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  • Problems with real-valued deep belief networks (of RBMs)

    - by Junier
    I am trying to recreate the results reported in Reducing the dimensionality of data with neural networks of autoencoding the olivetti face dataset with an adapted version of the MNIST digits matlab code, but am having some difficulty. It seems that no matter how much tweaking I do on the number of epochs, rates, or momentum the stacked RBMs are entering the fine-tuning stage with a large amount of error and consequently fail to improve much at the fine-tuning stage. I am also experiencing a similar problem on another real-valued dataset. For the first layer I am using a RBM with a smaller learning rate (as described in the paper) and with negdata = poshidstates*vishid' + repmat(visbiases,numcases,1); I'm fairly confident I am following the instructions found in the supporting material but I cannot achieve the correct errors. Is there something I am missing? See the code I'm using for real-valued visible unit RBMs below, and for the whole deep training. The rest of the code can be found here. rbmvislinear.m: epsilonw = 0.001; % Learning rate for weights epsilonvb = 0.001; % Learning rate for biases of visible units epsilonhb = 0.001; % Learning rate for biases of hidden units weightcost = 0.0002; initialmomentum = 0.5; finalmomentum = 0.9; [numcases numdims numbatches]=size(batchdata); if restart ==1, restart=0; epoch=1; % Initializing symmetric weights and biases. vishid = 0.1*randn(numdims, numhid); hidbiases = zeros(1,numhid); visbiases = zeros(1,numdims); poshidprobs = zeros(numcases,numhid); neghidprobs = zeros(numcases,numhid); posprods = zeros(numdims,numhid); negprods = zeros(numdims,numhid); vishidinc = zeros(numdims,numhid); hidbiasinc = zeros(1,numhid); visbiasinc = zeros(1,numdims); sigmainc = zeros(1,numhid); batchposhidprobs=zeros(numcases,numhid,numbatches); end for epoch = epoch:maxepoch, fprintf(1,'epoch %d\r',epoch); errsum=0; for batch = 1:numbatches, if (mod(batch,100)==0) fprintf(1,' %d ',batch); end %%%%%%%%% START POSITIVE PHASE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% data = batchdata(:,:,batch); poshidprobs = 1./(1 + exp(-data*vishid - repmat(hidbiases,numcases,1))); batchposhidprobs(:,:,batch)=poshidprobs; posprods = data' * poshidprobs; poshidact = sum(poshidprobs); posvisact = sum(data); %%%%%%%%% END OF POSITIVE PHASE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% poshidstates = poshidprobs > rand(numcases,numhid); %%%%%%%%% START NEGATIVE PHASE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% negdata = poshidstates*vishid' + repmat(visbiases,numcases,1);% + randn(numcases,numdims) if not using mean neghidprobs = 1./(1 + exp(-negdata*vishid - repmat(hidbiases,numcases,1))); negprods = negdata'*neghidprobs; neghidact = sum(neghidprobs); negvisact = sum(negdata); %%%%%%%%% END OF NEGATIVE PHASE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% err= sum(sum( (data-negdata).^2 )); errsum = err + errsum; if epoch>5, momentum=finalmomentum; else momentum=initialmomentum; end; %%%%%%%%% UPDATE WEIGHTS AND BIASES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% vishidinc = momentum*vishidinc + ... epsilonw*( (posprods-negprods)/numcases - weightcost*vishid); visbiasinc = momentum*visbiasinc + (epsilonvb/numcases)*(posvisact-negvisact); hidbiasinc = momentum*hidbiasinc + (epsilonhb/numcases)*(poshidact-neghidact); vishid = vishid + vishidinc; visbiases = visbiases + visbiasinc; hidbiases = hidbiases + hidbiasinc; %%%%%%%%%%%%%%%% END OF UPDATES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% end fprintf(1, '\nepoch %4i error %f \n', epoch, errsum); end dofacedeepauto.m: clear all close all maxepoch=200; %In the Science paper we use maxepoch=50, but it works just fine. numhid=2000; numpen=1000; numpen2=500; numopen=30; fprintf(1,'Pretraining a deep autoencoder. \n'); fprintf(1,'The Science paper used 50 epochs. This uses %3i \n', maxepoch); load fdata %makeFaceData; [numcases numdims numbatches]=size(batchdata); fprintf(1,'Pretraining Layer 1 with RBM: %d-%d \n',numdims,numhid); restart=1; rbmvislinear; hidrecbiases=hidbiases; save mnistvh vishid hidrecbiases visbiases; maxepoch=50; fprintf(1,'\nPretraining Layer 2 with RBM: %d-%d \n',numhid,numpen); batchdata=batchposhidprobs; numhid=numpen; restart=1; rbm; hidpen=vishid; penrecbiases=hidbiases; hidgenbiases=visbiases; save mnisthp hidpen penrecbiases hidgenbiases; fprintf(1,'\nPretraining Layer 3 with RBM: %d-%d \n',numpen,numpen2); batchdata=batchposhidprobs; numhid=numpen2; restart=1; rbm; hidpen2=vishid; penrecbiases2=hidbiases; hidgenbiases2=visbiases; save mnisthp2 hidpen2 penrecbiases2 hidgenbiases2; fprintf(1,'\nPretraining Layer 4 with RBM: %d-%d \n',numpen2,numopen); batchdata=batchposhidprobs; numhid=numopen; restart=1; rbmhidlinear; hidtop=vishid; toprecbiases=hidbiases; topgenbiases=visbiases; save mnistpo hidtop toprecbiases topgenbiases; backpropface; Thanks for your time

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  • Disable .htaccess from apache allowoverride none, still reads .htaccess files

    - by John Magnolia
    I have moved all of our .htaccess config into <Directory> blocks and set AllowOverride None in the default and default-ssl. Although after restarting apache it is still reading the .htaccess files. How can I completely turn off reading these files? Update of all files with "AllowOverride" /etc/apache2/mods-available/userdir.conf <IfModule mod_userdir.c> UserDir public_html UserDir disabled root <Directory /home/*/public_html> AllowOverride FileInfo AuthConfig Limit Indexes Options MultiViews Indexes SymLinksIfOwnerMatch IncludesNoExec <Limit GET POST OPTIONS> Order allow,deny Allow from all </Limit> <LimitExcept GET POST OPTIONS> Order deny,allow Deny from all </LimitExcept> </Directory> </IfModule> /etc/apache2/mods-available/alias.conf <IfModule alias_module> # # Aliases: Add here as many aliases as you need (with no limit). The format is # Alias fakename realname # # Note that if you include a trailing / on fakename then the server will # require it to be present in the URL. So "/icons" isn't aliased in this # example, only "/icons/". If the fakename is slash-terminated, then the # realname must also be slash terminated, and if the fakename omits the # trailing slash, the realname must also omit it. # # We include the /icons/ alias for FancyIndexed directory listings. If # you do not use FancyIndexing, you may comment this out. # Alias /icons/ "/usr/share/apache2/icons/" <Directory "/usr/share/apache2/icons"> Options Indexes MultiViews AllowOverride None Order allow,deny Allow from all </Directory> </IfModule> /etc/apache2/httpd.conf # # Directives to allow use of AWStats as a CGI # Alias /awstatsclasses "/usr/share/doc/awstats/examples/wwwroot/classes/" Alias /awstatscss "/usr/share/doc/awstats/examples/wwwroot/css/" Alias /awstatsicons "/usr/share/doc/awstats/examples/wwwroot/icon/" ScriptAlias /awstats/ "/usr/share/doc/awstats/examples/wwwroot/cgi-bin/" # # This is to permit URL access to scripts/files in AWStats directory. # <Directory "/usr/share/doc/awstats/examples/wwwroot"> Options None AllowOverride None Order allow,deny Allow from all </Directory> Alias /awstats-icon/ /usr/share/awstats/icon/ <Directory /usr/share/awstats/icon> Options None AllowOverride None Order allow,deny Allow from all </Directory> /etc/apache2/sites-available/default-ssl <IfModule mod_ssl.c> <VirtualHost _default_:443> ServerAdmin webmaster@localhost DocumentRoot /var/www <Directory /> Options FollowSymLinks AllowOverride None </Directory> <Directory /var/www/> Options Indexes FollowSymLinks MultiViews AllowOverride None </Directory> ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/ <Directory "/usr/lib/cgi-bin"> AllowOverride None Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch Order allow,deny Allow from all </Directory> ErrorLog ${APACHE_LOG_DIR}/error.log # Possible values include: debug, info, notice, warn, error, crit, # alert, emerg. LogLevel warn CustomLog ${APACHE_LOG_DIR}/ssl_access.log combined # SSL Engine Switch: # Enable/Disable SSL for this virtual host. SSLEngine on # A self-signed (snakeoil) certificate can be created by installing # the ssl-cert package. See # /usr/share/doc/apache2.2-common/README.Debian.gz for more info. # If both key and certificate are stored in the same file, only the # SSLCertificateFile directive is needed. SSLCertificateFile /etc/ssl/certs/ssl-cert-snakeoil.pem SSLCertificateKeyFile /etc/ssl/private/ssl-cert-snakeoil.key # Server Certificate Chain: # Point SSLCertificateChainFile at a file containing the # concatenation of PEM encoded CA certificates which form the # certificate chain for the server certificate. Alternatively # the referenced file can be the same as SSLCertificateFile # when the CA certificates are directly appended to the server # certificate for convinience. #SSLCertificateChainFile /etc/apache2/ssl.crt/server-ca.crt # Certificate Authority (CA): # Set the CA certificate verification path where to find CA # certificates for client authentication or alternatively one # huge file containing all of them (file must be PEM encoded) # Note: Inside SSLCACertificatePath you need hash symlinks # to point to the certificate files. Use the provided # Makefile to update the hash symlinks after changes. #SSLCACertificatePath /etc/ssl/certs/ #SSLCACertificateFile /etc/apache2/ssl.crt/ca-bundle.crt # Certificate Revocation Lists (CRL): # Set the CA revocation path where to find CA CRLs for client # authentication or alternatively one huge file containing all # of them (file must be PEM encoded) # Note: Inside SSLCARevocationPath you need hash symlinks # to point to the certificate files. Use the provided # Makefile to update the hash symlinks after changes. #SSLCARevocationPath /etc/apache2/ssl.crl/ #SSLCARevocationFile /etc/apache2/ssl.crl/ca-bundle.crl # Client Authentication (Type): # Client certificate verification type and depth. Types are # none, optional, require and optional_no_ca. Depth is a # number which specifies how deeply to verify the certificate # issuer chain before deciding the certificate is not valid. #SSLVerifyClient require #SSLVerifyDepth 10 # Access Control: # With SSLRequire you can do per-directory access control based # on arbitrary complex boolean expressions containing server # variable checks and other lookup directives. The syntax is a # mixture between C and Perl. See the mod_ssl documentation # for more details. #<Location /> #SSLRequire ( %{SSL_CIPHER} !~ m/^(EXP|NULL)/ \ # and %{SSL_CLIENT_S_DN_O} eq "Snake Oil, Ltd." \ # and %{SSL_CLIENT_S_DN_OU} in {"Staff", "CA", "Dev"} \ # and %{TIME_WDAY} >= 1 and %{TIME_WDAY} <= 5 \ # and %{TIME_HOUR} >= 8 and %{TIME_HOUR} <= 20 ) \ # or %{REMOTE_ADDR} =~ m/^192\.76\.162\.[0-9]+$/ #</Location> # SSL Engine Options: # Set various options for the SSL engine. # o FakeBasicAuth: # Translate the client X.509 into a Basic Authorisation. This means that # the standard Auth/DBMAuth methods can be used for access control. The # user name is the `one line' version of the client's X.509 certificate. # Note that no password is obtained from the user. Every entry in the user # file needs this password: `xxj31ZMTZzkVA'. # o ExportCertData: # This exports two additional environment variables: SSL_CLIENT_CERT and # SSL_SERVER_CERT. These contain the PEM-encoded certificates of the # server (always existing) and the client (only existing when client # authentication is used). This can be used to import the certificates # into CGI scripts. # o StdEnvVars: # This exports the standard SSL/TLS related `SSL_*' environment variables. # Per default this exportation is switched off for performance reasons, # because the extraction step is an expensive operation and is usually # useless for serving static content. So one usually enables the # exportation for CGI and SSI requests only. # o StrictRequire: # This denies access when "SSLRequireSSL" or "SSLRequire" applied even # under a "Satisfy any" situation, i.e. when it applies access is denied # and no other module can change it. # o OptRenegotiate: # This enables optimized SSL connection renegotiation handling when SSL # directives are used in per-directory context. #SSLOptions +FakeBasicAuth +ExportCertData +StrictRequire <FilesMatch "\.(cgi|shtml|phtml|php)$"> SSLOptions +StdEnvVars </FilesMatch> <Directory /usr/lib/cgi-bin> SSLOptions +StdEnvVars </Directory> # SSL Protocol Adjustments: # The safe and default but still SSL/TLS standard compliant shutdown # approach is that mod_ssl sends the close notify alert but doesn't wait for # the close notify alert from client. When you need a different shutdown # approach you can use one of the following variables: # o ssl-unclean-shutdown: # This forces an unclean shutdown when the connection is closed, i.e. no # SSL close notify alert is send or allowed to received. This violates # the SSL/TLS standard but is needed for some brain-dead browsers. Use # this when you receive I/O errors because of the standard approach where # mod_ssl sends the close notify alert. # o ssl-accurate-shutdown: # This forces an accurate shutdown when the connection is closed, i.e. a # SSL close notify alert is send and mod_ssl waits for the close notify # alert of the client. This is 100% SSL/TLS standard compliant, but in # practice often causes hanging connections with brain-dead browsers. Use # this only for browsers where you know that their SSL implementation # works correctly. # Notice: Most problems of broken clients are also related to the HTTP # keep-alive facility, so you usually additionally want to disable # keep-alive for those clients, too. Use variable "nokeepalive" for this. # Similarly, one has to force some clients to use HTTP/1.0 to workaround # their broken HTTP/1.1 implementation. Use variables "downgrade-1.0" and # "force-response-1.0" for this. BrowserMatch "MSIE [2-6]" \ nokeepalive ssl-unclean-shutdown \ downgrade-1.0 force-response-1.0 # MSIE 7 and newer should be able to use keepalive BrowserMatch "MSIE [17-9]" ssl-unclean-shutdown </VirtualHost> </IfModule> /etc/apache2/sites-available/default <VirtualHost *:80> ServerAdmin webmaster@localhost DocumentRoot /var/www <Directory /> Options FollowSymLinks AllowOverride None </Directory> <Directory /var/www/> Options -Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny allow from all </Directory> ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/ <Directory "/usr/lib/cgi-bin"> AllowOverride None Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch Order allow,deny Allow from all </Directory> Alias /delboy /usr/share/phpmyadmin <Directory /usr/share/phpmyadmin> # Restrict phpmyadmin access Order Deny,Allow Allow from all </Directory> ErrorLog ${APACHE_LOG_DIR}/error.log # Possible values include: debug, info, notice, warn, error, crit, # alert, emerg. LogLevel warn CustomLog ${APACHE_LOG_DIR}/access.log combined Alias /doc/ "/usr/share/doc/" <Directory "/usr/share/doc/"> Options Indexes MultiViews FollowSymLinks AllowOverride None Order deny,allow Deny from all Allow from 127.0.0.0/255.0.0.0 ::1/128 </Directory> </VirtualHost> /etc/apache2/conf.d/security # # Disable access to the entire file system except for the directories that # are explicitly allowed later. # # This currently breaks the configurations that come with some web application # Debian packages. # #<Directory /> # AllowOverride None # Order Deny,Allow # Deny from all #</Directory> # Changing the following options will not really affect the security of the # server, but might make attacks slightly more difficult in some cases. # # ServerTokens # This directive configures what you return as the Server HTTP response # Header. The default is 'Full' which sends information about the OS-Type # and compiled in modules. # Set to one of: Full | OS | Minimal | Minor | Major | Prod # where Full conveys the most information, and Prod the least. # #ServerTokens Minimal ServerTokens OS #ServerTokens Full # # Optionally add a line containing the server version and virtual host # name to server-generated pages (internal error documents, FTP directory # listings, mod_status and mod_info output etc., but not CGI generated # documents or custom error documents). # Set to "EMail" to also include a mailto: link to the ServerAdmin. # Set to one of: On | Off | EMail # #ServerSignature Off ServerSignature On # # Allow TRACE method # # Set to "extended" to also reflect the request body (only for testing and # diagnostic purposes). # # Set to one of: On | Off | extended # TraceEnable Off #TraceEnable On /etc/apache2/apache2.conf # # Based upon the NCSA server configuration files originally by Rob McCool. # # This is the main Apache server configuration file. It contains the # configuration directives that give the server its instructions. # See http://httpd.apache.org/docs/2.2/ for detailed information about # the directives. # # Do NOT simply read the instructions in here without understanding # what they do. They're here only as hints or reminders. If you are unsure # consult the online docs. You have been warned. # # The configuration directives are grouped into three basic sections: # 1. Directives that control the operation of the Apache server process as a # whole (the 'global environment'). # 2. Directives that define the parameters of the 'main' or 'default' server, # which responds to requests that aren't handled by a virtual host. # These directives also provide default values for the settings # of all virtual hosts. # 3. Settings for virtual hosts, which allow Web requests to be sent to # different IP addresses or hostnames and have them handled by the # same Apache server process. # # Configuration and logfile names: If the filenames you specify for many # of the server's control files begin with "/" (or "drive:/" for Win32), the # server will use that explicit path. If the filenames do *not* begin # with "/", the value of ServerRoot is prepended -- so "foo.log" # with ServerRoot set to "/etc/apache2" will be interpreted by the # server as "/etc/apache2/foo.log". # ### Section 1: Global Environment # # The directives in this section affect the overall operation of Apache, # such as the number of concurrent requests it can handle or where it # can find its configuration files. # # # ServerRoot: The top of the directory tree under which the server's # configuration, error, and log files are kept. # # NOTE! If you intend to place this on an NFS (or otherwise network) # mounted filesystem then please read the LockFile documentation (available # at <URL:http://httpd.apache.org/docs/2.2/mod/mpm_common.html#lockfile>); # you will save yourself a lot of trouble. # # Do NOT add a slash at the end of the directory path. # #ServerRoot "/etc/apache2" # # The accept serialization lock file MUST BE STORED ON A LOCAL DISK. # LockFile ${APACHE_LOCK_DIR}/accept.lock # # PidFile: The file in which the server should record its process # identification number when it starts. # This needs to be set in /etc/apache2/envvars # PidFile ${APACHE_PID_FILE} # # Timeout: The number of seconds before receives and sends time out. # Timeout 300 # # KeepAlive: Whether or not to allow persistent connections (more than # one request per connection). Set to "Off" to deactivate. # KeepAlive On # # MaxKeepAliveRequests: The maximum number of requests to allow # during a persistent connection. Set to 0 to allow an unlimited amount. # We recommend you leave this number high, for maximum performance. # MaxKeepAliveRequests 100 # # KeepAliveTimeout: Number of seconds to wait for the next request from the # same client on the same connection. # KeepAliveTimeout 4 ## ## Server-Pool Size Regulation (MPM specific) ## # prefork MPM # StartServers: number of server processes to start # MinSpareServers: minimum number of server processes which are kept spare # MaxSpareServers: maximum number of server processes which are kept spare # MaxClients: maximum number of server processes allowed to start # MaxRequestsPerChild: maximum number of requests a server process serves <IfModule mpm_prefork_module> StartServers 5 MinSpareServers 5 MaxSpareServers 10 MaxClients 150 MaxRequestsPerChild 500 </IfModule> # worker MPM # StartServers: initial number of server processes to start # MaxClients: maximum number of simultaneous client connections # MinSpareThreads: minimum number of worker threads which are kept spare # MaxSpareThreads: maximum number of worker threads which are kept spare # ThreadLimit: ThreadsPerChild can be changed to this maximum value during a # graceful restart. ThreadLimit can only be changed by stopping # and starting Apache. # ThreadsPerChild: constant number of worker threads in each server process # MaxRequestsPerChild: maximum number of requests a server process serves <IfModule mpm_worker_module> StartServers 2 MinSpareThreads 25 MaxSpareThreads 75 ThreadLimit 64 ThreadsPerChild 25 MaxClients 150 MaxRequestsPerChild 0 </IfModule> # event MPM # StartServers: initial number of server processes to start # MaxClients: maximum number of simultaneous client connections # MinSpareThreads: minimum number of worker threads which are kept spare # MaxSpareThreads: maximum number of worker threads which are kept spare # ThreadsPerChild: constant number of worker threads in each server process # MaxRequestsPerChild: maximum number of requests a server process serves <IfModule mpm_event_module> StartServers 2 MaxClients 150 MinSpareThreads 25 MaxSpareThreads 75 ThreadLimit 64 ThreadsPerChild 25 MaxRequestsPerChild 0 </IfModule> # These need to be set in /etc/apache2/envvars User ${APACHE_RUN_USER} Group ${APACHE_RUN_GROUP} # # AccessFileName: The name of the file to look for in each directory # for additional configuration directives. See also the AllowOverride # directive. # AccessFileName .htaccess # # The following lines prevent .htaccess and .htpasswd files from being # viewed by Web clients. # <Files ~ "^\.ht"> Order allow,deny Deny from all Satisfy all </Files> # # DefaultType is the default MIME type the server will use for a document # if it cannot otherwise determine one, such as from filename extensions. # If your server contains mostly text or HTML documents, "text/plain" is # a good value. If most of your content is binary, such as applications # or images, you may want to use "application/octet-stream" instead to # keep browsers from trying to display binary files as though they are # text. # DefaultType text/plain # # HostnameLookups: Log the names of clients or just their IP addresses # e.g., www.apache.org (on) or 204.62.129.132 (off). # The default is off because it'd be overall better for the net if people # had to knowingly turn this feature on, since enabling it means that # each client request will result in AT LEAST one lookup request to the # nameserver. # HostnameLookups Off # ErrorLog: The location of the error log file. # If you do not specify an ErrorLog directive within a <VirtualHost> # container, error messages relating to that virtual host will be # logged here. If you *do* define an error logfile for a <VirtualHost> # container, that host's errors will be logged there and not here. # ErrorLog ${APACHE_LOG_DIR}/error.log # # LogLevel: Control the number of messages logged to the error_log. # Possible values include: debug, info, notice, warn, error, crit, # alert, emerg. # LogLevel warn # Include module configuration: Include mods-enabled/*.load Include mods-enabled/*.conf # Include all the user configurations: Include httpd.conf # Include ports listing Include ports.conf # # The following directives define some format nicknames for use with # a CustomLog directive (see below). # If you are behind a reverse proxy, you might want to change %h into %{X-Forwarded-For}i # LogFormat "%v:%p %h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" vhost_combined LogFormat "%h %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"" combined LogFormat "%h %l %u %t \"%r\" %>s %O" common LogFormat "%{Referer}i -> %U" referer LogFormat "%{User-agent}i" agent # Include of directories ignores editors' and dpkg's backup files, # see README.Debian for details. # Include generic snippets of statements Include conf.d/ # Include the virtual host configurations: Include sites-enabled/

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