Mojtaba Safari, Shansong Wang, Zach Eidex, Qiang Li, Erik H Middlebrooks, David S Yu, Xiaofeng Yang
{"title":"MRI super-resolution reconstruction using efficient diffusion probabilistic model with residual shifting.","authors":"Mojtaba Safari, Shansong Wang, Zach Eidex, Qiang Li, Erik H Middlebrooks, David S Yu, Xiaofeng Yang","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Objective: </strong>MRI offers superior soft-tissue contrast yet suffers from long acquisition times that can induce patient discomfort and motion artifacts. Super-resolution (SR) methods reconstruct high-resolution (HR) images from low-resolution (LR) scans, but diffusion models typically require numerous sampling steps, hindering real-time use. Here, we introduce a residual error-shifting strategy that reduce sampling steps without compromising anatomical fidelity, thereby improving MRI SR for clinical deployment.</p><p><strong>Approach: </strong>We propose a novel diffusion-based SR framework called Res-SRDiff, which integrates residual error shifting into the forward diffusion process. This approach enables efficient HR image reconstruction by aligning the degraded HR image distribution with the LR image distribution. Our model was evaluated on two MRI datasets: ultra-high-field brain T1 MP2RAGE maps and T2-weighted prostate images. We compared Res-SRDiff against established methods, including Bicubic, Pix2pix, CycleGAN, and a conventional denoising diffusion probabilistic model with vision transformer backbone (TM-DDPM), using quantitative metrics such as peak signal-to-noise ratio (PSNR), structural similarity index (SSIM), gradient magnitude similarity deviation (GMSD), and learned perceptual image patch similarity (LPIPS).</p><p><strong>Main results: </strong>Res-SRDiff significantly outperformed all comparative methods in terms of PSNR, SSIM, and GMSD across both datasets, with statistically significant improvements ( <math><mrow><mi>p</mi></mrow> </math> -values ≪ 0.05). The model achieved high-fidelity image restoration with only four sampling steps, drastically reducing computational time to under one second per slice, which is substantially faster than conventional TM-DDPM with around 20 seconds per slice. Qualitative analyses further demonstrated that Res-SRDiff effectively preserved fine anatomical details and lesion morphology in both brain and pelvic MRI images.</p><p><strong>Significance: </strong>Our findings show that Res-SRDiff is an efficient and accurate MRI SR method, markedly improving computational efficiency and image quality. By integrating residual error shifting into the diffusion process, it allows for rapid and robust HR image reconstruction, enhancing clinical MRI workflows and advancing medical imaging research. The source at: https://github.com/mosaf/Res-SRDiff.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Penalized Principal Component Analysis Using Smoothing.","authors":"Rebecca M Hurwitz, Georg Hahn","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Principal components computed via PCA (principal component analysis) are traditionally used to reduce dimensionality in genomic data or to correct for population stratification. In this paper, we explore the penalized eigenvalue problem (PEP) which reformulates the computation of the first eigenvector as an optimization problem and adds an $L_1$ penalty constraint to enforce sparseness of the solution. The contribution of our article is threefold. First, we extend PEP by applying smoothing to the original LASSO-type $L_1$ penalty. This allows one to compute analytical gradients which enable faster and more efficient minimization of the objective function associated with the optimization problem. Second, we demonstrate how higher order eigenvectors can be calculated with PEP using established results from singular value decomposition (SVD). Third, we present four experimental studies to demonstrate the usefulness of the smoothed penalized eigenvectors. Using data from the 1000 Genomes Project dataset, we empirically demonstrate that our proposed smoothed PEP allows one to increase numerical stability and obtain meaningful eigenvectors. We also employ the penalized eigenvector approach in two additional real data applications (computation of a polygenic risk score and clustering), demonstrating that exchanging the penalized eigenvectors for their smoothed counterparts can increase prediction accuracy in polygenic risk scores and enhance discernibility of clusterings. Moreover, we compare our proposed smoothed PEP to seven state-of-the-art algorithms for sparse PCA and evaluate the accuracy of the obtained eigenvectors, their support recovery, and their runtime.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10557800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41164740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isaac Lin, Tianye Wang, Shang Gao, Shiming Tang, Tai Sing Lee
{"title":"Self-Attention-Based Contextual Modulation Improves Neural System Identification.","authors":"Isaac Lin, Tianye Wang, Shang Gao, Shiming Tang, Tai Sing Lee","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Convolutional neural networks (CNNs) have been shown to be state-of-the-art models for visual cortical neurons. Cortical neurons in the primary visual cortex are sensitive to contextual information mediated by extensive horizontal and feedback connections. Standard CNNs integrate global contextual information to model contextual modulation via two mechanisms: successive convolutions and a fully connected readout layer. In this paper, we find that self-attention (SA), an implementation of non-local network mechanisms, can improve neural response predictions over parameter-matched CNNs in two key metrics: tuning curve correlation and peak tuning. We introduce peak tuning as a metric to evaluate a model's ability to capture a neuron's top feature preference. We factorize networks to assess each context mechanism, revealing that information in the local receptive field is most important for modeling overall tuning, but surround information is critically necessary for characterizing the tuning peak. We find that self-attention can replace posterior spatial-integration convolutions when learned incrementally, and is further enhanced in the presence of a fully connected readout layer, suggesting that the two context mechanisms are complementary. Finally, we find that decomposing receptive field learning and contextual modulation learning in an incremental manner may be an effective and robust mechanism for learning surround-center interactions.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Deep Learning Approach to Multi-Fiber Parameter Estimation and Uncertainty Quantification in Diffusion MRI.","authors":"William Consagra, Lipeng Ning, Yogesh Rathi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Diffusion MRI (dMRI) is the primary imaging modality used to study brain microstructure in vivo. Reliable and computationally efficient parameter inference for common dMRI biophysical models is a challenging inverse problem, due to factors such as variable dimensionalities (reflecting the unknown number of distinct white matter fiber populations in a voxel), low signal-to-noise ratios, and non-linear forward models. These challenges have led many existing methods to use biologically implausible simplified models to stabilize estimation, for instance, assuming shared microstructure across all fiber populations within a voxel. In this work, we introduce a novel sequential method for multi-fiber parameter inference that decomposes the task into a series of manageable subproblems. These subproblems are solved using deep neural networks tailored to problem-specific structure and symmetry, and trained via simulation. The resulting inference procedure is largely amortized, enabling scalable parameter estimation and uncertainty quantification across all model parameters. Simulation studies and real imaging data analysis using the Human Connectome Project (HCP) demonstrate the advantages of our method over standard alternatives. In the case of the standard model of diffusion, our results show that under HCP-like acquisition schemes, estimates for extra-cellular parallel diffusivity are highly uncertain, while those for the intra-cellular volume fraction can be estimated with relatively high precision.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Minibeam-pLATTICE: A novel proton LATTICE modality using minibeams.","authors":"Nimita Shinde, Weijie Zhang, Yuting Lin, Hao Gao","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Purpose: </strong>LATTICE, a form of spatially fractionated radiation therapy (SFRT) that delivers high-dose peaks and low-dose valleys within the target volume, has been clinically utilized for treating bulky tumors. However, its application to small-to-medium-sized target volumes remains challenging due to beam size limitations. To address this challenge, this work proposes a novel proton LATTICE (pLATTICE) modality using minibeams, namely minibeam-pLATTICE, that can extend the LATTICE approach for small-to-medium target volumes.</p><p><strong>Methods: </strong>Three minibeam-pLATTICE methods are introduced. (1) M0: a fixed minibeam aperture orientation (e.g., 0°) for all beam angles; (2) M1: alternated minibeam aperture orientations (e.g., between 0° and 90°), for consecutive beam angles; (3) M2: multiple minibeam aperture orientations (e.g., 0° and 90°) for each beam angle. The purpose of M1 or M2 is to correct anisotropic dose distribution at lattice peaks due to the planar spatial modulation of minibeams. For each minibeam-pLATTICE method, an optimization problem is formulated to optimize dose uniformity in target peaks and valleys, as well as dose-volume-histogram-based objectives. This optimization problem is solved using iterative convex relaxation and alternating direction method of multipliers (ADMM).</p><p><strong>Results: </strong>Three minibeam-pLATTICE methods are validated to demonstrate the feasibility of minibeam-pLATTICE for the head-and-neck (HN) patients. The advantages of this modality over conventional beam (CONV) pLATTICE are evaluated by comparing peak-to-valley dose ratio (PVDR) and dose delivered to organs at risk (OAR). All three minibeam-pLATTICE modalities achieved improved plan quality compared to CONV, with M2 yielding the best results. For example, in terms of PVDR, M2=5.89, compared to CONV=4.13, M0=4.87 and M1=4.7; in terms of max brainstem dose, M2=5.8 Gy, compared to CONV=16.57 Gy, M0=6.54 Gy and M1=7.04 Gy.</p><p><strong>Conclusions: </strong>A novel minibeam-pLATTICE modality is proposed that can generate lattice dose patterns for small-to-medium target volumes, which are not achievable with conventional pLATTICE due to beam size limitations. Peak dose anisotropy due to 1D planar minibeam apertures is corrected through inverse treatment planning with alternating or multiple minibeam apertures per beam angle.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Association of normalization, non-differentially expressed genes and data source with machine learning performance in intra-dataset or cross-dataset modelling of transcriptomic and clinical data.","authors":"Fei Deng, Lanjing Zhang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Cross-dataset testing is critical for examining machine learning (ML) model's performance. However, most studies on modelling transcriptomic and clinical data only conducted intra-dataset testing. It is also unclear whether normalization and non-differentially expressed genes (NDEG) can improve cross-dataset modeling performance of ML. We thus aim to understand whether normalization, NDEG and data source are associated with performance of ML in cross-dataset testing. The transcriptomic and clinical data shared by the lung adenocarcinoma cases in TCGA and ONCOSG were used. The best cross-dataset ML performance was reached using transcriptomic data alone and statistically better than those using transcriptomic and clinical data. The best balance accuracy (BA), area under curve (AUC) and accuracy were significantly better in ML algorithms training on TCGA and tested on ONCOSG than those trained on ONCOSG and tested on TCGA (p<0.05 for all). Normalization and NDEG greatly improved intra-dataset ML performances in both datasets, but not in cross-dataset testing. Strikingly, modelling transcriptomic data of ONCOSG alone outperformed modelling transcriptomic and clinical data whereas including clinical data in TCGA did not significantly impact ML performance, suggesting limited clinical data value or an overwhelming influence of transcriptomic data in TCGA. Performance gains in intra-dataset testing were more pronounced for ML models trained on ONCOSG than TCGA. Among the six ML models compared, Support vector machine was the most frequent best-performer in both intra-dataset and cross-dataset testing. Therefore, our data show data source, normalization and NDEG are associated with intra-dataset and cross-dataset ML performance in modelling transcriptomic and clinical data.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Guillermo Lorenzo, David A Hormuth, Chengyue Wu, Graham Pash, Anirban Chaudhuri, Ernesto A B F Lima, Lois C Okereke, Reshmi Patel, Karen Willcox, Thomas E Yankeelov
{"title":"Validating the predictions of mathematical models describing tumor growth and treatment response.","authors":"Guillermo Lorenzo, David A Hormuth, Chengyue Wu, Graham Pash, Anirban Chaudhuri, Ernesto A B F Lima, Lois C Okereke, Reshmi Patel, Karen Willcox, Thomas E Yankeelov","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Despite advances in methods to interrogate tumor biology, the observational and population-based approach of classical cancer research and clinical oncology does not enable anticipation of tumor outcomes to hasten the discovery of cancer mechanisms and personalize disease management. To address these limitations, individualized cancer forecasts have been shown to predict tumor growth and therapeutic response, inform treatment optimization, and guide experimental efforts. These predictions are obtained <i>via</i> computer simulations of mathematical models that are constrained with data from a patient's cancer and experiments. This book chapter addresses the validation of these mathematical models to forecast tumor growth and treatment response. We start with an overview of mathematical modeling frameworks, model selection techniques, and fundamental metrics. We then describe the usual strategies employed to validate cancer forecasts in preclinical and clinical scenarios. Finally, we discuss existing barriers in validating these predictions along with potential strategies to address them.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fanglei Xue, Meihan Zhang, Shuqi Li, Xinyu Gao, James A Wohlschlegel, Wenbing Huang, Yi Yang, Weixian Deng
{"title":"SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation.","authors":"Fanglei Xue, Meihan Zhang, Shuqi Li, Xinyu Gao, James A Wohlschlegel, Wenbing Huang, Yi Yang, Weixian Deng","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered \"undruggable.\" This strategy induces the degradation of target proteins rather than inhibiting their activity, achieving desirable therapeutic outcomes. Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) are the primary small molecules that induce TPD. Both types of molecules form a ternary complex linking an E3 ubiquitin ligase with a target protein, a crucial step for drug discovery. While significant advances have been made in in-silico binary structure prediction for proteins and small molecules, ternary structure prediction remains challenging due to obscure interaction mechanisms and insufficient training data. Traditional methods relying on manually assigned rules perform poorly and are computationally demanding due to extensive random sampling. In this work, we introduce DeepTernary, a novel deep learning-based approach that directly predicts ternary structures in an end-to-end manner using an encoder-decoder architecture. DeepTernary leverages an SE(3)-equivariant graph neural network (GNN) with both intra-graph and ternary inter-graph attention mechanisms to capture intricate ternary interactions from our collected high-quality training dataset, TernaryDB. The proposed query-based Pocket Points Decoder extracts the 3D structure of the final binding ternary complex from learned ternary embeddings, demonstrating state-of-the-art accuracy and speed in existing PROTAC benchmarks without prior knowledge from known PROTACs. It also achieves notable accuracy on the more challenging MGD benchmark under the blind docking protocol. Remarkably, our experiments reveal that the buried surface area calculated from DeepTernary-predicted structures correlates with experimentally obtained degradation potency-related metrics. Consequently, DeepTernary shows potential in effectively assisting and accelerating the development of TPDs for previously undruggable targets.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Luis A Álvarez-García, Wolfram Liebermeister, Ian Leifer, Hernán A Makse
{"title":"Complexity reduction by symmetry: uncovering the minimal regulatory network for logical computation in bacteria.","authors":"Luis A Álvarez-García, Wolfram Liebermeister, Ian Leifer, Hernán A Makse","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Symmetry principles play an important role in geometry, and physics, allowing for the reduction of complicated systems to simpler, more comprehensible models that preserve the system's features of interest. Biological systems are often highly complex and may consist of a large number of interacting parts. Using symmetry fibrations, the relevant symmetries for biological \"message-passing\" networks, we introduce a scheme, called Complexity Reduction by Symmetry or ComSym, to reduce the gene regulatory networks of <i>Escherichia coli</i> and <i>Bacillus subtilis</i> bacteria to core networks in a way that preserves the dynamics and uncovers the computational capabilities of the network. Gene nodes in the original network that share isomorphic input trees are collapsed by the fibration into equivalence classes called fibers, whereby nodes that receive signals with the same \"history\" belong to one fiber and synchronize. Then we reduce the networks to its minimal computational core via k-core decomposition. This computational core consists of a few strongly connected components or \"signal vortices\", in which signals can cycle through. While between them, these \"signal vortices\" transmit signals in a feedforward manner. These connected components perform signal processing and decision making in the bacterial cell by employing a series of genetic toggle-switch circuits that store memory, plus oscillator circuits. These circuits act as the central computation device of the network, whose output signals then spread to the rest of the network. Our reduction method opens the door to narrow the vast complexity of biological systems to their minimal parts in a systematic way by using fundamental theoretical principles of symmetry.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10614959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71415970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chaitanya K Joshi, Arian R Jamasb, Ramon Viñas, Charles Harris, Simon V Mathis, Alex Morehead, Rishabh Anand, Pietro Liò
{"title":"gRNAde: Geometric Deep Learning for 3D RNA inverse design.","authors":"Chaitanya K Joshi, Arian R Jamasb, Ramon Viñas, Charles Harris, Simon V Mathis, Alex Morehead, Rishabh Anand, Pietro Liò","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. gRNAde uses a multi-state Graph Neural Network and autoregressive decoding to generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. (2010), gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Experimental wet lab validation on 10 different structured RNA backbones finds that gRNAde has a success rate of 50% at designing pseudoknotted RNA structures, a significant advance over 35% for Rosetta. Open source code and tutorials are available at: https://github.com/chaitjo/geometric-rna-design.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11142323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}