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T-Cell Receptor Optimization with Reinforcement learning and Mutation Polices for Precision Immunotherapy 27th

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T-Cell Receptor Optimization with Reinforcement Learning an...

27th International Conference on Research in Computational Molecular Biology, RECOMB 2023

作者： Chen, Ziqi Min, Martin Renqiang Guo, Hongyu Cheng, Chao Clancy, Trevor Ning, Xia Computer Science and Engineering The Ohio State University ColumbusOH43210 United States Machine Learning Department NEC Labs PrincetonNJ08540 United States Digital Technologies Research Centre National Research Council Canada Ontario Canada Department of Medicine Baylor College of Medicine HoustonTX77030 United States NEC Oncolmmunity AS Oslo Cancer Cluster Innovation Park Ullernchausséen 64 Oslo0379 Norway Biomedical Informatics The Ohio State University ColumbusOH43210 United States Translational Data Analytics Institute The Ohio State University ColumbusOH43210 United States

ISBN: (纸本)9783031291180

T cells monitor the health status of cells by identifying foreign peptides displayed on their surface. T-cell receptors (TCRs), which are protein complexes found on the surface of T cells, are able to bind to these peptides. This process is known as TCR recognition and constitutes a key step for immune response. Optimizing TCR sequences for TCR recognition represents a fundamental step towards the development of personalized treatments to trigger immune responses killing cancerous or virus-infected cells. In this paper, we formulated the search for these optimized TCRs as a reinforcement learning (Formula Presented) problem, and presented a framework (Formula Presented) with a mutation policy using proximal policy optimization. (Formula Presented) mutates TCRs into effective ones that can recognize given peptides. (Formula Presented) leverages a reward function that combines the likelihoods of mutated sequences being valid TCRs measured by a new scoring function based on deep autoencoders, with the probabilities of mutated sequences recognizing peptides from a peptide-TCR interaction predictor. We compared (Formula Presented) with multiple baseline methods and demonstrated that (Formula Presented) significantly outperforms all the baseline methods to generate positive binding and valid TCRs. These results demonstrate the potential of(Formula Presented) for both precision immunotherapy and peptide-recognizing TCR motif discovery. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Reinforcement learning

Heat flux for semilocal machine-learning potentials

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Physical Review B 2023年第10期108卷 L100302-L100302页

作者： Marcel F. Langer Florian Knoop Christian Carbogno Matthias Scheffler Matthias Rupp Machine Learning Group Technische Universität Berlin 10587 Berlin Germany Berlin Institute for the Foundations of Learning and Data 10623 Berlin Germany The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS Adlershof of the Humboldt Universität zu Berlin 14195 Berlin Germany Theoretical Physics Division Department of Physics Chemistry and Biology (IFM) Linköping University 581 83 Linköping Sweden Department of Computer and Information Science University of Konstanz 78464 Konstanz Germany Materials Research and Technology Department Luxembourg Institute of Science and Technology Belvaux Luxembourg

The Green-Kubo (GK) method is a rigorous framework for heat transport simulations in materials. However, it requires an accurate description of the potential-energy surface and carefully converged statistics. machine-learning potentials can achieve the accuracy of first-principles simulations while allowing to reach well beyond their simulation time and length scales at a fraction of the cost. In this Letter, we explain how to apply the GK approach to the recent class of message-passing machine-learning potentials, which iteratively consider semilocal interactions beyond the initial interaction cutoff. We derive an adapted heat flux formulation that can be implemented using automatic differentiation without compromising computational efficiency. The approach is demonstrated and validated by calculating the thermal conductivity of zirconium dioxide across temperatures.

关键词： Lattice thermal conductivity machine learning Molecular dynamics Neural network simulations

SPEAR: Design and Implementation of an Advanced Virtual Assistant

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SPEAR: Design and Implementation of an Advanced Virtual Assi...

Sustainable Expert Systems (ICSES), International Conference on

作者： Garima Jain Amita Shukla Nitesh Kumar Bairwa Anamika Chaudhary Ashish Patel Ankush Jain Department of Computer Science and Buisness Systems Noida Institute of Engineering and Technology Greater Noida India Department of Artificial Intelligence Noida Institute of Engineering and Technology Greater Noida India Department of Data Science Noida Institute of Engineering and Technology Greater Noida India Department of Artificial Intelligence and Machine Learning Dronacharya Group of Institutions Greater Noida India Department of Computer Science and Enginnering Netaji Subhash University of Technology Delhi India

ISBN: (数字)9798331540364

ISBN: (纸本)9798331540371

This research presents the development and evaluation of SPEAR, an advanced voice-activated personal desktop assistant designed to address challenges in existing virtual assistant technology, such as limited language support, low recognition accuracy, and inadequate task automation. Despite recent advancements in Natural Language Processing (NLP) and machine learning, implementation in current systems remains subpar. SPEAR achieves an 88% overall command execution success rate, with a speech recognition accuracy of 92% and an average response time of 1.8 seconds, demonstrating efficiency in real-time interactions. Developed using Python and machine learning libraries, SPEAR supports 15 voice commands across multiple platforms, excelling in note creation (95% success), web searching (94%), and information retrieval (92%). Its natural language understanding score of 0.86 and context retention rate of 75% highlight its conversational capabilities. While the assistant performs well in messaging functionality (85% success) and currently supports three languages, expanding its multilingual capabilities is essential for broader user engagement. Metrics indicate a satisfaction score of 8.2/10 and an average of 12 daily interactions per user, showcasing its practical utility. Additionally, the system's text-to-speech quality (8.5/10) and error recovery rate (82 %) affirm its robustness. These findings contribute valuable insights for future research, focusing on enhancing multilingual support, broadening task categories, and improving context retention, ultimately positioning SPEAR to rival established industry leaders by offering a comprehensive suite of services.

关键词： Accuracy Personal voice assistants machine learning Information retrieval Natural language processing Real-time systems Robustness Text to speech Time factors Web search

PAM: A Propagation-Based Model for Segmenting Any 3D Objects across Multi-Modal Medical Images

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arXiv 2024年

作者： Chen, Zifan Nan, Xinyu Li, Jiazheng Zhao, Jie Li, Haifeng Lin, Ziling Li, Haoshen Chen, Heyun Liu, Yiting Tang, Lei Zhang, Li Dong, Bin Center for Data Science Peking University Beijing China Department of Radiology Key Laboratory of Carcinogenesis and Translational Research Ministry of Education Peking University Cancer Hospital and Institute Beijing China National Engineering Laboratory for Big Data Analysis and Applications Peking University Beijing China Peking University Beijing China Center for Machine Learning Research Peking University Beijing China National Biomedical Imaging Center Peking University Beijing China

Background: Volumetric segmentation is crucial for medical imaging applications but faces significant challenges. Current approaches often require extensive manual annotations and scenario-specific model training, limiting their transferability across different tasks or modalities. While general segmentation models offer some versatility in natural image processing, they struggle with the unique characteristics of medical images. There is an urgent need in clinical practice for a new segmentation approach that can effectively handle medical imagery features while maintaining adaptability across various three-dimensional objects and imaging modalities. Methods: We introduce PAM (Propagating Anything Model), a propagation-based segmentation approach that operates on 3D medical image volumes using a 2D prompt (bounding box or sketch mask). PAM extrapolates this initial input to generate a complete 3D segmentation by modeling inter-slice structural relationships, establishing a continuous information flow within 3D medical structures. This approach enhances segmentation effectiveness across various imaging modalities by focusing on structural and semantic continuities rather than isolating specific objects. The model combines a CNN-based UNet architecture for intra-slice information processing with a Transformer-based attention module to facilitate inter-slice propagation. This innovative framework results in a method with unique generalizability, capable of segmenting diverse 3D objects across different medical imaging modalities. Results: PAM demonstrated superior performance on 44 diverse medical datasets, notably improving the dice similarity coefficient (DSC) for hundreds of segmentation object types and various medical imaging modalities. Compared to modern models like MedSAM and SegVol, PAM achieved an average DSC improvement of over 18.1%, while maintaining stable predictions despite prompt deviation (one-way ANOVA test, P ≥ 0.5985) and varying propagation confi

关键词： Semantic Segmentation

Improving generative model-based unfolding with Schrödinger bridges

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Physical Review D 2024年第7期109卷 076011-076011页

作者： Sascha Diefenbacher Guan-Horng Liu Vinicius Mikuni Benjamin Nachman Weili Nie Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Autonomous Control and Decision Systems Laboratory Georgia Institute of Technology Atlanta Georgia 30332 USA National Energy Research Scientific Computing Center Berkeley Lab Berkeley California 94720 USA Berkeley Institute for Data Science University of California Berkeley California 94720 USA Machine Learning Research Group NVIDIA Research

machine learning-based unfolding has enabled unbinned and high-dimensional differential cross section measurements. Two main approaches have emerged in this research area; one based on discriminative models and one based on generative models. The main advantage of discriminative models is that they learn a small correction to a starting simulation while generative models scale better to regions of phase space with little data. We propose to use Schrödinger bridges and diffusion models to create sbunfold, an unfolding approach that combines the strengths of both discriminative and generative models. The key feature of sbunfold is that its generative model maps one set of events into another without having to go through a known probability density as is the case for normalizing flows and standard diffusion models. We show that sbunfold achieves excellent performance compared to state of the art methods on a synthetic Z+jets dataset.

关键词： machine learning Particle detectors Probability theory

Towards Symbolic XAI – Explanation Through Human Understandable Logical Relationships Between Features

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arXiv 2024年

作者： Schnake, Thomas Jafari, Farnoush Rezaei Lederer, Jonas Xiong, Ping Nakajima, Shinichi Gugler, Stefan Montavon, Grégoire Müller, Klaus-Robert Berlin Institute for the Foundations of Learning and Data – BIFOLD Berlin10623 Germany Machine Learning Group Technical University of Berlin Berlin10623 Germany RIKEN AIP Tokyo103-0027 Japan Department of Artificial Intelligence Korea University Seoul136-713 Korea Republic of Max Planck Institut für Informatik Saarbrücken66123 Germany Department of Mathematics and Computer Science Free University of Berlin Berlin14195 Germany

Explainable Artificial Intelligence (XAI) plays a crucial role in fostering transparency and trust in AI systems, where traditional XAI approaches typically offer one level of abstraction for explanations, often in the form of heatmaps highlighting single or multiple input features. However, we ask whether abstract reasoning or problem-solving strategies of a model may also be relevant, as these align more closely with how humans approach solutions to problems. We propose a framework, called Symbolic XAI, that attributes relevance to symbolic queries expressing logical relationships between input features, thereby capturing the abstract reasoning behind a model’s predictions. The methodology is built upon a simple yet general multi-order decomposition of model predictions. This decomposition can be specified using higher-order propagation-based relevance methods, such as GNN-LRP, or perturbation-based explanation methods commonly used in XAI. The effectiveness of our framework is demonstrated in the domains of natural language processing (NLP), vision, and quantum chemistry (QC), where abstract symbolic domain knowledge is abundant and of significant interest to users. The Symbolic XAI framework provides an understanding of the model’s decision-making process that is both flexible for customization by the user and human-readable through logical formulas. Copyright © 2024, The Authors. All rights reserved.

关键词： Decision making

learning with group Noise

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arXiv 2021年

作者： Wang, Qizhou Yao, Jiangchao Gong, Chen Liu, Tongliang Gong, Mingming Yang, Hongxia Han, Bo Department of Computer Science Hong Kong Baptist University Hong Kong Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of MoE School of Computer Science and Engineering Nanjing University of Science and Technology China Data Analytics and Intelligence Lab Alibaba Group China Department of Computing Hong Kong Polytechnic University Hong Kong Trustworthy Machine Learning Lab School of Computer Science University of Sydney Australia School of Mathematics and Statistics University of Melbourne Australia

machine learning in the context of noise is a challenging but practical setting to plenty of real-world applications. Most of the previous approaches in this area focus on the pairwise relation (casual or correlational relationship) with noise, such as learning with noisy labels. However, the group noise, which is parasitic on the coarse-grained accurate relation with the fine-grained uncertainty, is also universal and has not been well investigated. The challenge under this setting is how to discover true pairwise connections concealed by the group relation with its fine-grained noise. To overcome this issue, we propose a novel Max-Matching method for learning with group noise. Specifically, it utilizes a matching mechanism to evaluate the relation confidence of each object (cf. Figure 1) w.r.t. the target, meanwhile considering the Non-IID characteristics among objects in the group. Only the most confident object is considered to learn the model, so that the fine-grained noise is mostly dropped. The performance on a range of real-world datasets in the area of several learning paradigms demonstrates the effectiveness of Max-Matching. Copyright © 2021, The Authors. All rights reserved.

关键词： machine learning

Big data = Big Insights? Operationalising Brooks’ Law in a Massive GitHub data Set

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arXiv 2022年

作者： Gote, Christoph Schweitzer, Frank Mavrodiev, Pavlin Scholtes, Ingo Department of Systems Design ETH Zurich Weinbergstrasse 56/58 Zurich8092 Switzerland Department of Computer Science XV - Machine Learning for Complex Networks Julius-Maximilians-Universität Würzburg Friedrich-Bergius-Ring 30 Würzburg97076 Germany Data Analytics Group University of Zurich Binzmühlestrasse 14 Zurich8050 Switzerland

Massive data from software repositories and collaboration tools are widely used to study social aspects in software development. One question that several recent works have addressed is how a software project’s size and structure influence team productivity, a question famously considered in Brooks’ law. Recent studies using massive repository data suggest that developers in larger teams tend to be less productive than smaller teams. Despite using similar methods and data, other studies argue for a positive linear or even super-linear relationship between team size and productivity, thus contesting the view of software economics that software projects are diseconomies of scale. In our work, we study challenges that can explain the disagreement between recent studies of developer productivity in massive repository data. We further provide, to the best of our knowledge, the largest, curated corpus of GitHub projects tailored to investigate the influence of team size and collaboration patterns on individual and collective productivity. Our work contributes to the ongoing discussion on the choice of productivity metrics in the operationalisation of hypotheses about determinants of successful software projects. It further highlights general pitfalls in big data analysis and shows that the use of bigger data sets does not automatically lead to more reliable insights. Copyright © 2022, The Authors. All rights reserved.

关键词： Productivity

COMPUTER AUDITION: FROM TASK-SPECIFIC machine learning TO FOUNDATION MODELS

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arXiv 2024年

作者： Triantafyllopoulos, Andreas Tsangko, Iosif Gebhard, Alexander Mesaros, Annamaria Virtanen, Tuomas Schuller, Björn W. CHI – Chair of Health Informatics Technical University of Munich MRI Munich Germany Audio Research Group Tampere University Tampere Finland EIHW – Chair of Embedded Intelligence for Health Care and Wellbeing University of Augsburg Augsburg Germany GLAM – Group on Language Audio & Music Imperial College London United Kingdom MCML – Munich Center for Machine Learning Munich Germany MDSI – Munich Data Science Institute Munich Germany

Foundation models (FMs) are increasingly spearheading recent advances on a variety of tasks that fall under the purview of computer audition – the use of machines to understand sounds. They feature several advantages over traditional pipelines: among others, the ability to consolidate multiple tasks in a single model, the option to leverage knowledge from other modalities, and the readily-available interaction with human users. Naturally, these promises have created substantial excitement in the audio community, and have led to a wave of early attempts to build new, general-purpose foundation models for audio. In the present contribution, we give an overview of computational audio analysis as it transitions from traditional pipelines towards auditory foundation models. Our work highlights the key operating principles that underpin those models, and showcases how they can accommodate multiple tasks that the audio community previously tackled separately. Copyright © 2024, The Authors. All rights reserved.

关键词： Pipelines