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

The large-scale analysis task of deciphering gravitational wave signals in the LISA data stream will be difficult, requiring a large amount of computational resources and extensive development of computational methods. Its high…

Reinforcement learning (RL) algorithms involve the deep nesting of highly irregular computation patterns, each of which typically exhibits opportunities for distributed computation. We argue for distributing RL components in a composable…

Quantitative analysis of multidimensional biological images is useful for understanding complex cellular phenotypes and accelerating advances in biomedical research. As modern microscopy generates ever-larger 2D and 3D datasets, existing…

Retrieval-augmented generation (RAG) can enhance the generation quality of large language models (LLMs) by incorporating external token databases. However, retrievals from large databases can constitute a substantial portion of the overall…

Classifying structural variability in noisy projections of biological macromolecules is a central problem in Cryo-EM. In this work, we build on a previous method for estimating the covariance matrix of the three-dimensional structure…

We introduce eCLIP, an enhanced version of the CLIP model that integrates expert annotations in the form of radiologist eye-gaze heatmaps. It tackles key challenges in contrastive multi-modal medical imaging analysis, notably data scarcity…

Velocity estimation is a cornerstone of the recently introduced near-field predictive beamforming. This paper derives the Cramer-Rao bounds (CRBs) for joint radial and transverse velocity estimation within a predictive beamforming framework…

Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied…

Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method to resolve biological macromolecules. In a cryo-EM experiment, the microscope produces…

Electrocardiogram (ECG) diagnosis remains challenging due to limited labeled data and the need to capture subtle yet clinically meaningful variations in rhythm and morphology. We present CREMA (Contrastive Regularized Masked Autoencoder), a…

Multimodal Large Language Models (MLLMs) have significantly advanced AI-assisted medical diagnosis, but they often generate factually inconsistent responses that deviate from established medical knowledge. Retrieval-Augmented Generation…

Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic…

Multi-agent reinforcement learning (MARL) research is inherently computationally expensive and it is often difficult to obtain a sufficient number of experiment samples to test hypotheses and make robust statistical claims. Furthermore,…

Reinforcement learning (RL) provides a principled framework for decision-making in partially observable environments, which can be modeled as Markov decision processes and compactly represented through dynamic decision Bayesian networks.…

In this work we propose Neuro-Nav, an open-source library for neurally plausible reinforcement learning (RL). RL is among the most common modeling frameworks for studying decision making, learning, and navigation in biological organisms. In…

Machine-learning interatomic potentials (MLIPs) such as neuroevolution potentials (NEP) combine quantum-mechanical accuracy with computational efficiency significantly accelerate atomistic dynamic simulations. Trained by derivative-free…

Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alternative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC…

Neural networks achieve strong empirical performance, but robustness concerns still hinder deployment in safety-critical applications. Formal verification provides robustness guarantees, but current methods face a scalability-completeness…

One of the difficulties in 3D reconstruction of molecules from images in single particle Cryo-Electron Microscopy (Cryo-EM), in addition to high levels of noise and unknown image orientations, is heterogeneity in samples: in many cases, the…

We present our work on scalable, GPU-accelerated algorithms for diffeomorphic image registration. The associated software package is termed CLAIRE. Image registration is a non-linear inverse problem. It is about computing a spatial mapping…