An increasing threshold on this probability was used to generate precision-recall curves using two approaches for defining precision and recall. In the second case, we defined only assignments with probability above the threshold to single class proteins as correct and thus all assignments above the threshold made to proteins with two or more labels were considered incorrect. In our preliminary work on classification of subcellular location patterns using HPA images  , a subset of images of single pattern proteins were evaluated by both SVM and Random Forest  methods.
The results indicated slightly better performance for the latter approach, and we therefore also evaluated Random Forest classifiers for the tasks on the larger datasets used in this paper. As an alternative to classification which requires labels for training , we used an unsupervised machine learning method, hierarchical clustering, to identify candidate proteins for reannotation in two rounds. For this we used the same features and a normalized Euclidean distance metric with Stepwise Discriminant Analysis feature selection.
Since there was more than one cell for each protein and some of these might be atypical , we chose the cell closest to the multivariate median normalized feature value for a given protein to represent that protein in the clustering.
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The resulting tree can be cut at various values of the distance measure to give different numbers of clusters. We defined the cluster annotation for each protein as the dominant human annotation in the cluster in which the protein is found. To choose the optimal number of clusters, Akaike information criterion was used. It balances the log-likelihood of the data given the clustering against the number of clusters.
After we decided the clustering of proteins, the clusters were ordered by optimal leaf ordering  using the associated annotations. Once we obtained the clustering of proteins, we computed two scores for each protein to measure and identify the proteins whose annotations might be not correct.click
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In the first round, we found a subset of all proteins with the below one value of the first score in total lowest scores by the first definition and another subset of proteins with the lowest scores by the second definition which were from the range between zero and the value around the peak of the histogram of the second score, data not shown , and then selected proteins in the intersection of the two subsets as candidates for reannotation.
However, we restricted the final list by requiring that each cluster could only have one protein in this list to minimize the effect that the presence of more than one mis-annotated protein might have on the quality of a cluster. In the second round, we released these restrictions. Proteins were sorted with the first score and with the second score respectively in ascending order; then they were sorted with the sum of the two ranks ascendingly.
As a result, we had all proteins sorted in one list, and the more confidence we had on one protein for its being incorrectly annotated, the higher it would be in the sorting. The final subset of proteins that would be reexamined by annotators was thus generated from the top until we thought that the number of proteins in the subset would not be an inappropriate burden of work for the annotators.
To serve as a baseline for evaluating the reannotation enrichments we would obtain from automated methods SVM and hierarchical clustering , we created another list of proteins to be reexamined. Due to the highly imbalanced dataset, we made a compromise schema for the random sampling. For each class, we uniformly randomly sampled a small number r of proteins with replacement.
Thus we were easily able to ensure that we sampled proteins from all classes especially those with small size and meanwhile to control the number of proteins in this list to reduce the burden of reannotation work. On the other hand, we could reduce the chances of selecting the majority or even all proteins from some small classes with replacement sampling.
Then the unique set of proteins without the duplicates was merged with those identified from the automated methods and subjected to reexamination. Classification results after first round of reannotation. Classification results using Random Forest classifier after second round of reannotation.
Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Abstract The Human Protein Atlas contains immunofluorescence images showing subcellular locations for thousands of proteins. Introduction Knowledge of the subcellular locations of proteins provides critical context necessary for understanding their functions within the cell. Download: PPT. Figure 1. An overview of the framework introduced in this paper. Results In the following sub-sections, we present our results for two rounds of analyses.
Automated Selection of Proteins for Reannotation We began by segmenting confocal immunofluorescence images from the A cell line in release 4. Table 1. Classification results before first round of reannotation. Figure 2. Examples of mis-annotated proteins identified by the SVM classification reannotation algorithm. Figure 3. Examples of mis-annotated proteins identified by the hierarchical clustering reannotation method. Figure 4. Example of detection of mixed patterns by clustering. Second Round Reannotation After incorporating the results from the first round analysis i.
Table 3. Classification results before second round of reannotation. Table 5. Classification results after second round of reannotation. Figure 6. Precision-recall curves for protein annotations for single and multi-class classifiers.
Discussion Microscopy images are rich sources of information about cell structure and function for systems biology. Cell Segmentation and Feature Calculation We used the same cell segmentation and feature calculation strategies as in our previous work . Hierarchical Clustering for Reannotation As an alternative to classification which requires labels for training , we used an unsupervised machine learning method, hierarchical clustering, to identify candidate proteins for reannotation in two rounds.
Random Sampling for Reannotation To serve as a baseline for evaluating the reannotation enrichments we would obtain from automated methods SVM and hierarchical clustering , we created another list of proteins to be reexamined. Supporting Information. Table S1. List of proteins reannotated after first round. Table S2. Table S List of proteins reannotated after second round. Table S4. Acknowledgments We thank Drs. Arvind Rao and Aabid Shariff for helpful discussions. References 1.
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View Article Google Scholar 7. BMC Bioinformatics 8 View Article Google Scholar 8. Bioinformatics i66—i View Article Google Scholar 9. Proteome Res. View Article Google Scholar Proteomics 4: — Bioinformatics i7—i Lowe DG Object recognition from local scale-invariant features. Conf Computer Vision 2: — Huang K, Velliste M, Murphy RF Feature reduction for improved recognition of subcellular location patterns in fluorescence microscope images.
SPIE — Breiman L Random forests. She has a fresh eye and unique approach to her work with her clients and projects. The most significant piece of work that I have hired Carolyn for is for photography for the members of the Dundee Hills Winegrowers Association. An association with nearly 50 members primarily vineyard and winery owners , we contracted with Carolyn to photograph each of our members — in their unique environment — to tell a story of our AVA and its members.
This was an exhaustive task, not only finding the right way to tell the story of each individual winery and vineyard owner through photo — but the planning and execution of the project was also significant. Our association and individual members were thrilled with the outcome and the association now has a library of photos that we can use to tell the story of the Dundee Hills. The photographs Carolyn has taken of my winery and our staff Winderlea Vineyard and Winery have been the best photographs we have ever had taken.
They have become iconic components to our story and have been picked up in a range of publications and have become the foundational pieces of many of our ads and our brochures. She puts her subjects at ease and is able to capture the essence of a person — or a space. Carolyn is also highly professional, meets deadlines and is flexible with her approach to working on projects.
Bergstrom Wines is a family owned and operated winery who specializes in Oregon Pinot Noir and Chardonnay. We grow, produce and sell our products across the entire United States and in 15 foreign markets. I can say without a doubt that working closely with Carolyn Wells Kramer over the past two years has been the highlight of all of these relationships thus far. She has a great eye for detail and a knack for portraying a subject or a subject matter in the best light which also best reflects the individual mood or situation.
I would recommend Carolyn Wells Kramer for any photography project. She has surpassed all of our expectations on our photography projects including: portraits, aerial photography, landscapes, product shots and much more. She has the professionalism, skill sets and integrity to do any photography project in my humble opinion. We have worked with CWK photography for many years on various projects.
In addition, she photographed our staff in action shots during harvest, portraits of our staff for the website and an official portrait of our owners. She has an amazing ability to capture a sense of place with her landscape photography which conveys the beauty of the Willamette Valley and specifically our vineyards. Her portraits capture a real sense of the subject that is thoughtful and genuine.
CWK has provided Adelsheim Vineyard with photography for our special events, website, tasting room and the bottle shots that are used in promotional materials. Over the past year she has done extraordinary work for the winery. From bottle shots, which we use on all our printed materials, to product placement images that are a part of our national advertising campaigns, to dramatic harvest images and breathtaking vineyard shots; one of which hangs proudly in the main entrance to our facility.
Live out of state, however must come here every visit I have. Try the kozzie special; if u like meat, you won't be disappointed. Hi Duane, Thank you so much for the legendary review! It's fantastic you visit us every time you're in town. We will see you soon. We went for lunch recently they have a terrific lunch special!
That said, it took 30 minutes for us to get our pizzas, and that's a long, long time to wait. Christina, we are really happy that you discovered the lunch special! We apologize for the wait, thank you so much for the great review anyways. Have a wonderful weekend. Flights Vacation Rentals Restaurants Things to do. Tip: All of your saved places can be found here in My Trips. Log in Join.
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