14 research outputs found
Efficient Representation Learning for Healthcare with Cross-Architectural Self-Supervision
In healthcare and biomedical applications, extreme computational requirements
pose a significant barrier to adopting representation learning. Representation
learning can enhance the performance of deep learning architectures by learning
useful priors from limited medical data. However, state-of-the-art
self-supervised techniques suffer from reduced performance when using smaller
batch sizes or shorter pretraining epochs, which are more practical in clinical
settings. We present Cross Architectural - Self Supervision (CASS) in response
to this challenge. This novel siamese self-supervised learning approach
synergistically leverages Transformer and Convolutional Neural Networks (CNN)
for efficient learning. Our empirical evaluation demonstrates that CASS-trained
CNNs and Transformers outperform existing self-supervised learning methods
across four diverse healthcare datasets. With only 1% labeled data for
finetuning, CASS achieves a 3.8% average improvement; with 10% labeled data, it
gains 5.9%; and with 100% labeled data, it reaches a remarkable 10.13%
enhancement. Notably, CASS reduces pretraining time by 69% compared to
state-of-the-art methods, making it more amenable to clinical implementation.
We also demonstrate that CASS is considerably more robust to variations in
batch size and pretraining epochs, making it a suitable candidate for machine
learning in healthcare applications.Comment: Accepted at MLHC 2023. Extended conference version of
arXiv:2206.0417
Enhancing Medical Image Segmentation: Optimizing Cross-Entropy Weights and Post-Processing with Autoencoders
The task of medical image segmentation presents unique challenges,
necessitating both localized and holistic semantic understanding to accurately
delineate areas of interest, such as critical tissues or aberrant features.
This complexity is heightened in medical image segmentation due to the high
degree of inter-class similarities, intra-class variations, and possible image
obfuscation. The segmentation task further diversifies when considering the
study of histopathology slides for autoimmune diseases like dermatomyositis.
The analysis of cell inflammation and interaction in these cases has been less
studied due to constraints in data acquisition pipelines. Despite the
progressive strides in medical science, we lack a comprehensive collection of
autoimmune diseases. As autoimmune diseases globally escalate in prevalence and
exhibit associations with COVID-19, their study becomes increasingly essential.
While there is existing research that integrates artificial intelligence in the
analysis of various autoimmune diseases, the exploration of dermatomyositis
remains relatively underrepresented. In this paper, we present a deep-learning
approach tailored for Medical image segmentation. Our proposed method
outperforms the current state-of-the-art techniques by an average of 12.26% for
U-Net and 12.04% for U-Net++ across the ResNet family of encoders on the
dermatomyositis dataset. Furthermore, we probe the importance of optimizing
loss function weights and benchmark our methodology on three challenging
medical image segmentation tasksComment: Accepted at ICCV CVAMD 202
Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization
Publisher Copyright: Copyright © 2021 The Authors, some rights reserved;In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation.Peer reviewe
SuperNoder: a tool to discover over-represented modular structures in networks
Background: Networks whose nodes have labels can seem complex. Fortunately, many have substructures that occur often ("motifs"). A societal example of a motif might be a household. Replacing such motifs by named supernodes reduces the complexity of the network and can bring out insightful features. Doing so repeatedly may give hints about higher level structures of the network. We call this recursive process Recursive Supernode Extraction.
Results: This paper describes algorithms and a tool to discover disjoint (i.e. non-overlapping) motifs in a network, replacing those motifs by new nodes, and then recursing. We show applications in food-web and protein-protein interaction (PPI) networks where our methods reduce the complexity of the network and yield insights.
Conclusions: SuperNoder is a web-based and standalone tool which enables the simplification of big graphs based on the reduction of high frequency motifs. It applies various strategies for identifying disjoint motifs with the goal of enhancing the understandability of networks
Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions
International audienceCharting a temporal path in gene networks requires linking early transcription factor (TF)-triggered events to downstream effects. We scale-up a cell-based TF-perturbation assay to identify direct regulated targets of 33 nitrogen (N)-early response TFs encompassing 88% of N-responsive Arabidopsis genes. We uncover a duality where each TF is an inducer and repressor, and in vitro cis-motifs are typically specific to regulation directionality. Validated TF-targets (71,836) are used to refine precision of a time-inferred root network, connecting 145 N-responsive TFs and 311 targets. These data are used to chart network paths from direct TF 1-regulated targets identified in cells to indirect targets responding only in planta via Network Walking. We uncover network paths from TGA1 and CRF4 to direct TF 2 targets, which in turn regulate 76% and 87% of TF 1 indirect targets in planta, respectively. These results have implications for N-use and the approach can reveal temporal networks for any biological system
Data from: Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants
This study exploits time, the relatively unexplored fourth dimension of gene regulatory networks (GRNs), to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. Our âjust-in-timeâ analysis of time-series transcriptome data uncovered a temporal cascade of cis elements underlying dynamic N signaling. To infer transcription factor (TF)-target edges in a GRN, we applied a time-based machine learning method to 2,174 dynamic N-responsive genes. We experimentally determined a network precision cutoff, using TF-regulated genome-wide targets of three TF hubs (CRF4, SNZ, and CDF1), used to âpruneâ the network to 155 TFs and 608 targets. This network precision was reconfirmed using genome-wide TF-target regulation data for four additional TFs (TGA1, HHO5/6, and PHL1) not used in network pruning. These higher-confidence edges in the GRN were further filtered by independent TF-target binding data, used to calculate a TF âN-specificityâ index. This refined GRN identifies the temporal relationship of known/validated regulators of N signaling (NLP7/8, TGA1/4, NAC4, HRS1, and LBD37/38/39) and 146 additional regulators. Six TFsâCRF4, SNZ, CDF1, HHO5/6, and PHL1âvalidated herein regulate a significant number of genes in the dynamic N response, targeting 54% of N-uptake/assimilation pathway genes. Phenotypically, inducible overexpression of CRF4 in planta regulates genes resulting in altered biomass, root development, and 15NO3â uptake, specifically under low-N conditions. This dynamic N-signaling GRN now provides the temporal âtranscriptional logicâ for 155 candidate TFs to improve nitrogen use efficiency with potential agricultural applications. Broadly, these time-based approaches can uncover the temporal transcriptional logic for any biological response system in biology, agriculture, or medicine. External links: 1. DFG: http://cs.nyu.edu/~mirowski/pub/GRN_Krouk_Mirowski_GenomeBiology.zip, 2. GEO dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9750
ShootRawCounts
Raw counts of total RNA-Seq reads aligned to each gene model in the Arabidopsis thaliana genome (TAIR10 version). These counts are from the RNA-Seq libraries constructed from shoot samples
RootRawCounts
Raw counts of total RNA-Seq reads aligned to each gene model in the Arabidopsis thaliana genome (TAIR10 version). These counts are from the RNA-Seq libraries constructed from root samples