LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Your last searches

  1. AU="Bassett, Dani S."
  2. AU="James Lemon"
  3. AU="Gros, Stephanie J"
  4. AU="Saeed Khademi"
  5. AU="Lallet-Daher, Helene"
  6. AU="Greenblatt, M"
  7. AU="Patwa, Ajay K"
  8. AU=Mastaglia F L
  9. AU="De Croock, Femke"
  10. AU=Robinson Michael J
  11. AU=Singh Romil
  12. AU="Martin, S J"
  13. AU="Szendrői, Miklós"
  14. AU="Moncel, Marie-Hélène"
  15. AU=Otu Akaninyene AU=Otu Akaninyene
  16. AU="Chiba, Kentaro"
  17. AU="Zhou, Jihua"
  18. AU="Ronald Bartels"
  19. AU="Liñares, J"
  20. AU="Valle, Valentina"
  21. AU="Tóth, András"
  22. AU="Pawar, Atul Darasing"
  23. AU="Semper, Chelsea"
  24. AU="Kraus, Joanne F"

Search results

Result 1 - 10 of total 92

Search options

  1. Article ; Online: Information decomposition in complex systems via machine learning.

    Murphy, Kieran A / Bassett, Dani S

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 13, Page(s) e2312988121

    Abstract: One of the fundamental steps toward understanding a complex system is identifying variation at the scale of the system's components that is most relevant to behavior on a macroscopic scale. Mutual information provides a natural means of linking variation ...

    Abstract One of the fundamental steps toward understanding a complex system is identifying variation at the scale of the system's components that is most relevant to behavior on a macroscopic scale. Mutual information provides a natural means of linking variation across scales of a system due to its independence of functional relationship between observables. However, characterizing the manner in which information is distributed across a set of observables is computationally challenging and generally infeasible beyond a handful of measurements. Here, we propose a practical and general methodology that uses machine learning to decompose the information contained in a set of measurements by jointly optimizing a lossy compression of each measurement. Guided by the distributed information bottleneck as a learning objective, the information decomposition identifies the variation in the measurements of the system state most relevant to specified macroscale behavior. We focus our analysis on two paradigmatic complex systems: a Boolean circuit and an amorphous material undergoing plastic deformation. In both examples, the large amount of entropy of the system state is decomposed, bit by bit, in terms of what is most related to macroscale behavior. The identification of meaningful variation in data, with the full generality brought by information theory, is made practical for studying the connection between micro- and macroscale structure in complex systems.
    Language English
    Publishing date 2024-03-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2312988121
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Causation in neuroscience: keeping mechanism meaningful.

    Ross, Lauren N / Bassett, Dani S

    Nature reviews. Neuroscience

    2024  Volume 25, Issue 2, Page(s) 81–90

    Abstract: A fundamental goal of research in neuroscience is to uncover the causal structure of the brain. This focus on causation makes sense, because causal information can provide explanations of brain function and identify reliable targets with which to ... ...

    Abstract A fundamental goal of research in neuroscience is to uncover the causal structure of the brain. This focus on causation makes sense, because causal information can provide explanations of brain function and identify reliable targets with which to understand cognitive function and prevent or change neurological conditions and psychiatric disorders. In this research, one of the most frequently used causal concepts is 'mechanism' - this is seen in the literature and language of the field, in grant and funding inquiries that specify what research is supported, and in journal guidelines on which contributions are considered for publication. In these contexts, mechanisms are commonly tied to expressions of the main aims of the field and cited as the 'fundamental', 'foundational' and/or 'basic' unit for understanding the brain. Despite its common usage and perceived importance, mechanism is used in different ways that are rarely distinguished. Given that this concept is defined in different ways throughout the field - and that there is often no clarification of which definition is intended - there remains a marked ambiguity about the fundamental goals, orientation and principles of the field. Here we provide an overview of causation and mechanism from the perspectives of neuroscience and philosophy of science, in order to address these challenges.
    MeSH term(s) Humans ; Cognition ; Brain ; Neurosciences ; Philosophy ; Mental Disorders
    Language English
    Publishing date 2024-01-11
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2034150-7
    ISSN 1471-0048 ; 1471-0048 ; 1471-003X
    ISSN (online) 1471-0048
    ISSN 1471-0048 ; 1471-003X
    DOI 10.1038/s41583-023-00778-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Tracking Disordered Brain Dynamics in Psychiatry.

    Parkes, Linden / Bassett, Dani S

    Biological psychiatry

    2023  Volume 94, Issue 7, Page(s) 528–530

    MeSH term(s) Brain ; Psychiatry
    Language English
    Publishing date 2023-09-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 209434-4
    ISSN 1873-2402 ; 0006-3223
    ISSN (online) 1873-2402
    ISSN 0006-3223
    DOI 10.1016/j.biopsych.2023.07.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: Understanding divergence: Placing developmental neuroscience in its dynamic context.

    Astle, Duncan E / Bassett, Dani S / Viding, Essi

    Neuroscience and biobehavioral reviews

    2024  Volume 157, Page(s) 105539

    Abstract: Neurodevelopment is not merely a process of brain maturation, but an adaptation to constraints unique to each individual and to the environments we co-create. However, our theoretical and methodological toolkits often ignore this reality. There is ... ...

    Abstract Neurodevelopment is not merely a process of brain maturation, but an adaptation to constraints unique to each individual and to the environments we co-create. However, our theoretical and methodological toolkits often ignore this reality. There is growing awareness that a shift is needed that allows us to study divergence of brain and behaviour across conventional categorical boundaries. However, we argue that in future our study of divergence must also incorporate the developmental dynamics that capture the emergence of those neurodevelopmental differences. This crucial step will require adjustments in study design and methodology. If our ultimate aim is to incorporate the developmental dynamics that capture how, and ultimately when, divergence takes place then we will need an analytic toolkit equal to these ambitions. We argue that the over reliance on group averages has been a conceptual dead-end with regard to the neurodevelopmental differences. This is in part because any individual differences and developmental dynamics are inevitably lost within the group average. Instead, analytic approaches which are themselves new, or simply newly applied within this context, may allow us to shift our theoretical and methodological frameworks from groups to individuals. Likewise, methods capable of modelling complex dynamic systems may allow us to understand the emergent dynamics only possible at the level of an interacting neural system.
    MeSH term(s) Humans ; Brain ; Research Design
    Language English
    Publishing date 2024-01-09
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 282464-4
    ISSN 1873-7528 ; 0149-7634
    ISSN (online) 1873-7528
    ISSN 0149-7634
    DOI 10.1016/j.neubiorev.2024.105539
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Book ; Online: Optimized measurements of chaotic dynamical systems via the information bottleneck

    Murphy, Kieran A. / Bassett, Dani S.

    2023  

    Abstract: Deterministic chaos permits a precise notion of a "perfect measurement" as one that, when obtained repeatedly, captures all of the information created by the system's evolution with minimal redundancy. Finding an optimal measurement is challenging, and ... ...

    Abstract Deterministic chaos permits a precise notion of a "perfect measurement" as one that, when obtained repeatedly, captures all of the information created by the system's evolution with minimal redundancy. Finding an optimal measurement is challenging, and has generally required intimate knowledge of the dynamics in the few cases where it has been done. We establish an equivalence between a perfect measurement and a variant of the information bottleneck. As a consequence, we can employ machine learning to optimize measurement processes that efficiently extract information from trajectory data. We obtain approximately optimal measurements for multiple chaotic maps and lay the necessary groundwork for efficient information extraction from general time series.

    Comment: Project page: https://distributed-information-bottleneck.github.io
    Keywords Computer Science - Machine Learning ; Computer Science - Information Theory ; Nonlinear Sciences - Chaotic Dynamics
    Subject code 006
    Publishing date 2023-11-08
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  6. Book ; Online: Information decomposition to identify relevant variation in complex systems with machine learning

    Murphy, Kieran A. / Bassett, Dani S.

    2023  

    Abstract: One of the fundamental steps toward understanding a complex system is identifying variation at the scale of the system's components that is most relevant to behavior on a macroscopic scale. Mutual information is a natural means of linking variation ... ...

    Abstract One of the fundamental steps toward understanding a complex system is identifying variation at the scale of the system's components that is most relevant to behavior on a macroscopic scale. Mutual information is a natural means of linking variation across scales of a system due to its independence of the particular functional relationship between variables. However, estimating mutual information given high-dimensional, continuous-valued data is notoriously difficult, and the desideratum -- to reveal important variation in a comprehensible manner -- is only readily achieved through exhaustive search. Here we propose a practical, efficient, and broadly applicable methodology to decompose the information contained in a set of measurements by lossily compressing each measurement with machine learning. Guided by the distributed information bottleneck as a learning objective, the information decomposition sorts variation in the measurements of the system state by relevance to specified macroscale behavior, revealing the most important subsets of measurements for different amounts of predictive information. Additional granularity is achieved by inspection of the learned compression schemes: the variation transmitted during compression is composed of distinctions among measurement values that are most relevant to the macroscale behavior. We focus our analysis on two paradigmatic complex systems: a Boolean circuit and an amorphous material undergoing plastic deformation. In both examples, specific bits of entropy are identified out of the high entropy of the system state as most related to macroscale behavior for insight about the connection between micro- and macro- in the complex system. The identification of meaningful variation in data, with the full generality brought by information theory, is made practical for the study of complex systems.

    Comment: Project page: https://distributed-information-bottleneck.github.io/
    Keywords Computer Science - Machine Learning ; Condensed Matter - Soft Condensed Matter ; Computer Science - Information Theory ; Physics - Data Analysis ; Statistics and Probability
    Subject code 006
    Publishing date 2023-07-10
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  7. Article ; Online: Epilepsy imaging meets machine learning: a new era of individualized patient care.

    Caciagli, Lorenzo / Bassett, Dani S

    Brain : a journal of neurology

    2021  Volume 145, Issue 3, Page(s) 807–810

    MeSH term(s) Epilepsy/diagnostic imaging ; Humans ; Machine Learning ; Magnetic Resonance Imaging/methods ; Patient Care
    Language English
    Publishing date 2021-12-11
    Publishing country England
    Document type Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 80072-7
    ISSN 1460-2156 ; 0006-8950
    ISSN (online) 1460-2156
    ISSN 0006-8950
    DOI 10.1093/brain/awac027
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article: Breaking reflection symmetry: evolving long dynamical cycles in Boolean systems.

    Ouellet, Mathieu / Kim, Jason Z / Guillaume, Harmange / Shaffer, Sydney M / Bassett, Lee C / Bassett, Dani S

    New journal of physics

    2024  Volume 26, Issue 2, Page(s) 23006

    Abstract: In interacting dynamical systems, specific local interaction rules for system components give rise to diverse and complex global dynamics. Long dynamical cycles are a key feature of many natural interacting systems, especially in biology. Examples of ... ...

    Abstract In interacting dynamical systems, specific local interaction rules for system components give rise to diverse and complex global dynamics. Long dynamical cycles are a key feature of many natural interacting systems, especially in biology. Examples of dynamical cycles range from circadian rhythms regulating sleep to cell cycles regulating reproductive behavior. Despite the crucial role of cycles in nature, the properties of network structure that give rise to cycles still need to be better understood. Here, we use a Boolean interaction network model to study the relationships between network structure and cyclic dynamics. We identify particular structural motifs that support cycles, and other motifs that suppress them. More generally, we show that the presence of
    Language English
    Publishing date 2024-02-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 1464444-7
    ISSN 1367-2630
    ISSN 1367-2630
    DOI 10.1088/1367-2630/ad1bdd
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article: Neural Dynamics During the Generation and Evaluation of Creative and Non-Creative Ideas.

    Kenett, Yoed N / Chrysikou, Evangelia G / Bassett, Dani S / Thompson-Schill, Sharon L

    bioRxiv : the preprint server for biology

    2024  

    Abstract: What are the neural dynamics that drive creative thinking? Recent studies have provided much insight into the neural mechanisms of creative thought. Specifically, the interaction between the executive control, default mode, and salience brain networks ... ...

    Abstract What are the neural dynamics that drive creative thinking? Recent studies have provided much insight into the neural mechanisms of creative thought. Specifically, the interaction between the executive control, default mode, and salience brain networks has been shown to be an important marker of individual differences in creative ability. However, how these different brain systems might be recruited dynamically during the two key components of the creative process-generation and evaluation of ideas-remains far from understood. In the current study we applied state-of-the-art network neuroscience methodologies to examine the neural dynamics related to the generation and evaluation of creative and non-creative ideas using a novel within-subjects design. Participants completed two functional magnetic resonance imaging sessions, taking place a week apart. In the first imaging session, participants generated either creative (alternative uses) or non-creative (common characteristics) responses to common objects. In the second imaging session, participants evaluated their own creative and non-creative responses to the same objects. Network neuroscience methods were applied to examine and directly compare reconfiguration, integration, and recruitment of brain networks during these four conditions. We found that generating creative ideas led to significantly higher network reconfiguration than generating non-creative ideas, whereas evaluating creative and non-creative ideas led to similar levels of network integration. Furthermore, we found that these differences were attributable to different dynamic patterns of neural activity across the executive control, default mode, and salience networks. This study is the first to show within-subject differences in neural dynamics related to generating and evaluating creative and non-creative ideas.
    Language English
    Publishing date 2024-04-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.15.589621
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Book ; Online: Interpretability with full complexity by constraining feature information

    Murphy, Kieran A. / Bassett, Dani S.

    2022  

    Abstract: Interpretability is a pressing issue for machine learning. Common approaches to interpretable machine learning constrain interactions between features of the input, rendering the effects of those features on a model's output comprehensible but at the ... ...

    Abstract Interpretability is a pressing issue for machine learning. Common approaches to interpretable machine learning constrain interactions between features of the input, rendering the effects of those features on a model's output comprehensible but at the expense of model complexity. We approach interpretability from a new angle: constrain the information about the features without restricting the complexity of the model. Borrowing from information theory, we use the Distributed Information Bottleneck to find optimal compressions of each feature that maximally preserve information about the output. The learned information allocation, by feature and by feature value, provides rich opportunities for interpretation, particularly in problems with many features and complex feature interactions. The central object of analysis is not a single trained model, but rather a spectrum of models serving as approximations that leverage variable amounts of information about the inputs. Information is allocated to features by their relevance to the output, thereby solving the problem of feature selection by constructing a learned continuum of feature inclusion-to-exclusion. The optimal compression of each feature -- at every stage of approximation -- allows fine-grained inspection of the distinctions among feature values that are most impactful for prediction. We develop a framework for extracting insight from the spectrum of approximate models and demonstrate its utility on a range of tabular datasets.

    Comment: project page: https://distributed-information-bottleneck.github.io
    Keywords Computer Science - Machine Learning
    Subject code 004
    Publishing date 2022-11-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

To top