Xiao Fei

Sarah Almeida Carneiro, Christos Xypolopoulos, Xiao Fei et al.

We introduce CARTE 1 (Culturally Anchored Regional-Territorial Evaluation), a multiplechoice benchmark for evaluating the ability of large language models (LLMs) to perform fine-grained reasoning over geographically grounded and regionally differentiated knowledge within France. While prior benchmarks focus on national-level cultural understanding, they largely overlook intra-country variation and the need to distinguish between closely related regional contexts. CARTE addresses this gap by introducing 2,431 questions spanning the 13 metropolitan regions of France and covering 14 thematic domains, including culture, language, demographics, economy, environment, and mobility. We further introduce CARTE-LV, a subset targeting Linguistic Variation across French regions, enabling focused evaluation of language-related differences. We evaluate 27 LLMs ranging from 1B to 12B parameters under few-shot settings. Our experiments reveal performance disparities across regions and model scales, suggesting systematic gaps in pretraining coverage and limited robustness to intra-national variation.

Xiao Fei, Philippe Martins, Jialiang Lu

The classification of fifth-generation New-Radio (5G-NR) mobile network traffic is an emerging topic in the field of telecommunications. It can be utilized for quality of service (QoS) management and dynamic resource allocation. However, traditional approaches such as Deep Packet Inspection (DPI) can not be directly applied to encrypted data flows. Therefore, new real-time encrypted traffic classification algorithms need to be investigated to handle dynamic transmission. In this study, we examine the real-time encrypted 5G Non-Standalone (NSA) application-level traffic classification using physical channel records. Due to the vastness of their features, decision-tree-based gradient boosting algorithms are a viable approach for classification. We generate a noise-limited 5G NSA trace dataset with traffic from multiple applications. We develop a new pipeline to convert sequences of physical channel records into numerical vectors. A set of machine learning models are tested, and we propose our solution based on Light Gradient Boosting Machine (LGBM) due to its advantages in fast parallel training and low computational burden in practical scenarios. Our experiments demonstrate that our algorithm can achieve 95% accuracy on the classification task with a state-of-the-art response time as quick as 10ms.

Xiao Fei, Sarah Almeida Carneiro, Yang Zhang et al.

Protein-protein interaction (PPI) modeling has been widely studied as a binary or multi-label classification task. While emerging multimodal large language models (LLMs) can now describe single proteins, they remain unable to generate free-form descriptions of interactions between protein pairs. Moving beyond controlled vocabulary annotations, we propose to model PPI using free-text description, enabling richer expressiveness, improved interpretability, and better integration with literature knowledge base. We present PPI2Text, a multimodal LLM for free-form PPI captioning from amino acid sequences, that encodes each protein using ESM3 encoder, constructs a pair map from the two representations to capture interactions across all residue pairs, and autoregressively generates descriptions using a Qwen3 language decoder. We further introduce PaCo-RoPE, a coordinate-aligned positional encoding that aligns each axis of the pair grid with the residue positions of the corresponding protein. In addition, we release PPI2Text-Dataset, a 351k-pair corpus of free-form PPI descriptions aggregated from ten curated biological databases and further synthesized with Gemini under evidence-tiered prompting. PPI2Text consistently outperforms strong baselines across multiple ablation settings and evaluation protocols. It not only achieves higher scores on linguistic metrics against synthesized references, but also excels on factuality metrics, where an LLM-based judge evaluates outputs against raw biological evidence.

Christos Xypolopoulos, Guokan Shang, Xiao Fei et al.

Large language models have evolved to process multiple modalities beyond text, such as images and audio, which motivates us to explore how to effectively leverage them for graph reasoning tasks. The key question, therefore, is how to transform graphs into linear sequences of tokens, a process we term "graph linearization", so that LLMs can handle graphs naturally. We consider that graphs should be linearized meaningfully to reflect certain properties of natural language text, such as local dependency and global alignment, in order to ease contemporary LLMs, trained on trillions of textual tokens, better understand graphs. To achieve this, we developed several graph linearization methods based on graph centrality and degeneracy. These methods are further enhanced using node relabeling techniques. The experimental results demonstrate the effectiveness of our methods compared to the random linearization baseline. Our work introduces novel graph representations suitable for LLMs, contributing to the potential integration of graph machine learning with the trend of multimodal processing using a unified transformer model.

Oussama Kharouiche, Aris Markogiannakis, Xiao Fei et al.

Single-cell RNA sequencing has transformed biology by enabling the measurement of gene expression at cellular resolution, providing information for cell types, states, and disease contexts. Recently, single-cell foundation models have emerged as powerful tools for learning transferable representations directly from expression profiles, improving performance on classification and clustering tasks. However, these models are limited to discrete prediction heads, which collapse cellular complexity into predefined labels that fail to capture the richer, contextual explanations biologists need. We introduce Cell2Text, a multimodal generative framework that translates scRNA-seq profiles into structured natural language descriptions. By integrating gene-level embeddings from single-cell foundation models with pretrained large language models, Cell2Text generates coherent summaries that capture cellular identity, tissue origin, disease associations, and pathway activity, generalizing to unseen cells. Empirically, Cell2Text outperforms baselines on classification accuracy, demonstrates strong ontological consistency using PageRank-based similarity metrics, and achieves high semantic fidelity in text generation. These results demonstrate that coupling expression data with natural language offers both stronger predictive performance and inherently interpretable outputs, pointing to a scalable path for label-efficient characterization of unseen cells.