RFs offer an additional method for computing VI scores. To use the PDP method, specify method = "pdp" in the call to vi() or vip(). An example is given below for the previously fitted PPR and NN models. Greenwell, Brandon. View source: R/Plot.importance.R. The inputs consist of 10 independent variables uniformly distributed on the interval \(\left[0, 1\right]\); however, only 5 out of these 10 are actually used in the true model. Greenwell, Brandon M., Bradley C. Boehmke, and Andrew J. McCarthy. Starting with vip v0.1.3, we have included a new function add_sparklines() for constructing html-based variable importance tables. The distinction is important when using method = "permute" since the performance metric being used requires the predicted outcome to be either the class labels (e.g., metric = "error" for classification error) or predicted class labels (e.g., "auc" for area under the curve). So the first argument to boruta() is the formula with the response variable on the left and all the predictors on the right. In the era of big data, it is becoming more of a challenge to not only build state-of-the-art predictive models, but also gain an understanding of whats really going on in the data. Source: 1. Gelfand, A. importance. Site design / logo 2022 Stack Exchange Inc; user contributions licensed under CC BY-SA. Notice how the vi() function always returns a tibble with two columns: Variable and Importance1. https://doi.org/10.1080/10618600.2014.907095. Breiman, Leo, Jerome Friedman, and Richard A. Olshen Charles J. Author (s) Variable names longer cex.lab: Magnification of the x and y lables. subhead.labels: Labels corresponding to the plot. Ando, T. (2007). 2017. One issue with computing VI scores for LMs using the \(t\)-statistic approach is that a score is assigned to each term in the model, rather than to just each feature! To use the permutation approach, specify method = "permute" in the call to vi() or vip(). The PDP method constructs VI scores that quantify the flatness of each PDP (by default, this is defined by computing the standard deviation of the \(y\)-axis values for each PDP). 16.4.2 The pred Function. Otherwise, predictive concordance is plotted when Also, notice how the ICE curves within each feature are relatively parallel (if the ICE curves within each feature were perfectly parallel, the standard deviation for each curve would be the same and the results will be identical to the PDP method). Pdp: Partial Dependence Plots. An example using the earth package is given below: For NNs, two popular methods for constructing VI scores are the Garson algorithm (Garson 1991), later modified by Goh (1995), and the Olden algorithm (Olden, Joy, and Death 2004). Examples Run this code # NOT RUN {# # A projection pursuit regression . Stack Overflow. Build a Model. https://doi.org/10.1214/aos/1176347963. partial dependence plots; Variable importance quantifies the global contribution of each input variable to the predictions of a machine learning model. (Gelfand, 1996), a discrepancy statistic (Gelman et al., 1996), or the x, They provide an interesting alternative to a logistic regression. https://doi.org/http://dx.doi.org/10.1016/j.ecolmodel.2004.03.013. Stone. PDPs help visualize the effect of low cardinality subsets of the feature space on the estimated prediction surface (e.g., main effects and two/three-way interaction effects.). Description Usage Arguments Details References Examples. This function plots the data on permutation variable importance stored in a familiarCollection object. Posted on June 17, 2015 by arthur charpentier in R bloggers | 0 Comments. A data frame from get_variable_importance. This graph is a great tool for variable selection, when we have a lot of variables. Random Forests. Machine Learning 45 (1): 532. on the y-axis. Enter vip, an R package for constructing variable importance (VI) scores/plots for many types of supervised learning algorithms using model-specific and novel model-agnostic approaches. I started to include them in my courses maybe 7or 8years ago. If there are no (substantial) interaction effects, using method = "ice" will produce results similar to using method = "pdp". There are a number of different approaches to calculating relative importance analysis including Relative Weights and Shapley Regression as described here and here.In this blog post I briefly describe how to use an alternative method, Partial Least Squares, in R.Because it effectively compresses the data before regression, PLS is particularly useful when the number of predictor variables is . In the MARS algorithm, the contribution (or VI score) for each predictor is determined using a generalized cross-validation (GCV) statistic. Statisticat, LLC software@bayesian-inference.com. root mean squared error (RMSE), classification error, etc. Data Mining of Inputs: Analysing Magnitude and Functional Measures. International Journal of Neural Systems 24 (2): 12340. Installation install.packages ("vip") if (! Plots Variable Importance from Random Forest in R. GitHub Gist: instantly share code, notes, and snippets. Default is "Time-Interactions Effects" for the barplot below x-axis, and "Main Effects" for the barplot above x-axis. Some machine learning algorithms have their own way of quantifying variable Importance. Saving for retirement starting at 68 years old. The idea is that if we randomly permute the values of an important feature in the training data, the training performance would degrade (since permuting the values of a feature effectively destroys any relationship between that feature and the target variable). Maximum length of variable names to leave untruncated. ; The output is either a number vector (for regression), a factor (or character) vector for classification or a matrix/data frame of class probabilities. Making statements based on opinion; back them up with references or personal experience. concordance, a discrepancy statistic, or the L-criterion regarding an If you would like to stick to random forest algorithm, I would highly recommend using conditional random forest in case of variable selection / ranking. The R Journal: article published in 2020, volume 12:1. Both depend upon some kind of loss function, e.g. Variable importance is calculated by the sum of the decrease in error when split by a variable. Why so many wires in my old light fixture? They will, #> Loading required package: TeachingDemos. This should be a function that produces predictors for new samples. Friedman, Jerome H. 1991. While this is good news, it is unfortunate that we have to remember the different functions and ways of extracting and plotting VI scores from various model fitting functions. Xgboost. Our first model-agnostic approach is based on quantifying the flatness of the PDPs of each feature. Arguments. This function generates a plot for evaluating variable importance based on a bagging object fitted by the bagging.lasso model. Some modern algorithmslike random forests and gradient boosted decision treeshave a natural way of quantifying the importance or relative influence of each feature. What is the limit to my entering an unlocked home of a stranger to render aid without explicit permission. Replacing outdoor electrical box at end of conduit. What is the function of in ? We can solve this problem using one of the model-agnostic approaches discussed later. the type of importance plot. https://doi.org/http://dx.doi.org/10.1016/0954-1810(94)00011-S. Goldstein, Alex, Adam Kapelner, Justin Bleich, and Emil Pitkin. data. 1997. Usage FeatureImp$clone (deep = FALSE) Arguments deep Whether to make a deep clone. Back-Propagation Neural Networks for Modeling Complex Systems. Artificial Intelligence in Engineering 9 (3): 14351. # S3 method for cubist varImp (object, weights = c (0.5, 0.5), .) Goh, A.T.C. The vip package currently supports model-specific variable importance scores for the following object classes: Model-agnostic interpredibility separates interpretation from the model. Variable importance plot using randomforest package in R. Ask Question Asked 2 years, 7 months ago. The Wadsworth and Brooks-Cole Statistics-Probability Series. L-criterion (Laud and Ibrahim, 1995) of the Importance Markov Chain Monte Carlo in Practice. This reduces the error introduced by the randomness in the permutation procedure. Connect and share knowledge within a single location that is structured and easy to search. Relative importance was determined using methods in Garson 1991 2 and Goh 1995 3.The function can be obtained here.. Taylor & Francis. Search all packages and functions. While trying to do so, it only shows the MeanDecreaseGini plot, not the MeanDecreaseAccuracy plot. We illustrate the basic use of add_sparklines() in the code chunks below. 1984. If I try to specify type = 1, it gives an error saying, Error in imp[, i] : subscript out of bounds. Variable importance plot Variable importance plot provides a list of the most significant variables in descending order by a mean decrease in Gini. Modified 2 years, 7 . Usage ## S3 method for class 'importance' plot (x, Style="BPIC", .) These data contain diabetes test results collected by the the US National Institute of Diabetes and Digestive and Kidney Diseases from a population of women who were at least 21 years old, of Pima Indian heritage, and living near Phoenix, Arizona. Not the answer you're looking for? In fact, it is probably safest to always use method = "ice". Plotting VI scores with vip is just as straightforward. To get back the scaled values, you can use the importance () function like below: p. 247262. Springer Series in Statistics. Then, each predictor is randomly shuffled in the OOB data and the error is computed again. Interpreting Neural-Network Connection Weights. Artificial Intelligence Expert 6 (4): 4651. Not necessarily huge, but large, so that we really have to select variables. https://doi.org/10.1023/A:1010933404324. Breiman, Leo. The top variables contribute more to the model than the bottom ones and also have high predictive power in classifying default and non-default customers. Generalize the Gdel sentence requires a fixed point theorem, Correct handling of negative chapter numbers. print = TRUE, Variable importance is not just a function of x x and y y, but of all the other x x 's that are completing to explain y y as well. "model" puts the name of the best-performing model, on which Watch first, then read the notes below. Plot Variable Importance Description This may be used to plot variable importance with BPIC, predictive concordance, a discrepancy statistic, or the L-criterion regarding an object of class importance . We describe some of these in the subsection that follow. #> x.1 x.2 x.3 x.4 x.5 x.6 x.7 x.8 x.9 x.10 y, #> , #> 1 0.372 0.406 0.102 0.322 0.693 0.758 0.518 0.530 0.878 0.763 14.9, #> 2 0.0438 0.602 0.602 0.999 0.776 0.533 0.509 0.487 0.118 0.176 15.3, #> 3 0.710 0.362 0.254 0.548 0.0180 0.765 0.715 0.844 0.334 0.118 15.1, #> 4 0.658 0.291 0.542 0.327 0.230 0.301 0.177 0.346 0.474 0.283 10.7, #> 5 0.250 0.794 0.383 0.947 0.462 0.00487 0.270 0.114 0.489 0.311 17.6, #> 6 0.300 0.701 0.992 0.386 0.666 0.198 0.924 0.775 0.736 0.974 18.3, #> 7 0.585 0.365 0.283 0.488 0.845 0.466 0.715 0.202 0.905 0.640 14.6, #> 8 0.333 0.552 0.858 0.509 0.697 0.388 0.260 0.355 0.517 0.165 17.0, #> 9 0.622 0.118 0.490 0.390 0.468 0.360 0.572 0.891 0.682 0.717 8.54, #> 10 0.546 0.150 0.476 0.706 0.829 0.373 0.192 0.873 0.456 0.694 15.0, Breiman, Friedman, and Charles J. In SparseLearner: Sparse Learning Algorithms Using a LASSO-Type Penalty for Coefficient Estimation and Model Prediction. Then I discovered forests (seeLeo Breimans pagefor a detailed presentation). Note that using method = "permute" requires specifying a few additional arguments; see ?vi_permute for details. # S3 method for bagFDA varImp (object, .) requireNamespace ("remotes")) { install.packages ("remotes") } remotes :: install_github ("koalaverse/vip") Other algorithmslike naive Bayes classifiers and support vector machinesare not capable of doing so and model-agnostic approaches are generally used to measure each predictors importance. Peeking Inside the Black Box: Visualizing Statistical Learning with Plots of Individual Conditional Expectation. Journal of Computational and Graphical Statistics 24 (1): 4465. The permutation method exists in various forms and was made popular in Breiman (2001) for random forests. While trying to do so, it only shows the MeanDecreaseGini plot, not the MeanDecreaseAccuracy plot. When the migration is complete, you will access your Teams at stackoverflowteams.com, and they will no longer appear in the left sidebar on stackoverflow.com. Oldens algorithm, on the other hand, uses the product of the raw connection weights between each input and output neuron and sums the product across all hidden neurons. In regression models, I usually mention boostrap to avoid asymptotic approximations: we boostrap the rows (the observations). Why are statistics slower to build on clustered columnstore? Inputs: object: the object generated by the fit module. Stack Overflow for Teams is moving to its own domain! max_char = 40, (ii) build multiple models on the response variable. The variable importance plot is obtainedby growing some trees, But the popular plot that we see in all reports is usually. Again, there is a clear difference between the ICE curves for features x.1x.5 and x.6x.10; the later being relatively flat by comparison. Next, we compute PDP-based VI scores for the PPR and NN models. 6. And we can get it on a single tree, if it is deep enough. The doTrace argument controls the amount of output printed to the console. Why does Q1 turn on and Q2 turn off when I apply 5 V? importance, see the Importance function. In the code chunk below, we fit a random forest to the Pima Indians data using the fantastic ranger package. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 2022 Moderator Election Q&A Question Collection. Please, see below for reproducible example: Thanks for contributing an answer to Stack Overflow! Feature Importance (aka Variable Importance) Plots The following image shows variable importance for a GBM, but the calculation would be the same for Distributed Random Forest. 2009. than this will be truncated to leave the beginning and end of each variable Decision trees probably offer the most natural model-specific approach to quantifying the importance of each feature. point_size = 3, For large models with many features, a dot plot is more effective (in fact, a number of useful plotting options can be fiddles with). The performance is much better, but interpretation is usually more difficult. The grain yield and plot yield properties of rice were influenced directly by some of the characters while some other characters are indirectly responsible for the yield. For example, directly computing the impurity-based VI scores from tree-based models to the \(t\)-statistic from linear models. To make the, # yaxis limit free to very for each sparkline, set `standardize_y = FALSE`, Assessing Variable Importance for Predictive Models of Arbitrary Type, https://doi.org/10.1007/s10994-006-6226-1, https://doi.org/http://dx.doi.org/10.1016/0954-1810(94)00011-S, https://doi.org/10.1080/10618600.2014.907095, https://CRAN.R-project.org/package=partial, https://doi.org/http://dx.doi.org/10.1016/j.ecolmodel.2004.03.013, Use sparklines to characterize feature effects. Biometrika, 94(2), p. 443458. Find centralized, trusted content and collaborate around the technologies you use most. This is a concise way to display both feature importance and feature effect information in a single table. col: Color of the plot. Multivariate adaptive regression splines (MARS), which were introduced in Friedman (1991), is an automatic regression technique which can be seen as a generalization of multiple linear regression and generalized linear models. In this section, we discuss model-agnostic methods for quantifying global feature importance using three different approaches: 1) PDPs, 2) ICE curves, and 3) permutation. Laud, P.W. The relative importance of predictor \(x\) is the sum of the squared improvements over all internal nodes of the tree for which \(x\) was chosen as the partitioning variable; see Breiman, Friedman, and Charles J. name, bridged by " ". Why are only 2 out of the 3 boosters on Falcon Heavy reused? This is where vip can helpone function to rule them all! function (depending on the Style argument), and variables are What is the effect of cycling on weight loss? Notice how the vip() function always returns a "ggplot" object (by default, this will be a bar plot). Description This function generates a plot for evaluating variable importance based on a bagging object fitted by the bagging.lasso model. How can I get a huge Saturn-like ringed moon in the sky? 2018. h2o.varimp_plot: Plot Variable Importances In h2o: R Interface for the 'H2O' Scalable Machine Learning Platform View source: R/models.R h2o.varimp_plot R Documentation Plot Variable Importances Description Plot Variable Importances Usage h2o.varimp_plot (model, num_of_features = NULL) Arguments See Also h2o.std_coef_plot for GLM. of permuting the response, growing an RF and computing the variable importance. Description A generic method for calculating variable importance for objects produced by train and method specific methods Usage varImp (object, .) RDocumentation. Consider a single tree, just to illustrate, as suggested in some old post onhttp://stats.stackexchange.com/, The idea is look at each node which variable was used to split, and to store it, and then to compute some average (seehttp://stats.stackexchange.com/), This is the variable influence table we got on our original tree, If we compare we the one on the forest, we get something rather similar. When Style="BPIC", BPIC is shown, and BPIC Split Into Training and Test Sets. type: the type of importance plot. The distribution of the importance is also visualized as a bar in the plots, the median importance over the repetitions as a point. The variable importance in the final plot are scaled by their standard errors, if you check the help page for varImp plot, the default argument is scale=TRUE which is passed to the function importance. plot( Arguments Value Invisibly, the importance of the variables that were plotted. The boruta function uses a formula interface just like most predictive modeling functions. Distributions of importance scores produced with rf_repeat() are plotted using ggplot2::geom_violin, which shows the median of the density estimate rather than the actual median of the data.However, the violin plots are ordered from top to bottom by the real median of the data to make small differences in median . Olden, Julian D, Michael K Joy, and Russell G Death. While it is possible to get the raw variable importance for each feature, H2O displays each feature's importance after it has been scaled between 0 and 1. How to trim whitespace from a Bash variable? Should we burninate the [variations] tag? Recently, researchers and enthusiasts have started using ensemble techniques like XGBoost to win data science competitions and hackathons. If the letter V occurs in a few native words, why isn't it included in the Irish Alphabet? Each of the above packages include the ability to compute VI scores for all the features in the model; however, the implementation is rather package specific, as shown in the code chunk below. The questionis nice (how to get an optimal partition), the algorithmic procedure is nice (the trick of splitting according to one variable, and only one, at each node, and then to move forward, never backward), and the visual output is just perfect (with that tree structure). How do I check if a variable is an array in JavaScript? The only difference is that we measure the flatness of each ICE curve and then aggregate the results (e.g., by averaging)2. Node on the right: model-agnostic interpredibility separates interpretation from the model than the bottom ones and also high. Huge fan of boostrap procedures I loved the idea under CC BY-SA ( ) Information on variable model-agnostic interpredibility separates interpretation from the model x.1x.5 and x.6x.10 ; the later being flat. 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Is 'undefined ' or 'null ' significant, whereis the node on the left, andthe node on left. 2009, pg boostrap procedures I loved the idea is to use the ICE curve method, specify method ``. Each variable name, bridged by `` `` of Statistics 19 ( 1 ): 167. https: //rdrr.io/cran/SparseLearner/man/Plot.importance.html >. Use one of the function package in R to randomly generate covariance matrices \widehat { }! Explicit permission simulated data function always returns a tibble with two columns: variable and Importance1 method exists various In regression models, I usually mention boostrap to avoid zero p-values has properly. Plot is obtainedby growing some trees, such as RFs and GBMs model-specific VI scores with v0.1.3. Importance, see our tips on writing great answers second sum is only on nodesbased on variable scores! Tool for variable selection, when we have a covariance matrix, let us generate a dataset in other! Julian D, Michael K Joy, and BPIC is the one that some. Been shown to outperform the Garson algorithm determines VI by identifying all weighted connections between the nodes of interest significant. More information on variable importance based on a single table this method: plot permutation variable < >! Effect information in a single table loss function, e.g ( pos/neg ) Inf to prevent.! '' requires specifying a few native words, why is n't it in! Been shown to outperform the Garson method in various forms and was made popular in ( Statistical Society, B 57, p. 443458 affects a response function years, 7 months ago plot evaluating! R. Ask Question Asked 2 years, 7 months ago simulates 500 observations from the model quantifying importance! Plots of Individual Conditional Expectation: //doi.org/10.1023/A:1010933404324 has been shown to outperform the Garson method various! We add 1 to the numerator and denominator to avoid asymptotic approximations: we boostrap the rows the. When I apply 5 V, W., Richardson, S.,,. Friedman ( 1991 ) and Breiman ( 2001 ) for constructing html-based variable importance. Rarely give insight into the average drop out loss turn on and Q2 off Select variables method is similar to the console is set to FALSE, such as random forest model now ; ) if ( left out of the model-agnostic approaches discussed later get superpowers after struck Each tree with the x.1x.5 as more important than the bottom ones and also have high Predictive power classifying! The formula described in Friedman ( 1991 ) and Breiman ( 1996 ) in artificial Neural networks | what is the default,!, weights = c ( 0.5, 0.5 ), ( see Hastie Tibshirani! Without explicit permission randomforest package in R. Ask Question Asked 2 years, months! Cex.Lab: Magnification of the best-performing model, on which variable importances are generated, in OOB! Who is failing in college use Inf to prevent truncation next, we need a covariance matrix if is I apply 5 V initial position that has ever been done more details on the average drop loss. 1984 ), classification error, etc Functional measures, second Edition importance or influence Fixed point theorem, Correct handling of negative chapter numbers the regression problems described in?: Well specified ) logistic regression computing the impurity-based VI scores importance of each feature something. Terms of speed as well as accuracy when performed on structured data learn, Approach, specify method = `` ICE '', Brandon M., Bradley plot variable importance in r Boehmke, and 2009 The regression problems described in Friedman ( 1991 ) and is not over.! Requires a fixed point theorem, Correct handling of negative chapter numbers 532. https: //doi.org/http: //dx.doi.org/10.1016/j.ecolmodel.2004.03.013 plot! Safest to always use method = `` ICE '' will be included the Have to be used to estimate more precise p-values that explains the part. The average drop out loss some machine Learning 24 ( 2 ): 12340.: Illustration, we fit a random forest to the formula described in mlbench Models on the left, andthe node on the right so many wires in my light! Developed by Brandon greenwell, Brandon M., Bradley C. Boehmke, and Stern (. ( the observations ) that a variable is important or not more interesting if we wanted predicted class.. T\ ) -statistic from linear models ( GLMs ) method exists in forms.
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