141 research outputs found
Representing Alzheimer's Disease Progression via Deep Prototype Tree
For decades, a variety of predictive approaches have been proposed and
evaluated in terms of their predicting capability for Alzheimer's Disease (AD)
and its precursor - mild cognitive impairment (MCI). Most of them focused on
prediction or identification of statistical differences among different
clinical groups or phases (e.g., longitudinal studies). The continuous nature
of AD development and transition states between successive AD related stages
have been overlooked, especially in binary or multi-class classification.
Though a few progression models of AD have been studied recently, they mainly
designed to determine and compare the order of specific biomarkers. How to
effectively predict the individual patient's status within a wide spectrum of
AD progression has been understudied. In this work, we developed a novel
structure learning method to computationally model the continuum of AD
progression as a tree structure. By conducting a novel prototype learning with
a deep manner, we are able to capture intrinsic relations among different
clinical groups as prototypes and represent them in a continuous process for AD
development. We named this method as Deep Prototype Learning and the learned
tree structure as Deep Prototype Tree - DPTree. DPTree represents different
clinical stages as a trajectory reflecting AD progression and predict clinical
status by projecting individuals onto this continuous trajectory. Through this
way, DPTree can not only perform efficient prediction for patients at any
stages of AD development (77.8% accuracy for five groups), but also provide
more information by examining the projecting locations within the entire AD
progression process.Comment: Submitted to Information Processing in Medical Imaging (IPMI) 202
Robust Core-Periphery Constrained Transformer for Domain Adaptation
Unsupervised domain adaptation (UDA) aims to learn transferable
representation across domains. Recently a few UDA works have successfully
applied Transformer-based methods and achieved state-of-the-art (SOTA) results.
However, it remains challenging when there exists a large domain gap between
the source and target domain. Inspired by humans' exceptional transferability
abilities to adapt knowledge from familiar to uncharted domains, we try to
apply the universally existing organizational structure in the human functional
brain networks, i.e., the core-periphery principle to design the Transformer
and improve its UDA performance. In this paper, we propose a novel
brain-inspired robust core-periphery constrained transformer (RCCT) for
unsupervised domain adaptation, which brings a large margin of performance
improvement on various datasets. Specifically, in RCCT, the self-attention
operation across image patches is rescheduled by an adaptively learned weighted
graph with the Core-Periphery structure (CP graph), where the information
communication and exchange between images patches are manipulated and
controlled by the connection strength, i.e., edge weight of the learned
weighted CP graph. Besides, since the data in domain adaptation tasks can be
noisy, to improve the model robustness, we intentionally add perturbations to
the patches in the latent space to ensure generating robust learned weighted
core-periphery graphs. Extensive evaluations are conducted on several widely
tested UDA benchmarks. Our proposed RCCT consistently performs best compared to
existing works, including 88.3\% on Office-Home, 95.0\% on Office-31, 90.7\% on
VisDA-2017, and 46.0\% on DomainNet.Comment: Core-Periphery, ViT, Unsupervised domain adaptatio
Exploring the Influence of Information Entropy Change in Learning Systems
In this work, we explore the influence of entropy change in deep learning
systems by adding noise to the inputs/latent features. The applications in this
paper focus on deep learning tasks within computer vision, but the proposed
theory can be further applied to other fields. Noise is conventionally viewed
as a harmful perturbation in various deep learning architectures, such as
convolutional neural networks (CNNs) and vision transformers (ViTs), as well as
different learning tasks like image classification and transfer learning.
However, this paper aims to rethink whether the conventional proposition always
holds. We demonstrate that specific noise can boost the performance of various
deep architectures under certain conditions. We theoretically prove the
enhancement gained from positive noise by reducing the task complexity defined
by information entropy and experimentally show the significant performance gain
in large image datasets, such as the ImageNet. Herein, we use the information
entropy to define the complexity of the task. We categorize the noise into two
types, positive noise (PN) and harmful noise (HN), based on whether the noise
can help reduce the complexity of the task. Extensive experiments of CNNs and
ViTs have shown performance improvements by proactively injecting positive
noise, where we achieved an unprecedented top 1 accuracy of over 95% on
ImageNet. Both theoretical analysis and empirical evidence have confirmed that
the presence of positive noise can benefit the learning process, while the
traditionally perceived harmful noise indeed impairs deep learning models. The
different roles of noise offer new explanations for deep models on specific
tasks and provide a new paradigm for improving model performance. Moreover, it
reminds us that we can influence the performance of learning systems via
information entropy change.Comment: Information Entropy, CNN, Transforme
Silk Fibroin/Polyvinyl Pyrrolidone Interpenetrating Polymer Network Hydrogels
Silk fibroin hydrogel is an ideal model as biomaterial matrix due to its excellent biocompatibility and used in the field of medical polymer materials. Nevertheless, native fibroin hydrogels show poor transparency and resilience. To settle these drawbacks, an interpenetrating network (IPN) of hydrogels are synthesized with changing ratios of silk fibroin/N-Vinyl-2-pyrrolidonemixtures that crosslink by H2O2 and horseradish peroxidase. Interpenetrating polymer network structure can shorten the gel time and the pure fibroin solution gel time for more than a week. This is mainly due to conformation from the random coil to the β-sheet structure changes of fibroin. Moreover, the light transmittance of IPN hydrogel can be as high as more than 97% and maintain a level of 90% within a week. The hydrogel, which mainly consists of random coil, the apertures inside can be up to 200 μm. Elastic modulus increases during the process of gelation. The gel has nearly 95% resilience under the compression of 70% eventually, which is much higher than native fibroin gel. The results suggest that the present IPN hydrogels have excellent mechanical properties and excellent transparency.This work was supported by The National Key Research and Development Program of China
(Grant No. 2017YFC1103602), National Natural Science Foundation of China (Grant No. 51373114, 51741301),
PAPD and Nature Science Foundation of Jiangsu, China (Grant No. BK20171239, BK20151242).info:eu-repo/semantics/publishedVersio
Core-Periphery Principle Guided Redesign of Self-Attention in Transformers
Designing more efficient, reliable, and explainable neural network
architectures is critical to studies that are based on artificial intelligence
(AI) techniques. Previous studies, by post-hoc analysis, have found that the
best-performing ANNs surprisingly resemble biological neural networks (BNN),
which indicates that ANNs and BNNs may share some common principles to achieve
optimal performance in either machine learning or cognitive/behavior tasks.
Inspired by this phenomenon, we proactively instill organizational principles
of BNNs to guide the redesign of ANNs. We leverage the Core-Periphery (CP)
organization, which is widely found in human brain networks, to guide the
information communication mechanism in the self-attention of vision transformer
(ViT) and name this novel framework as CP-ViT. In CP-ViT, the attention
operation between nodes is defined by a sparse graph with a Core-Periphery
structure (CP graph), where the core nodes are redesigned and reorganized to
play an integrative role and serve as a center for other periphery nodes to
exchange information. We evaluated the proposed CP-ViT on multiple public
datasets, including medical image datasets (INbreast) and natural image
datasets. Interestingly, by incorporating the BNN-derived principle (CP
structure) into the redesign of ViT, our CP-ViT outperforms other
state-of-the-art ANNs. In general, our work advances the state of the art in
three aspects: 1) This work provides novel insights for brain-inspired AI: we
can utilize the principles found in BNNs to guide and improve our ANN
architecture design; 2) We show that there exist sweet spots of CP graphs that
lead to CP-ViTs with significantly improved performance; and 3) The core nodes
in CP-ViT correspond to task-related meaningful and important image patches,
which can significantly enhance the interpretability of the trained deep model.Comment: Core-periphery, functional brain networks, Vi
Hierarchical Semantic Tree Concept Whitening for Interpretable Image Classification
With the popularity of deep neural networks (DNNs), model interpretability is
becoming a critical concern. Many approaches have been developed to tackle the
problem through post-hoc analysis, such as explaining how predictions are made
or understanding the meaning of neurons in middle layers. Nevertheless, these
methods can only discover the patterns or rules that naturally exist in models.
In this work, rather than relying on post-hoc schemes, we proactively instill
knowledge to alter the representation of human-understandable concepts in
hidden layers. Specifically, we use a hierarchical tree of semantic concepts to
store the knowledge, which is leveraged to regularize the representations of
image data instances while training deep models. The axes of the latent space
are aligned with the semantic concepts, where the hierarchical relations
between concepts are also preserved. Experiments on real-world image datasets
show that our method improves model interpretability, showing better
disentanglement of semantic concepts, without negatively affecting model
classification performance
Segment Anything Model (SAM) for Radiation Oncology
In this study, we evaluate the performance of the Segment Anything Model
(SAM) model in clinical radiotherapy. We collected real clinical cases from
four regions at the Mayo Clinic: prostate, lung, gastrointestinal, and head \&
neck, which are typical treatment sites in radiation oncology. For each case,
we selected the OARs of concern in radiotherapy planning and compared the Dice
and Jaccard outcomes between clinical manual delineation, automatic
segmentation using SAM's "segment anything" mode, and automatic segmentation
using SAM with box prompt. Our results indicate that SAM performs better in
automatic segmentation for the prostate and lung regions, while its performance
in the gastrointestinal and head \& neck regions was relatively inferior. When
considering the size of the organ and the clarity of its boundary, SAM displays
better performance for larger organs with clear boundaries, such as the lung
and liver, and worse for smaller organs with unclear boundaries, like the
parotid and cochlea. These findings align with the generally accepted
variations in difficulty level associated with manual delineation of different
organs at different sites in clinical radiotherapy. Given that SAM, a single
trained model, could handle the delineation of OARs in four regions, these
results also demonstrate SAM's robust generalization capabilities in automatic
segmentation for radiotherapy, i.e., achieving delineation of different
radiotherapy OARs using a generic automatic segmentation model. SAM's
generalization capabilities across different regions make it technically
feasible to develop a generic model for automatic segmentation in radiotherapy
Predictive models of resting state networks for assessment of altered functional connectivity in mild cognitive impairment
Due to the difficulties in establishing correspondences between functional regions across individuals and populations, systematic elucidation of functional connectivity alterations in mild cognitive impairment (MCI) in comparison with normal controls (NC) is still a challenging problem. In this paper, we assessed the functional connectivity alterations in MCI via novel, alternative predictive models of resting state networks (RSNs) learned from multimodal resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI) data. First, ICA-clustering was used to construct RSNs from R-fMRI data in NC group. Second, since the RSNs in MCI are already altered and can hardly be constructed directly from R-fMRI data, structural landmarks derived from DTI data were employed as the predictive models of RSNs for MCI. Third, given that the landmarks are structurally consistent and correspondent across NC and MCI, functional connectivities in MCI were assessed based on the predicted RSNs and compared with those in NC. Experimental results demonstrated that the predictive models of RSNs based on multimodal R-fMRI and DTI data systematically and comprehensively revealed widespread functional connectivity alterations in MCI in comparison with NC
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