained in a city-specific manner, which hinders their generalizability and limits scalability across diverse urban contexts. To overcome these limitations, we introduce TrafficPPT, a Pretrained Probabilistic Transformer designed to model traffic volume as a distributional aggregation of trajectories. Our framework fuses heterogeneous data sources-including real-time observations, historical trajectory data, and road network topology-enabling robust and uncertainty-aware traffic inference. TrafficPPT is initially pretrained on large-scale simulated data spanning multiple urban scenarios, and later fine-tuned on target cities to ensure effective domain adaptation. Experiments on real-world datasets show that TrafficPPT consistently surpasses state-of-the-art baselines, particularly under conditions of extreme data sparsity. Code will be open.