Related papers: BioT5+: Towards Generalized Biological Understandi…

Generative artificial intelligence (GenAI) has become a transformative approach in bioinformatics that often enables advancements in genomics, proteomics, transcriptomics, structural biology, and drug discovery. To systematically identify…

In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation…

Recent advances in large language models (LLMs) and biomedical foundation models (BioFMs) have achieved strong results in biological text reasoning, molecular modeling, and single-cell analysis, yet they remain siloed in disjoint embedding…

Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem…

Automated retinal image medical description generation is crucial for streamlining medical diagnosis and treatment planning. Existing challenges include the reliance on learned retinal image representations, difficulties in handling…

A substantial proportion (45\%) of maternal deaths, neonatal deaths, and stillbirths occur during the intrapartum phase, with a particularly high burden in low- and middle-income countries. Intrapartum biometry plays a critical role in…

Background and Objective: Biomedical Named Entity Recognition (BioNER) is a foundational task in medical informatics, crucial for downstream applications like drug discovery and clinical trial matching. However, adapting general-domain…

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in…

Prompt learning has become a prevalent strategy for adapting vision-language foundation models (VLMs) such as CLIP to downstream tasks. With the emergence of large language models (LLMs), recent studies have explored the potential of using…

Multi-instrument music transcription aims to convert polyphonic music recordings into musical scores assigned to each instrument. This task is challenging for modeling as it requires simultaneously identifying multiple instruments and…

The accelerated evolution of large language models has raised questions about their comparative performance across domains of practical importance. GPT-4 by OpenAI introduced advances in reasoning, multimodality, and task generalization,…

Agentic AI is rapidly advancing in healthcare and biomedical research. However, in medical image analysis, their performance and adoption remain limited due to the lack of a robust ecosystem, insufficient toolsets, and the absence of…

Instruction fine-tuned language models on a collection of instruction annotated datasets (FLAN) have shown highly effective to improve model performance and generalization to unseen tasks. However, a majority of standard parsing tasks…

Large Language Models have demonstrated remarkable capabilities in generating contextually relevant and grammatically correct text. However, they fundamentally lack the ability to process and respond to emotional context in a manner…

Software is constantly changing, requiring developers to perform several derived tasks in a timely manner, such as writing a description for the intention of the code change, or identifying the defect-prone code changes. Considering that…

Tracking individual cells in live-cell imaging provides fundamental insights, inevitable for studying causes and consequences of phenotypic heterogeneity, responses to changing environmental conditions or stressors. Microbial cell tracking,…

Motivated by the success of T5 (Text-To-Text Transfer Transformer) in pre-trained natural language processing models, we propose a unified-modal SpeechT5 framework that explores the encoder-decoder pre-training for self-supervised…

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive…

Using machine learning, especially deep learning, to facilitate biological research is a fascinating research direction. However, in addition to the standard classification or regression problems, in bioinformatics, we often need to predict…

Detecting user interface (UI) controls from software screenshots is a critical task for automated testing, accessibility, and software analytics, yet it remains challenging due to visual ambiguities, design variability, and the lack of…