Related papers: Cryo-RALib -- a modular library for accelerating a…

Graph-based Retrieval Augmented Generation (GraphRAG) extends retrieval-augmented generation to support structured reasoning over complex corpora, but its reliability under resource-constrained, privacy-sensitive deployments remains…

A common task in single particle electron cryomicroscopy (cryo-EM) is the rigid alignment of images and/or volumes. In the context of images, a rigid alignment involves estimating the inner-product between one image of $N\times N$ pixels…

The SARS-CoV-2 pandemic has created a global race for a cure. One approach focuses on designing a novel variant of the human angiotensin-converting enzyme 2 (ACE2) that binds more tightly to the SARS-CoV-2 spike protein and diverts it from…

Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrates particle…

Single particle electron cryomicroscopy (cryo-EM) allows for structures of proteins and protein complexes to be determined from images of non-crystalline specimens. Cryo-EM data analysis requires electron microscope images of randomly…

Motivated by the task of 2-D classification in single particle reconstruction by cryo-electron microscopy (cryo-EM), we consider the problem of heterogeneous multireference alignment of images. In this problem, the goal is to estimate a…

The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular…

The multi-resolution approximation (MRA) of Gaussian processes was recently proposed to conduct likelihood-based inference for massive spatial data sets. An advantage of the methodology is that it can be parallelized. We implemented the MRA…

Understanding protein flexibility and its dynamic interactions with other molecules is essential for studying protein function. Although cryogenic electron microscopy(cryo-EM) provides an opportunity to observe macromolecular dynamics…

In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly-oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy 2D…

Retrieval-augmented generation (RAG) enhances large language models (LLMs) with external knowledge but still suffers from long contexts and disjoint retrieval-generation optimization. In this work, we propose CLaRa (Continuous Latent…

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale,…

Time-resolved MR angiography (tMRA) has been widely used for dynamic contrast enhanced MRI (DCE-MRI) due to its highly accelerated acquisition. In tMRA, the periphery of the k-space data are sparsely sampled so that neighbouring frames can…

Machine learning (ML) models utilizing structure-based features provide an efficient means for accurate property predictions across diverse chemical spaces. However, obtaining equilibrium crystal structures typically requires expensive…

The deployment of Large Language Models (LLMs) in recommender systems for predicting Click-Through Rates (CTR) necessitates a delicate balance between computational efficiency and predictive accuracy. This paper presents an optimization…

Retrieval-augmented generation (RAG) has become a widely adopted paradigm for enabling knowledge-grounded large language models (LLMs). However, standard RAG pipelines often fail to ensure that model reasoning remains consistent with the…

Pretrained vision-language models such as CLIP exhibit strong zero-shot generalization but remain sensitive to distribution shifts. Test-time adaptation adapts models during inference without access to source data or target labels, offering…

Simultaneously optimizing multiple, frequently conflicting, molecular properties is a key bottleneck in the development of novel therapeutics. Although a promising approach, the efficacy of multi-task learning is often compromised by…

Computing-in-Memory (CIM) accelerators are a promising solution for accelerating Machine Learning (ML) workloads, as they perform Matrix-Vector Multiplications (MVMs) on crossbar arrays directly in memory. Although the bit widths of the…

Deploying Vision-Language Models on resource-constrained hardware typically requires INT8 quantization, but in joint-embedding architectures such as CLIP this introduces a failure mode distinct from quantized CNN classifiers: activation…