Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning, which calls for fast algorithms. We present fastcore, a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X. fastcore takes as input a core set of reactions that are known to be active in the context of interest (e.g., cell or tissue), and it searches for a flux consistent subnetwork of the global network that contains all reactions from the core set and a minimal set of additional reactions. Our key observation is that a minimal consistent reconstruction can be defined via a set of sparse modes of the global network, and fastcore iteratively computes such a set via a series of linear programs. Experiments on liver data demonstrate speedups of several orders of magnitude, and significantly more compact reconstructions, over a rival method. Given its simplicity and its excellent performance, fastcore can form the backbone of many future metabolic network reconstruction algorithms.
Several algorithms have been published in the last years for extracting condition-specific models from generic genome-wide models like Recon ,1. Among them, mCADRE @cite_22 , INIT @cite_40 , iMAT @cite_11 , MBA @cite_6 and GIMME @cite_24 are the most commonly used (see table3 for an overview). Here we provide a short outline of the different algorithms, and refer to @cite_7 for a more extensive overview. For GIMME, iMAT, and MBA, we briefly discuss some notable differences to .
@cite_22 @cite_7 @cite_6 @cite_24 @cite_40 @cite_11
2833943491 2170881581 2950940417 1811254738
Genome-scale models of metabolism and macromolecular expression (ME-models) explicitly compute the optimal proteome composition of a growing cell. ME-models expand upon the well-established genome-scale models of metabolism (M-models), and they enable a new fundamental understanding of cellular growth. ME-models have increased predictive capabilities and accuracy due to their inclusion of the biosynthetic costs for the machinery of life, but they come with a significant increase in model size and complexity. This challenge results in models which are both difficult to compute and challenging to understand conceptually. As a result, ME-models exist for only two organisms (Escherichia coli and Thermotoga maritima) and are still used by relatively few researchers. To address these challenges, we have developed a new software framework called COBRAme for building and simulating ME-models. It is coded in Python and built on COBRApy, a popular platform for using M-models. COBRAme streamlines computation and analysis of ME-models. It provides tools to simplify constructing and editing ME-models to enable ME-model reconstructions for new organisms. We used COBRAme to reconstruct a condensed E. coli ME-model called iJL1678b-ME. This reformulated model gives functionally identical solutions to previous E. coli ME-models while using 1 5 the number of free variables and solving in less than 10 minutes, a marked improvement over the 6 hour solve time of previous ME-model formulations. Errors in previous ME-models were also corrected leading to 52 additional genes that must be expressed in iJL1678b-ME to grow aerobically in glucose minimal in silico media. This manuscript outlines the architecture of COBRAme and demonstrates how ME-models can be created, modified, and shared most efficiently using the new software framework. We address the problem of cross-domain image retrieval, considering the following practical application: given a user photo depicting a clothing image, our goal is to retrieve the same or attribute-similar clothing items from online shopping stores. This is a challenging problem due to the large discrepancy between online shopping images, usually taken in ideal lighting pose background conditions, and user photos captured in uncontrolled conditions. To address this problem, we propose a Dual Attribute-aware Ranking Network (DARN) for retrieval feature learning. More specifically, DARN consists of two sub-networks, one for each domain, whose retrieval feature representations are driven by semantic attribute learning. We show that this attribute-guided learning is a key factor for retrieval accuracy improvement. In addition, to further align with the nature of the retrieval problem, we impose a triplet visual similarity constraint for learning to rank across the two subnetworks. Another contribution of our work is a large-scale dataset which makes the network learning feasible. We exploit customer review websites to crawl a large set of online shopping images and corresponding offline user photos with fine-grained clothing attributes, i.e., around 450,000 online shopping images and about 90,000 exact offline counterpart images of those online ones. All these images are collected from real-world consumer websites reflecting the diversity of the data modality, which makes this dataset unique and rare in the academic community. We extensively evaluate the retrieval performance of networks in different configurations. The top-20 retrieval accuracy is doubled when using the proposed DARN other than the current popular solution using pre-trained CNN features only (0.570 vs. 0.268). We address the problem of cross-domain image retrieval, considering the following practical application: given a user photo depicting a clothing image, our goal is to retrieve the same or attribute-similar clothing items from online shopping stores. This is a challenging problem due to the large discrepancy between online shopping images, usually taken in ideal lighting pose background conditions, and user photos captured in uncontrolled conditions. To address this problem, we propose a Dual Attribute-aware Ranking Network (DARN) for retrieval feature learning. More specifically, DARN consists of two sub-networks, one for each domain, whose retrieval feature representations are driven by semantic attribute learning. We show that this attribute-guided learning is a key factor for retrieval accuracy improvement. In addition, to further align with the nature of the retrieval problem, we impose a triplet visual similarity constraint for learning to rank across the two sub-networks. Another contribution of our work is a large-scale dataset which makes the network learning feasible. We exploit customer review websites to crawl a large set of online shopping images and corresponding offline user photos with fine-grained clothing attributes, i.e., around 450,000 online shopping images and about 90,000 exact offline counterpart images of those online ones. All these images are collected from real-world consumer websites reflecting the diversity of the data modality, which makes this dataset unique and rare in the academic community. We extensively evaluate the retrieval performance of networks in different configurations. The top-20 retrieval accuracy is doubled when using the proposed DARN other than the current popular solution using pre-trained CNN features only (0.570 vs. 0.268). In this paper, we present a multimodal Recurrent Neural Network (m-RNN) model for generating novel image captions. It directly models the probability distribution of generating a word given previous words and an image. Image captions are generated by sampling from this distribution. The model consists of two sub-networks: a deep recurrent neural network for sentences and a deep convolutional network for images. These two sub-networks interact with each other in a multimodal layer to form the whole m-RNN model. The effectiveness of our model is validated on four benchmark datasets (IAPR TC-12, Flickr 8K, Flickr 30K and MS COCO). Our model outperforms the state-of-the-art methods. In addition, we apply the m-RNN model to retrieval tasks for retrieving images or sentences, and achieves significant performance improvement over the state-of-the-art methods which directly optimize the ranking objective function for retrieval. The project page of this work is: www.stat.ucla.edu junhua.mao m-RNN.html .