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Current self-supervised learning methods for 3D medical imaging rely on simple pretext formulations and organ- or modality-specific datasets, limiting their generalizability and scalability. We present 3DINO, a cutting-edge SSL method…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
Most publicly available medical segmentation datasets are only partially labeled, with annotations provided for a subset of anatomical structures. When multiple datasets are combined for training, this incomplete annotation poses…
This paper presents an overview of Carnap, a free and open framework for the development of formal reasoning applications. Carnap's design emphasizes flexibility, extensibility, and rapid prototyping. Carnap-based applications are written…
Neural Architecture Search (NAS) algorithms are intended to remove the burden of manual neural network design, and have shown to be capable of designing excellent models for a variety of well-known problems. However, these algorithms…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
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…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…
Summary: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks.…
Stencil computations are a key part of many high-performance computing applications, such as image processing, convolutional neural networks, and finite-difference solvers for partial differential equations. Devito is a framework capable of…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Creating new fonts requires a lot of human effort and professional typographic knowledge. Despite the rapid advancements of automatic font generation models, existing methods require users to prepare pre-designed characters with target…
In dependently typed programming, proofs of basic, structural properties can be embedded implicitly into programs and do not need to be written explicitly. Besides saving the effort of writing separate proofs, a most distinguishing and…
Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level functionalities. Yet,…
CAD programs are a popular way to compactly encode shapes as a sequence of operations that are easy to parametrically modify. However, without sufficient semantic comments and structure, such programs can be challenging to understand, let…
This paper introduces CADgpt, an innovative plugin integrating Natural Language Processing (NLP) with Rhino3D for enhancing 3D modelling in computer-aided design (CAD) environments. Leveraging OpenAI's GPT-4, CADgpt simplifies the CAD…