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Proceedings of the 41st International Conference on Machine Learning

作者： Daniel Levine Syed Asad Rizvi Sacha Lévy Nazreen Pallikkavaliyaveetil David Zhang Xingyu Chen Sina Ghadermarzi Ruiming Wu Zihe Zheng Ivan Vrkic Anna Zhong Daphne Raskin Insu Han Antonio Henrique De Oliveira Fonseca Josue Ortega Caro Amin Karbasi Rahul M. Dhodapkar David Van Dijk Department of Computer Science Yale University New Haven CT School of Engineering Applied Science University of Pennsylvania Philadelphia PA School of Computer and Communication Sciences Swiss Federal Institute of Technology Lausanne Lausanne Switzerland Department of Computer Science Yale University New Haven CT and Department of Neuroscience Yale School of Medicine New Haven CT Department of Computer Science Yale University New Haven CT and Department of Neuroscience Yale School of Medicine New Haven CT and Wu Tsai Institute Yale University New Haven CT Google and Yale Institute for Foundations of Data Science New Haven CT and Department of Computer Science Yale University New Haven CT and Yale School of Engineering and Applied Science New Haven CT Roski Eye Institute University of Southern California Los Angeles CA and Department of Internal Medicine (Cardiology) Yale School of Medicine New Haven CT Department of Computer Science Yale University New Haven CT and Yale Institute for Foundations of Data Science New Haven CT and Wu Tsai Institute Yale University New Haven CT and Cardiovascular Research Center Yale School of Medicine New Haven CT and Interdepartmental Program in Computational Biology & Bioinformatics Yale University New Haven CT and Department of Internal Medicine (Cardiology) Yale School of Medicine New Haven CT

We introduce Cell2Sentence (C2S), a novel method to directly adapt large language models to a biological context, specifically single-cell transcriptomics. By transforming gene expression data into "cell sentences," C2S bridges the gap between natural language processing and biology. We demonstrate cell sentences enable the fine-tuning of language models for diverse tasks in biology, including cell generation, complex cell-type annotation, and direct data-driven text generation. Our experiments reveal that GPT-2, when fine-tuned with C2S, can generate biologically valid cells based on cell type inputs, and accurately predict cell types from cell sentences. This illustrates that language models, through C2S fine-tuning, can acquire a significant understanding of single-cell biology while maintaining robust text generation capabilities. C2S offers a flexible, accessible framework to integrate natural language processing with transcriptomics, utilizing existing models and libraries for a wide range of biological applications.

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Design of a SiPM-on-Tile ZDC for the future EIC, and its Performance with Graph Neural Networks

arXiv

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arXiv 2024年

作者： Milton, Ryan Paul, Sebouh J. Schmookler, Barak Arratia, Miguel Karande, Piyush Angerami, Aaron Acosta, Fernando Torales Nachman, Benjamin Department of Physics and Astronomy University of California RiversideCA92521 United States Nuclear and Chemical Science Division Lawrence Livermore National Laboratory LivermoreCA94550 United States Computational Engineering Division Lawrence Livermore National Laboratory LivermoreCA94550 United States Physics Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Berkeley Institute for Data Science University of California BerkeleyCA94720 United States

We present a design for a high-granularity zero-degree calorimeter (ZDC) for the upcoming Electron-Ion Collider (EIC). The design uses SiPM-on-tile technology and features a novel staggered-layer arrangement that improves spatial resolution. To fully leverage the design’s high granularity and non-trivial geometry, we employ graph neural networks (GNNs) for energy and angle regression as well as signal classification. The GNN-boosted performance metrics meet, and in some cases, significantly surpass the requirements set in the EIC Yellow Report, laying the groundwork for enhanced measurements that will facilitate a wide physics program. Our studies show that GNNs can significantly enhance the performance of high-granularity CALICE-style calorimeters by automating and optimizing the software compensation algorithms required for these systems. This improvement holds true even in the case of complicated geometries that pose challenges for image-based AI/ML methods. © 2024, CC BY.

关键词： Image enhancement

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Fuzzychain: An equitable consensus mechanism for blockchain networks

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Journal of Network and Computer Applications 2025年 241卷

作者： Ramos-Cruz, Bruno Andreu-Perez, Javier Quesada-Real, Francisco J. Martínez, Luis Computer Science Department University of Jaen Jaen Jaen23071 Spain Centre for Computational Intelligencer School of Computer Science and Electronic Engineering University of Essex Colchester United Kingdom Andalusian Research Institute in Data Science and Computational Intelligence Jaen Jaen23071 Spain

Blockchain technology has become a trusted method for establishing secure and transparent transactions through a distributed, encrypted network. The operation of blockchain is governed by consensus algorithms, among which Proof of Stake (PoS) is popular yet has its drawbacks, notably the potential for centralising power in nodes with larger stakes or higher rewards. Our proposed novel solution, Fuzzychain, leverages fuzzy sets to define stake semantics, introducing a degree of softness in validator selection. This approach mitigates rigid threshold-based decision-making by allowing gradual transitions between stake levels, reducing sharp disparities among validators. By incorporating this enhanced stake evaluation, Fuzzychain promotes a more adaptive and distributed selection process, ensuring a fairer and more inclusive blockchain network. A thorough assessment of a real-time multi-agent blockchain system to examine validator selection and reduce inequality, promoting a more equitable distribution of stakes among validators compared to other consensus mechanisms. This fosters a more inclusive selection process and a more equitably distributed network. © 2025 The Authors

关键词： Consensus algorithm

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An analysis of reconstruction noise from undersampled 4D flow MRI

arXiv

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arXiv 2022年

作者： Partin, Lauren Schiavazzi, Daniele E. Long, Carlos A. Sing Department Of Applied And Computational Mathematics And Statistics University Of Notre Dame Notre DameIN United States Institute For Mathematical And Computational Engineering Institute For Biological And Medical Engineering Pontificia Universidad Católica De Chile Santiago Chile ANID - Millennium Science Initiative Program Millennium Nucleus Center For The Discovery Of Structures In Complex Data Chile ANID - Millennium Science Initiative Program Millennium Nucleus Center For Cardiovascular Magnetic Resonance Chile

Novel Magnetic Resonance (MR) imaging modalities can quantify hemodynamics but require long acquisition times, precluding its widespread use for early diagnosis of cardiovascular disease. To reduce the acquisition times, reconstruction methods from undersampled measurements are routinely used, that leverage representations designed to increase image compressibility. Reconstructed anatomical and hemodynamic images may present visual artifacts. Although some of these artifact are essentially reconstruction errors, and thus a consequence of undersampling, others may be due to measurement noise or the random choice of the sampled frequencies. Said otherwise, a reconstructed image becomes a random variable, and both its bias and its covariance can lead to visual artifacts;the latter leads to spatial correlations that may be misconstrued for visual information. Although the nature of the former has been studied in the literature, the latter has not received as much attention. In this study, we investigate the theoretical properties of the random perturbations arising from the reconstruction process, and perform a number of numerical experiments on simulated and MR aortic flow. Our results show that the correlation length remains limited to two to three pixels when a Gaussian undersampling pattern is combined with recovery algorithms based on 1-norm minimization. However, the correlation length may increase significantly for other undersampling patterns, higher undersampling factors (i.e., 8× or 16× compression), and different reconstruction methods. © 2022, CC BY-NC-ND.

关键词： Magnetic resonance

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ANY GRAPH IS A MAPPER GRAPH

arXiv

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arXiv 2024年

作者： Alvarado, Enrique G. Belton, Robin Lee, Kang-Ju Palande, Sourabh Percival, Sarah Purvine, Emilie Tymochko, Sarah Department of Mathematics University of California at Davis DavisCA United States Department Mathematical Sciences Smith College NorthamptonMA United States Research Institute of Mathematics Seoul National University Seoul Korea Republic of Department of Computational Mathematics Science and Engineering Michigan State University East LansingMI United States Department of Mathematics and Statistics University of New Mexico AlbuquerqueNM United States Mathematics Statistics and Data Science Pacific Northwest National Laboratory SeattleWA United States Department of Mathematics University of California Los Angeles Los AngelesCA United States

The Mapper algorithm is a popular tool for visualization and data exploration in topological data analysis. We investigate an inverse problem for the Mapper algorithm: Given a dataset X and a graph G, does there exist a set of Mapper parameters such that the output Mapper graph of X is isomorphic to G? We provide constructions that affirmatively answer this question. Our results demonstrate that it is possible to engineer Mapper parameters to generate a desired graph. Copyright © 2024, The Authors. All rights reserved.

关键词： data centers

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Intra-datacenter Load Balancing in a Federated Cloud with Throttled Algorithm

Intra-Datacenter Load Balancing in a Federated Cloud with Th...

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science, engineering and Business for Sustainable Development Goals (SEB-SDG), International Conference on

作者： Damola Gideon Akinola Emmanuel Adetiba Abdultaofeek Abayomi Uche Nnaji Surendra Thakur Sibusiso Moyo Department of Electrical and Information Engineering Covenant Applied Informatics and Communications African Center of Excellence Covenant University Ota Nigeria HRA Institute for Systems Science Durban University of Technology Durban South Africa Department of Information and Communication Technology Mangosuthu University of Technology Durban South Africa Dept. of Computer and Information Science Covenant Applied Informatics and Communications African Center of Excellence Covenant University Ota Nigeria KZN e-Skills CoLab Durban University of Technology Durban South Africa School for Data Science and Computational Thinking and Department of Mathematical Sciences Stellenbosch University Stellenbosch South Africa

ISBN: (数字)9798350358155

ISBN: (纸本)9798350358162

The emergence of cloud computing technology has motivated a very high number of users in different organizations to access its services in running and delivering their various operations and services. However, this surge of cloud users has led to the problem of uneven load sharing among the cloud computing infrastructures. As a result, federated cloud infrastructure was initiated to provide more cloud computing resources to accommodate more cloud users’ requests and also to provide equal requests mapping with the available cloud resources. Nevertheless, the issue of unequal allocation of requests within the datacenter(s) that makes up the federated cloud environment still persists. This research work presents an intra-datacenter load balancing algorithm in a federated cloud environment named; the intra-balancer adapted throttled algorithm to evenly distribute requests in each datacenter that formulate the federated cloud infrastructures. The simulation of the intra-balancer was carried out in CloudAnalyst, the results of the implementation showed that the intra-balancer outperformed the Round-Robin and ESCE with 98.93ms and 2.26ms for the response and processing time respectively. The results assert that the intra-balancer algorithm provides a better load balancing solution in a federated cloud environment.

关键词： Computers Cloud computing Organizations Load management Resource management Time factors Task analysis

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Probabilistic partition of unity networks for high-dimensional regression problems

arXiv

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arXiv 2022年

作者： Fan, Tiffany Trask, Nathaniel D'Elia, Marta Darve, Eric Institute for Computational and Mathematical Engineering Stanford University CA United States Center for Computing Research Sandia National Laboratories New Mexico United States Data Science and Computing Sandia National Laboratories CA United States Department of Mechanical Engineering Stanford University CA United States

We explore the probabilistic partition of unity network (PPOU-Net) model in the context of high-dimensional regression problems and propose a general framework focusing on adaptive dimensionality reduction. With the proposed framework, the target function is approximated by a mixture of experts model on a low-dimensional manifold, where each cluster is associated with a local fixed-degree polynomial. We present a training strategy that leverages the expectation maximization (EM) algorithm. During the training, we alternate between (i) applying gradient descent to update the DNN coefficients;and (ii) using closed-form formulae derived from the EM algorithm to update the mixture of experts model parameters. Under the probabilistic formulation, step (ii) admits the form of embarrassingly parallelizable weighted least-squares solves. The PPOU-Nets consistently outperform the baseline fully-connected neural networks of comparable sizes in numerical experiments of various data dimensions. We also explore the proposed model in applications of quantum computing, where the PPOU-Nets act as surrogate models for cost landscapes associated with variational quantum circuits. Copyright © 2022, The Authors. All rights reserved.

关键词： Quantum computers

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MOST DISCRIMINATIVE STIMULI FOR FUNCTIONAL CELL TYPE CLUSTERING 12

MOST DISCRIMINATIVE STIMULI FOR FUNCTIONAL CELL TYPE CLUSTER...

引用

12th International Conference on Learning Representations, ICLR 2024

作者： Burg, Max F. Zenkel, Thomas Vystrčilová, Michaela Oesterle, Jonathan Höfling, Larissa Willeke, Konstantin F. Lause, Jan Müller, Sarah Fahey, Paul G. Ding, Zhiwei Restivo, Kelli Sridhar, Shashwat Gollisch, Tim Berens, Philipp Tolias, Andreas S. Euler, Thomas Bethge, Matthias Ecker, Alexander S. International Max Planck Research School for Intelligent Systems Tübingen Germany Institute of Computer Science and Campus Institute Data Science University of Göttingen Germany Tübingen AI Center University of Tübingen Germany Institute of Ophthalmic Research University of Tübingen Germany Centre for Integrative Neuroscience University of Tübingen Germany Institute for Bioinformatics and Medical Informatics Tübingen University Germany Hertie Institute for AI in Brain Health University of Tübingen Germany Department of Neuroscience Baylor College of Medicine HoustonTX United States Center for Neuroscience and Artificial Intelligence Baylor College of Medicine HoustonTX United States University Medical Center Göttingen Department of Ophthalmology Germany Bernstein Center for Computational Neuroscience Göttingen Germany University of Göttingen Germany Department of Electrical and Computer Engineering Rice University HoustonTX United States Max Planck Institute for Dynamics and Self-Organization Göttingen Germany

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron. © 2024 12th International Conference on Learning Representations, ICLR 2024. All rights reserved.

关键词： Maximum principle

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How to learn when data gradually reacts to your model

arXiv

引用

arXiv 2021年

作者： Izzo, Zachary Ying, Lexing Zou, James Department of Mathematics Stanford University United States Institute for Computational and Mathematical Engineering Stanford University United States Department of Biomedical Data Science Stanford University United States

A recent line of work has focused on training machine learning (ML) models in the performative setting, i.e. when the data distribution reacts to the deployed model. The goal in this setting is to learn a model which both induces a favorable data distribution and performs well on the induced distribution, thereby minimizing the test loss. Previous work on finding an optimal model assumes that the data distribution immediately adapts to the deployed model. In practice, however, this may not be the case, as the population may take time to adapt to the model. In many applications, the data distribution depends on both the currently deployed ML model and on the "state" that the population was in before the model was deployed. In this work, we propose a new algorithm, Stateful Performative Gradient Descent (Stateful PerfGD), for minimizing the performative loss even in the presence of these effects. We provide theoretical guarantees for the convergence of Stateful PerfGD. Our experiments confirm that Stateful PerfGD substantially outperforms previous state-of-the-art methods. Copyright © 2021, The Authors. All rights reserved.

关键词： Gradient methods

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How to learn when data reacts to your model: Performative gradient descent

arXiv

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arXiv 2021年

Performative distribution shift captures the setting where the choice of which ML model is deployed changes the data distribution. For example, a bank which uses the number of open credit lines to determine a customer’s risk of default on a loan may induce customers to open more credit lines in order to improve their chances of being approved. Because of the interactions between the model and data distribution, finding the optimal model parameters is challenging. Works in this area have focused on finding stable points, which can be far from optimal. Here we introduce performative gradient descent (PerfGD), which is the first algorithm which provably converges to the performatively optimal point. PerfGD explicitly captures how changes in the model affects the data distribution and is simple to use. We support our findings with theory and experiments. © 2021, CC BY.

关键词： Gradient methods

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