Related papers: Cryo-RALib -- a modular library for accelerating a…
Cryo-electron tomography (cryo-ET) enables structural characterization of biomolecules under near-native conditions. Existing approaches for interpreting the resulting three-dimensional volumes are computationally expensive and have…
We propose a highly parallel primal-dual algorithm for the multicut (a.k.a. correlation clustering) problem, a classical graph clustering problem widely used in machine learning and computer vision. Our algorithm consists of three steps…
Machine learning interatomic potentials (MLIPs) enable atomistic simulations with near ab initio accuracy at significantly reduced computational cost, but their broader adoption is often limited by fragmented tooling, limited scalability,…
In recent years, text-to-video retrieval methods based on CLIP have experienced rapid development. The primary direction of evolution is to exploit the much wider gamut of visual and textual cues to achieve alignment. Concretely, those…
Cryo-Electron Microscopy (cryo-EM) has emerged as a key technology to determine the structure of proteins, particularly large protein complexes and assemblies in recent years. A key challenge in cryo-EM data analysis is to automatically…
Large Language Models (LLMs) demand substantial computational resources, resulting in high energy consumption on GPUs. To address this challenge, we focus on Coarse-Grained Reconfigurable Arrays (CGRAs) as an effective alternative that…
One problem with researching cognitive modeling and reinforcement learning (RL) is that researchers spend too much time on setting up an appropriate computational framework for their experiments. Many open source implementations of current…
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the…
Multireference alignment (MRA) problem is to estimate an underlying signal from a large number of noisy circularly-shifted observations. The existing methods are always proposed under the hypothesis of a single Gaussian noise. However, the…
CLIP (Contrastive Language-Image Pre-training) uses contrastive learning from noise image-text pairs to excel at recognizing a wide array of candidates, yet its focus on broad associations hinders the precision in distinguishing subtle…
The computational pipelines of single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) include an early particle-picking stage, in which a micrograph or tomogram is scanned to extract candidate particles,…
Recent advances in transformer-based foundation models have made them the default choice for many tasks, but their rapidly growing size makes fitting a full model on a single GPU increasingly difficult and their computational cost…
We introduce a new rotationally invariant viewing angle classification method for identifying, among a large number of Cryo-EM projection images, similar views without prior knowledge of the molecule. Our rotationally invariant features are…
Class-incremental learning (CIL) in medical image-guided diagnosis requires retaining prior diagnostic knowledge while adapting to newly emerging disease categories, which is critical for scalable clinical deployment. This problem is…
Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the…
Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep…
Recent development in Retrieval-Augmented Large Language Models (LLMs) have shown great promise in biomedical applications. How ever, a critical gap persists in reliably evaluating their curation ability the process by which models select…
Cryo-electron microscopy (cryo-EM) is an emerging experimental method to characterize the structure of large biomolecular assemblies. Single particle cryo-EM records 2D images (so-called micrographs) of projections of the three-dimensional…
Dense retrieval systems increasingly need to handle complex queries. In many realistic settings, users express intent through long instructions or task-specific descriptions, while target documents remain relatively simple and static. This…
Remote Memory Access (RMA) enables direct access to remote memory to achieve high performance for HPC applications. However, most modern parallel programming models lack schemes for the remote process to detect the completion of RMA…