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This paper addresses the problems of missing reasoning chains and insufficient entity-level semantic understanding in large language models when dealing with tasks that require structured knowledge. It proposes a fine-tuning algorithm…

Computation and Language · Computer Science 2025-08-21 Wuyang Zhang , Yexin Tian , Xiandong Meng , Mengjie Wang , Junliang Du

Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…

Other Quantitative Biology · Quantitative Biology 2024-02-06 Juan F Poyatos

Feature-Imitating-Networks (FINs) are neural networks that are first trained to approximate closed-form statistical features (e.g. Entropy), and then embedded into other networks to enhance their performance. In this work, we perform the…

Image and Video Processing · Electrical Eng. & Systems 2024-04-24 Shangyang Min , Hassan B. Ebadian , Tuka Alhanai , Mohammad Mahdi Ghassemi

Visual image reconstruction from functional Magnetic Resonance Imaging (fMRI) is a fundamental task in brain decoding, providing a crucial pathway for understanding human perceptual mechanisms and developing advanced brain-computer…

Computer Vision and Pattern Recognition · Computer Science 2026-05-20 Yudan Ren , Pengcheng Shi , Zihan Ma , Xiaowei He , Xiao Li

From an enactive approach, some previous studies have demonstrated that social interaction plays a fundamental role in the dynamics of neural and behavioral complexity of embodied agents. In particular, it has been shown that agents with a…

Multiagent Systems · Computer Science 2020-11-04 Georgina Montserrat Reséndiz-Benhumea , Ekaterina Sangati , Tom Froese

Functional brain graphs are often characterized with separate graph-theoretic or spectral descriptors, overlooking how these properties covary and partially overlap across brains and conditions. We anticipate that dense, weighted functional…

Neurons and Cognition · Quantitative Biology 2025-11-07 Subati Abulikemu , Tiago Azevedo , Michail Mamalakis , John Suckling

The placenta is a complex organ, playing multiple roles during fetal development. Very little is known about the association between placental morphological abnormalities and fetal physiology. In this work, we present an open sourced,…

Computer Vision and Pattern Recognition · Computer Science 2018-05-29 Michael Ferlaino , Craig A. Glastonbury , Carolina Motta-Mejia , Manu Vatish , Ingrid Granne , Stephen Kennedy , Cecilia M. Lindgren , Christoffer Nellåker

Neural networks encode inputs as high-dimensional vectors, known as representations, that capture how models process data by encoding task-relevant structure and semantics. Representation alignment refers to the degree to which different…

Computational Geometry · Computer Science 2026-05-26 Xinyuan Yan , Rita Sevastjanova , Mennatallah El-Assady , Bei Wang

Foundation models have shown remarkable success in fitting biological visual systems; however, their black-box nature inherently limits their utility for understanding brain function. Here, we peek inside a SOTA foundation model of neural…

Neurons and Cognition · Quantitative Biology 2025-12-10 Johannes Bertram , Luciano Dyballa , T. Anderson Keller , Savik Kinger , Steven W. Zucker

The graph structure is a commonly used data storage mode, and it turns out that the low-dimensional embedded representation of nodes in the graph is extremely useful in various typical tasks, such as node classification, link prediction ,…

Social and Information Networks · Computer Science 2020-08-03 Xing Li , Wei Wei , Xiangnan Feng , Xue Liu , Zhiming Zheng

Network models describe the brain as sets of nodes and edges that represent its distributed organization. So far, most discoveries in network neuroscience have prioritized insights that highlight distinct groupings and specialized…

Neurons and Cognition · Quantitative Biology 2021-05-18 Joshua Faskowitz , Richard F. Betzel , Olaf Sporns

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…

Soft Condensed Matter · Physics 2024-07-23 Haiqian Yang , Anh Q. Nguyen , Dapeng Bi , Markus J. Buehler , Ming Guo

Topological data analyses are rapidly turning into key tools for quantifying large volumes of neurobiological data, e.g., for organizing the spiking outputs of large neuronal ensembles and thus gaining insights into the information produced…

Neurons and Cognition · Quantitative Biology 2019-09-18 Yuri Dabaghian

Intelligent biological systems are characterized by their embodiment in a complex environment and the intimate interplay between their nervous systems and the nonlinear mechanical properties of their bodies. This coordination, in which the…

Machine Learning · Computer Science 2023-02-02 Deniz Oktay , Mehran Mirramezani , Eder Medina , Ryan P. Adams

The genotype-phenotype map is an essential object in our understanding of organismal complexity and adaptive properties, determining at once genomic plasticity and those constraints that may limit the ability of genomes to attain…

Populations and Evolution · Quantitative Biology 2015-02-18 Clemente F. Arias , Pablo Catalán , Susanna Manrubia , José A. Cuesta

In the fields of brain-computer interaction and cognitive neuroscience, effective decoding of auditory signals from task-based functional magnetic resonance imaging (fMRI) is key to understanding how the brain processes complex auditory…

Neurons and Cognition · Quantitative Biology 2024-06-05 Wanli Ma , Xuegang Tang , Jin Gu , Ying Wang , Yuling Xia

The human brains are organized into hierarchically modular networks facilitating efficient and stable information processing and supporting diverse cognitive processes during the course of development. While the remarkable reconfiguration…

Neurons and Cognition · Quantitative Biology 2020-09-16 Xuyun Wen , Liming Hsu , Weili Lin , Han Zhang , Dinggang Shen

Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…

Populations and Evolution · Quantitative Biology 2022-08-01 Lakshwin Shreesha , Michael Levin

The intelligent behavior of robots does not emerge solely from control systems, but from the tight coupling between body and brain, a principle known as embodied intelligence. Designing soft robots that leverage this interaction remains a…

Robotics · Computer Science 2026-03-23 Jianqiang Wang , Shuaiqun Pan , Alvaro Serra-Gomez , Xiaohan Wei , Yue Xie

Various neuroimaging studies suffer from small sample size problem which often limit their reliability. Meta-analysis addresses this challenge by aggregating findings from different studies to identify consistent patterns of brain activity.…

Machine Learning · Computer Science 2025-11-27 Seunghun Baek , Jaejin Lee , Jaeyoon Sim , Minjae Jeong , Won Hwa Kim