Related papers: PROTOCOL: Late Interaction Retrieval for Protein H…

Unlocking the next generation of biotechnology and therapeutic innovation demands overcoming the inherent complexity and resource-intensity of conventional protein engineering methods. Recent GenAI-powered computational techniques often…

Vision-Language Models (VLMs) have demonstrated impressive performance on various visual tasks, yet they still require adaptation on downstream tasks to achieve optimal performance. Recently, various adaptation technologies have been…

In a partially observable Markov decision process (POMDP), an agent typically uses a representation of the past to approximate the underlying MDP. We propose to utilize a frozen Pretrained Language Transformer (PLT) for history…

Protein inverse folding aims to design an amino acid sequence that will fold into a given backbone structure, serving as a central task in protein design. Two main paradigms have been widely explored. Template-based methods exploit…

Traditional semantic image search methods aim to retrieve images that match the meaning of the text query. However, these methods typically search for objects on the whole image, without considering the localization of objects within the…

Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protein representations for predicting structures beyond…

Homologous proteins evolve from a common ancestral sequence, constrained by intricate patterns of co-evolving residues. Accurate reconstruction of evolutionary histories remains a challenge, primarily due to the inability of the existing…

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence…

This paper presents Prototypical Contrastive Learning (PCL), an unsupervised representation learning method that addresses the fundamental limitations of instance-wise contrastive learning. PCL not only learns low-level features for the…

Video-and-language pre-training has shown promising improvements on various downstream tasks. Most previous methods capture cross-modal interactions with a transformer-based multimodal encoder, not fully addressing the misalignment between…

Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…

The field of protein-ligand pose prediction has seen significant advances in recent years, with machine learning-based methods now being commonly used in lieu of classical docking methods or even to predict all-atom protein-ligand complex…

High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…

Latent representation alignment has become a foundational technique for constructing multimodal large language models (MLLM) by mapping embeddings from different modalities into a shared space, often aligned with the embedding space of…

Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…

Ad-hoc teamwork (AHT) requires agents to infer the behavior of previously unseen teammates and adapt their policy accordingly. Conventional approaches often rely on fixed probabilistic models or classifiers, which can be brittle under…

The long-tail recommendation is a challenging task for traditional recommender systems, due to data sparsity and data imbalance issues. The recent development of large language models (LLMs) has shown their abilities in complex reasoning,…

Pre-trained vision-language models are able to interpret visual concepts and language semantics. Prompt learning, a method of constructing prompts for text encoders or image encoders, elicits the potentials of pre-trained models and readily…

Protein language models leverage evolutionary information to perform state-of-the-art 3D structure and zero-shot variant prediction. Yet, extracting and explaining all the mutational interactions that govern model predictions remains…

Improving the ability to predict protein function can potentially facilitate research in the fields of drug discovery and precision medicine. Technically, the properties of proteins are directly or indirectly reflected in their sequence and…