Related papers: PRISM: Enhancing Protein Inverse Folding through F…
Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold relationship, as well as the difficulties to capture the…
Achieving precise alignment between user intent and generated visuals remains a central challenge in text-to-visual generation, as a single attempt often fails to produce the desired output. To handle this, prior approaches mainly scale the…
The pre-trained foundation models (PFMs) have become essential for facilitating large-scale multimodal learning. Researchers have effectively employed the ``pre-train, prompt, and predict'' paradigm through prompt learning to induce…
Fine-grained object retrieval aims to learn discriminative representation to retrieve visually similar objects. However, existing top-performing works usually impose pairwise similarities on the semantic embedding spaces or design a…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Multi-site MRI studies often suffer from site-specific variations arising from differences in methodology, hardware, and acquisition protocols, thereby compromising accuracy and reliability in clinical AI/ML tasks. We present PRISM…
Supervised fine-tuning (SFT) is a standard approach for adapting large language models to specialized domains, yet its application to protein sequence modeling and protein language models (PLMs) remains ad hoc. This is in part because…
The problem of phase retrieval (PR) involves recovering an unknown image from limited amplitude measurement data and is a challenge nonlinear inverse problem in computational imaging and image processing. However, many of the PR methods are…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
Video dataset condensation aims to reduce the immense computational cost of video processing. However, it faces a fundamental challenge regarding the inseparable interdependence between spatial appearance and temporal dynamics. Prior work…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
Diffusion models are now commonly used to solve inverse problems in computational imaging. However, most diffusion-based inverse solvers require complete knowledge of the forward operator to be used. In this work, we introduce a novel…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…
Contrastive image-text models such as CLIP form the building blocks of many state-of-the-art systems. While they excel at recognizing common generic concepts, they still struggle on fine-grained entities which are rare, or even absent from…
While DeepMind has tentatively solved protein folding, its inverse problem -- protein design which predicts protein sequences from their 3D structures -- still faces significant challenges. Particularly, the lack of large-scale standardized…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…