Related papers: Language-Enhanced Representation Learning for Sing…

Sequential sentence classification (SSC) in scientific publications is crucial for supporting downstream tasks such as fine-grained information retrieval and extractive summarization. However, current SSC methods are constrained by model…

This paper presents a novel training method, Conditional Masked Language Modeling (CMLM), to effectively learn sentence representations on large scale unlabeled corpora. CMLM integrates sentence representation learning into MLM training by…

Accurate and scalable cell type annotation remains a challenge in single-cell transcriptomics, especially when datasets exhibit strong batch effects or contain previously unseen cell populations. Here we introduce SpikGPT, a hybrid deep…

Spatial transcriptomics (ST) is an emerging technology that enables researchers to investigate the molecular relationships underlying tissue morphology. However, acquiring ST data remains prohibitively expensive, and traditional fixed-grid…

Single-cell multi-omics (scMulti-omics) refers to the paired multimodal data, such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), where the regulation of each cell was measured from different modalities, i.e.…

As a fundamental task in Information Retrieval and Computational Linguistics, sentence representation has profound implications for a wide range of practical applications such as text clustering, content analysis, question-answering…

Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research, as it enables the precise characterization of cellular heterogeneity. However, manual manipulation of various tools to achieve desired outcomes can be…

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that…

Multimodal Large Language Models (MLLMs) have achieved notable success in enhancing translation performance by integrating multimodal information. However, existing research primarily focuses on image-guided methods, whose applicability is…

Speech representations learned from Self-supervised learning (SSL) models can benefit various speech processing tasks. However, utilizing SSL representations usually requires fine-tuning the pre-trained models or designing task-specific…

Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional…

We present scPilot, the first systematic framework to practice omics-native reasoning: a large language model (LLM) converses in natural language while directly inspecting single-cell RNA-seq data and on-demand bioinformatics tools. scPilot…

Sequential Recommender Systems (SRS), which model a user's interaction history to predict the next item of interest, are widely used in various applications. However, existing SRS often struggle with low-popularity items, a challenge known…

Knowledge distillation plays a key role in compressing the Large Language Models (LLMs), which boosts a small-size student model under large teacher models' guidance. However, existing LLM distillation methods overly rely on…

Humans interpret and perceive the world by integrating sensory information from multiple modalities, such as vision and hearing. Spiking Neural Networks (SNNs), as brain-inspired computational models, exhibit unique advantages in emulating…

Traditional Automated Speaking Assessment (ASA) systems exhibit inherent modality limitations: text-based approaches lack acoustic information while audio-based methods miss semantic context. Multimodal Large Language Models (MLLM) offer…

Self-Supervised Learning (SSL) methods harness the concept of semantic invariance by utilizing data augmentation strategies to produce similar representations for different deformations of the same input. Essentially, the model captures the…

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling,…

In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become…

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex…