Related papers: AffinityFlow: Guided Flows for Antibody Affinity M…

AlphaFold is a neural-network-based tool for the prediction of 3D structures of protein. In CASP14, a blind structure prediction challenge, it performed significantly better than other competitors, which makes it the best available…

We introduce EvoFlows, a variable-length protein sequence-to-sequence modeling approach designed for protein engineering. Existing protein language models are poorly suited for optimization tasks: autoregressive models require full sequence…

We present FLOWR.root, an SE(3)-equivariant flow-matching model for pocket-aware 3D ligand generation with joint potency and binding affinity prediction and confidence estimation. The model supports de novo generation, interaction- and…

Flow matching models have emerged as a powerful framework for realistic image generation by learning to reverse a corruption process that progressively adds Gaussian noise. However, because noise is injected in the latent domain, its impact…

Breakthroughs in high-accuracy protein structure prediction, such as AlphaFold, have established receptor-based molecule design as a critical driver for rapid early-phase drug discovery. However, most approaches still struggle to balance…

Existing approaches to controllable generation typically rely on fine-tuning, auxiliary networks, or test-time search. We show that flow matching admits a different control interface: adaptation through examples. For deterministic…

Estimating three-dimensional conformations of a molecular graph allows insight into the molecule's biological and chemical functions. Fast generation of valid conformations is thus central to molecular modeling. Recent advances in…

Proteins are essential for almost all biological processes and derive their diverse functions from complex 3D structures, which are in turn determined by their amino acid sequences. In this paper, we exploit the rich biological inductive…

The rise of mobile devices equipped with numerous sensors, such as LiDAR and cameras, has spurred the adoption of multi-modal deep intelligence for distributed sensing tasks, such as smart cabins and driving assistance. However, the arrival…

Accurately determining a change in protein binding affinity upon mutations is important for the discovery and design of novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations…

Antibody-facilitated immune responses are central to the body's defense against pathogens, viruses, and other foreign invaders. The ability of antibodies to specifically bind and neutralize antigens is vital for maintaining immunity. Over…

We present NextFlow, a unified decoder-only autoregressive transformer trained on 6 trillion interleaved text-image discrete tokens. By leveraging a unified vision representation within a unified autoregressive architecture, NextFlow…

We present a novel, purely affinity-based natural image matting algorithm. Our method relies on carefully defined pixel-to-pixel connections that enable effective use of information available in the image. We control the information flow…

Data scarcity and weak supervision continue to limit the performance of machine learning models in many real-world applications, such as mammography, where Multiple Instance Learning (MIL) often offers the best formulation. While recent…

Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational…

Key objectives in conditional molecular generation include ensuring chemical validity, aligning generated molecules with target properties, promoting structural diversity, and enabling efficient sampling for discovery. Recent advances in…

Human action-reaction synthesis, a fundamental challenge in modeling causal human interactions, plays a critical role in applications ranging from virtual reality to social robotics. While diffusion-based models have demonstrated promising…

The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…

The high binding affinity of antibodies towards their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as research and therapeutic tools. Here, we propose ANTIPASTI, a Convolutional Neural…

Existing rectified flow models are based on linear trajectories between data and noise distributions. This linearity enforces zero curvature, which can inadvertently force the image generation process through low-probability regions of the…