Related papers: PPI2Text: Captioning Protein-Protein Interactions …
Current protein language models (pLMs) predominantly focus on single-chain protein sequences and often have not accounted for constraints on generative design imposed by protein-protein interactions. To address this gap, we present paired…
Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement…
Visual Question Answering (VQA) within the surgical domain, utilizing Large Language Models (LLMs), offers a distinct opportunity to improve intra-operative decision-making and facilitate intuitive surgeon-AI interaction. However, the…
Natural language sentence matching is the task of comparing two sentences and identifying the relationship between them.It has a wide range of applications in natural language processing tasks such as reading comprehension, question and…
The development of large language models (LLMs) has greatly advanced the field of multimodal understanding, leading to the emergence of large multimodal models (LMMs). In order to enhance the level of visual comprehension, recent studies…
Large Multimodal Models (LMMs) are increasingly applied to scientific research, yet it remains unclear whether they can reliably understand and reason over the multimodal complexity of papers. A central challenge lies in detecting and…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
The detection of Personally Identifiable Information (PII) is critical for privacy compliance but remains challenging in low-resource languages due to linguistic diversity and limited annotated data. We present RECAP, a hybrid framework…
Representation learning for protein biochemical space faces a difficult trade-off: protein language models excel at capturing long-range biological semantics but often miss fine-grained chemical details. Conversely, chemical language models…
The task of image captioning demands an algorithm to generate natural language descriptions of visual inputs. Recent advancements have seen a convergence between image captioning research and the development of Large Language Models (LLMs)…
This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron…
Recently, large-scale visual language pre-trained (VLP) models have demonstrated impressive performance across various downstream tasks. Motivated by these advancements, pioneering efforts have emerged in multi-label image recognition with…
In Track-1 of the BioCreative VII Challenge participants are asked to identify interactions between drugs/chemicals and proteins. In-context named entity annotations for each drug/chemical and protein are provided and one of fourteen…
Large language models (LLMs) are renowned for their extensive linguistic knowledge and strong generalization capabilities, but their high computational demands make them unsuitable for resource-constrained environments. In contrast, small…
(Renyi Qu's Master's Thesis) Recent advancements in interpretable models for vision-language tasks have achieved competitive performance; however, their interpretability often suffers due to the reliance on unstructured text outputs from…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
The alignment of protein-protein interaction (PPI) networks has many applications, such as the detection of conserved biological network motifs, the prediction of protein interactions, and the reconstruction of phylogenetic trees [1, 2, 3].…
Qualitative analysis of textual contents unpacks rich and valuable information by assigning labels to the data. However, this process is often labor-intensive, particularly when working with large datasets. While recent AI-based tools…
Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we…
The widespread adoption of Large Language Models (LLMs) has raised significant privacy concerns regarding the exposure of personally identifiable information (PII) in user prompts. To address this challenge, we propose a query-unrelated PII…