ArXiv最新文献

{"title":"Modeling Latent Neural Dynamics with Gaussian Process Switching Linear Dynamical Systems.","authors":"Amber Hu, David Zoltowski, Aditya Nair, David Anderson, Lea Duncker, Scott Linderman","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Understanding how the collective activity of neural populations relates to computation and ultimately behavior is a key goal in neuroscience. To this end, statistical methods which describe high-dimensional neural time series in terms of low-dimensional latent dynamics have played a fundamental role in characterizing neural systems. Yet, what constitutes a successful method involves two opposing criteria: (1) methods should be expressive enough to capture complex nonlinear dynamics, and (2) they should maintain a notion of interpretability often only warranted by simpler linear models. In this paper, we develop an approach that balances these two objectives: the Gaussian Process Switching Linear Dynamical System (gpSLDS). Our method builds on previous work modeling the latent state evolution via a stochastic differential equation whose nonlinear dynamics are described by a Gaussian process (GP-SDEs). We propose a novel kernel function which enforces smoothly interpolated locally linear dynamics, and therefore expresses flexible -- yet interpretable -- dynamics akin to those of recurrent switching linear dynamical systems (rSLDS). Our approach resolves key limitations of the rSLDS such as artifactual oscillations in dynamics near discrete state boundaries, while also providing posterior uncertainty estimates of the dynamics. To fit our models, we leverage a modified learning objective which improves the estimation accuracy of kernel hyperparameters compared to previous GP-SDE fitting approaches. We apply our method to synthetic data and data recorded in two neuroscience experiments and demonstrate favorable performance in comparison to the rSLDS.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061366","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":"Reusable specimen-level inference in computational pathology.","authors":"Jakub R Kaczmarzyk, Rishul Sharma, Peter K Koo, Joel H Saltz","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Foundation models for computational pathology have shown great promise for specimen-level tasks and are increasingly accessible to researchers. However, specimen-level models built on these foundation models remain largely unavailable, hindering their broader utility and impact. To address this gap, we developed SpinPath, a toolkit designed to democratize specimen-level deep learning by providing a zoo of pretrained specimen-level models, a Python-based inference engine, and a JavaScript-based inference platform. We demonstrate the utility of SpinPath in metastasis detection tasks across nine foundation models. SpinPath may foster reproducibility, simplify experimentation, and accelerate the adoption of specimen-level deep learning in computational pathology research.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049216","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":"MyESL: Sparse learning in molecular evolution and phylogenetic analysis.","authors":"Maxwell Sanderford, Sudip Sharma, Glen Stecher, Jun Liu, Jieping Ye, Sudhir Kumar","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Evolutionary sparse learning (ESL) uses a supervised machine learning approach, Least Absolute Shrinkage and Selection Operator (LASSO), to build models explaining the relationship between a hypothesis and the variation across genomic features (e.g., sites) in sequences alignments. ESL employs sparsity between and within the groups of genomic features (e.g., genomic loci or genes) by using sparse-group LASSO. Although some software packages are available for performing sparse group LASSO, we found them less well-suited for processing and analyzing genome-scale sequence data containing millions of features, such as bases. MyESL software fills the need for open-source software for conducting ESL analyses with facilities to pre-process the input hypotheses and large alignments, make LASSO flexible and computationally efficient, and post-process the output model to produce different metrics useful in functional or evolutionary genomics. MyESL takes binary response or phylogenetic trees as the regression response, processing them into class-balanced hypotheses as required. It also processes continuous and binary features or sequence alignments that are transformed into a binary one-hot encoded feature matrix for analysis. The model outputs are processed into user-friendly text and graphical files. The computational core of MyESL is written in C++, which offers model building with or without group sparsity, while the pre- and post-processing of inputs and model outputs is performed using customized functions written in Python. One of its applications in phylogenomics showcases the utility of MyESL. Our analysis of empirical genome-scale datasets shows that MyESL can build evolutionary models quickly and efficiently on a personal desktop, while other computational packages were unable due to their prohibitive requirements of computational resources and time. MyESL is available for Python environments on Linux and distributed as a standalone application for both Windows and macOS, which can be integrated into third-party software and pipelines.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049196","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":"How Large is the Universe of RNA-Like Motifs? A Clustering Analysis of RNA Graph Motifs Using Topological Descriptors.","authors":"Rui Wang, Tamar Schlick","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Identifying novel and functional RNA structures remains a significant challenge in RNA motif design and is crucial for developing RNA-based therapeutics. Here we introduce a computational topology-based approach with unsupervised machine-learning algorithms to estimate the database size and content of RNA-like graph topologies. Specifically, we apply graph theory enumeration to generate all 110,667 possible 2D dual graphs for vertex numbers ranging from 2 to 9. Among them, only 0.11% (121 dual graphs) correspond to approximately 200,000 known RNA atomic fragments/substructures (collected in 2021) using the RNA-as-Graphs (RAG) mapping method. The remaining 99.89% of the dual graphs may be RNA-like or non-RNA-like. To determine which dual graphs in the 99.89% hypothetical set are more likely to be associated with RNA structures, we apply computational topology descriptors using the Persistent Spectral Graphs (PSG) method to characterize each graph using 19 PSG-based features and use clustering algorithms that partition all possible dual graphs into two clusters. The cluster with the higher percentage of known dual graphs for RNA is defined as the \"RNA-like\" cluster, while the other is considered as \"non-RNA-like\". The distance of each dual graph to the center of the RNA-like cluster represents the likelihood of it belonging to RNA structures. From validation, our PSG-based RNA-like cluster includes 97.3% of the 121 known RNA dual graphs, suggesting good performance. Furthermore, 46.017% of the hypothetical RNAs are predicted to be RNA-like. Among the top 15 graphs identified as high-likelihood candidates for novel RNA motifs, 4 were confirmed from the RNA dataset collected in 2022. Significantly, we observe that all the top 15 RNA-like dual graphs can be separated into multiple subgraphs, whereas the top 15 non-RNA-like dual graphs tend not to have any subgraphs (subgraphs preserve pseudoknots and junctions). Moreover, a significant topological difference between top RNA-like and non-RNA-like graphs is evident when comparing their topological features (e.g. Betti-0 and Betti-1 numbers). These findings provide valuable insights into the size of the RNA motif universe and RNA design strategies, offering a novel framework for predicting RNA graph topologies and guiding the discovery of novel RNA motifs, perhaps anti-viral therapeutics by subgraph assembly.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049185","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":"Energy Dynamics Powered by Traction and Stress Control Formation and Motion of +1/2 Topological Defects in Epithelial Cell Monolayers.","authors":"Pradip K Bera, Molly McCord, Jun Zhang, Jacob Notbohm","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In confluent cell monolayers, patterns of cell forces and motion are systematically altered near topological defects in cell shape. In turn, defects have been proposed to alter cell density, extrusion, and invasion, but it remains unclear how the defects form and how they affect cell forces and motion. Here, we studied +1/2 defects, and, in contrast to prior studies, we observed both tail-to-head and head-to-tail defect motion occurring at the same time in the same cell monolayer. We quantified the cell velocities, the tractions at the cell-substrate interface, and stresses within the cell layer near +1/2 defects. Results revealed that both traction and stress are sources of activity within the epithelial cell monolayer, with their competition defining whether the cells inject or dissipate energy and determining the direction of motion of +1/2 defects. Interestingly, patterns of motion, traction, stress, and energy injection near +1/2 defects existed before defect formation, suggesting that defects form as a result of spatially coordinated patterns in cell forces and motion. These findings reverse the current picture, from one in which defects define the cell forces and motion to one in which coordinated patterns of cell forces and motion cause defects to form and move.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049098","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":"Curated loci prime editing (cliPE) for accessible multiplexed assays of variant effect (MAVEs).","authors":"Carina G Biar, Nicholas Bodkin, Gemma L Carvill, Jeffrey D Calhoun","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Multiplexed assays of variant effect (MAVEs) perform simultaneous characterization of many variants. Prime editing has been recently adopted for introducing many variants in their native genomic contexts. However, robust protocols and standards are limited, preventing widespread uptake. Herein, we describe curated loci prime editing (cliPE) which is an accessible, low-cost experimental pipeline to perform MAVEs using prime editing of a target gene, as well as a companion Shiny app (pegRNA Designer) to rapidly and easily design user-specific MAVE libraries.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049056","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":"Spatiotemporal Gaussian Optimization for 4D Cone Beam CT Reconstruction from Sparse Projections.","authors":"Yabo Fu, Hao Zhang, Weixing Cai, Huiqiao Xie, Licheng Kuo, Laura Cervino, Jean Moran, Xiang Li, Tianfang Li","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In image-guided radiotherapy (IGRT), four-dimensional cone-beam computed tomography (4D-CBCT) is critical for assessing tumor motion during a patients breathing cycle prior to beam delivery. However, generating 4D-CBCT images with sufficient quality requires significantly more projection images than a standard 3D-CBCT scan, leading to extended scanning times and increased imaging dose to the patient. To address these limitations, there is a strong demand for methods capable of reconstructing high-quality 4D-CBCT images from a 1-minute 3D-CBCT acquisition. The challenge lies in the sparse sampling of projections, which introduces severe streaking artifacts and compromises image quality. This paper introduces a novel framework leveraging spatiotemporal Gaussian representation for 4D-CBCT reconstruction from sparse projections, achieving a balance between streak artifact reduction, dynamic motion preservation, and fine detail restoration. Each Gaussian is characterized by its 3D position, covariance, rotation, and density. Two-dimensional X-ray projection images can be rendered from the Gaussian point cloud representation via X-ray rasterization. The properties of each Gaussian were optimized by minimizing the discrepancy between the measured projections and the rendered X-ray projections. A Gaussian deformation network is jointly optimized to deform these Gaussian properties to obtain a 4D Gaussian representation for dynamic CBCT scene modeling. The final 4D-CBCT images are reconstructed by voxelizing the 4D Gaussians, achieving a high-quality representation that preserves both motion dynamics and spatial detail. The code and reconstruction results can be found at https://github.com/fuyabo/4DGS_for_4DCBCT/tree/main.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049139","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":"<ArticleTitle xmlns:ns0=\"http://www.w3.org/1998/Math/MathML\">Rapid, High-resolution and Distortion-free <ns0:math> <ns0:msubsup><ns0:mrow><ns0:mi>R</ns0:mi></ns0:mrow> <ns0:mrow><ns0:mn>2</ns0:mn></ns0:mrow> <ns0:mrow><ns0:mi>*</ns0:mi></ns0:mrow> </ns0:msubsup> </ns0:math> Mapping of Fetal Brain using Multi-echo Radial FLASH and Model-based Reconstruction.","authors":"Xiaoqing Wang, Hongli Fan, Zhengguo Tan, Serge Vasylechko, Edward Yang, Ryne Didier, Onur Afacan, Martin Uecker, Simon K Warfield, Ali Gholipour","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Purpose: </strong>To develop a rapid, high-resolution and distortion-free quantitative <math> <msubsup><mrow><mi>R</mi></mrow> <mrow><mn>2</mn></mrow> <mrow><mi>*</mi></mrow> </msubsup> </math> mapping technique for fetal brain at 3 T.</p><p><strong>Methods: </strong>A 2D multi-echo radial FLASH sequence with blip gradients is adapted for fetal brain data acquisition during maternal free breathing at 3 T. A calibrationless model-based reconstruction with sparsity constraints is developed to jointly estimate water, fat, <math> <msubsup><mrow><mi>R</mi></mrow> <mrow><mn>2</mn></mrow> <mrow><mi>*</mi></mrow> </msubsup> </math> and <math> <msub><mrow><mi>B</mi></mrow> <mrow><mn>0</mn></mrow> </msub> </math> field maps directly from the acquired k-space data. Validations have been performed on numerical and NIST phantoms and five fetal subjects ranging from 27 weeks to 36 weeks gestation age.</p><p><strong>Results: </strong>Both numerical and experimental phantom studies confirm good accuracy and precision of the proposed method. In fetal studies, both the parallel imaging compressed sensing (PICS) technique with a Graph Cut algorithm and the model-based approach proved effective for parameter quantification, with the latter providing enhanced image details. Compared to commonly used multi-echo EPI approaches, the proposed radial technique shows improved spatial resolution (1.1 × 1.1 × 3 mm³ vs. 2-3 × 2-3 × 3 mm³) and reduced distortion. Quantitative <math> <msubsup><mrow><mi>R</mi></mrow> <mrow><mn>2</mn></mrow> <mrow><mi>*</mi></mrow> </msubsup> </math> results confirm good agreement between the two acquisition strategies. Additionally, high-resolution, distortion-free <math> <msubsup><mrow><mi>R</mi></mrow> <mrow><mn>2</mn></mrow> <mrow><mi>*</mi></mrow> </msubsup> </math> -weighted images can be synthesized, offering complementary information to HASTE.</p><p><strong>Conclusion: </strong>This work demonstrates the feasibility of radial acquisition for motion-robust quantitative <math> <msubsup><mrow><mi>R</mi></mrow> <mrow><mn>2</mn></mrow> <mrow><mi>*</mi></mrow> </msubsup> </math> mapping of the fetal brain. This proposed multi-echo radial FLASH, combined with calibrationless model-based reconstruction, achieves accurate, distortion-free fetal brain <math> <msubsup><mrow><mi>R</mi></mrow> <mrow><mn>2</mn></mrow> <mrow><mi>*</mi></mrow> </msubsup> </math> mapping at a nominal resolution of 1.1 × 1.1 × 3 mm³ within 2 seconds.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11722525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973766","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":"Advances in RNA secondary structure prediction and RNA modifications: Methods, data, and applications.","authors":"Shu Yang, Nhat Truong Pham, Ziyang Li, Jae Young Baik, Joseph Lee, Tianhua Zhai, Weicheng Yu, Bojian Hou, Tianqi Shang, Weiqing He, Duy Duong-Tran, Mayur Naik, Li Shen","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic. This review sets out to explore the computational prediction of RNA secondary structure and its connections to RNA modifications, which have emerged as an active domain in recent years. We first examine the progression of RNA secondary structure prediction methodology, focusing on a set of representative works categorized into thermodynamic, comparative, machine learning, and hybrid approaches. Next, we survey the advances in RNA modifications and computational methods for identifying RNA modifications, focusing on the prominent modification types. Subsequently, we highlight the interplay between RNA modifications and secondary structures, emphasizing how modifications such as m6A dynamically affect RNA folding and vice versa. In addition, we also review relevant data sources and provide a discussion of current challenges and opportunities in the field. Ultimately, we hope our review will be able to serve as a cornerstone to aid in the development of innovative methods for this emerging topic and foster therapeutic applications in the future.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049133","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":"Energy injection in an epithelial cell monolayer via negative viscosity.","authors":"Molly McCord, Jacob Notbohm","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Active fluids are driven out of thermodynamic equilibrium by internally generated forces, causing complex patterns of motion. Even when both the forces and motion are measurable, it is not yet possible to relate the two, because the sources of energy injection and dissipation are often unclear. Here, we study how energy is transferred by developing a method to measure viscosity from the shear stresses and strain rates within an epithelial cell monolayer. Surprisingly, there emerged multicellular regions in which the relationship between shear stress and shear strain rate was negatively proportional, indicating a negative viscosity. We provide direct experimental evidence that the negative viscosity results from cells aligning their stresses with the orientation of the flow. Regions of negative viscosity consistently exhibited greater cell speed and vorticity, and the cells had elevated metabolic activity, indicating that negative viscosity is a mechanism for injection of surplus energy. More broadly, our study shows that negative viscosity is a useful means of quantifying the flow of energy in active materials.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11759849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049179","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}