My Nguyen

Brydon P. G. Wall, My Nguyen, J. Chuck Harrell et al.

Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.

Minh Ngoc Ta, Dong Cao Van, Duc-Anh Hoang et al.

The growing collaboration between humans and AI models in generative tasks has introduced new challenges in distinguishing between human-written, LLM-generated, and human--LLM collaborative texts. In this work, we collect a multilingual, multi-domain, multi-generator dataset FAIDSet. We further introduce a fine-grained detection framework FAID to classify text into these three categories, and also to identify the underlying LLM family of the generator. Unlike existing binary classifiers, FAID is built to capture both authorship and model-specific characteristics. Our method combines multi-level contrastive learning with multi-task auxiliary classification to learn subtle stylistic cues. By modeling LLM families as distinct stylistic entities, we incorporate an adaptation to address distributional shifts without retraining for unseen data. Our experimental results demonstrate that FAID outperforms several baselines, particularly enhancing the generalization accuracy on unseen domains and new LLMs, thus offering a potential solution for improving transparency and accountability in AI-assisted writing.