Metadata-Version: 2.1
Name: sorn
Version: 0.2.9
Summary: Self-Organizing Recurrent Neural Networks
Home-page: https://github.com/Saran-nns/sorn
Author: Saranraj Nambusubramaniyan
Author-email: saran_nns@hotmail.com
License: OSI Approved :: MIT License
Description: ## Self-Organizing Recurrent Neural Networks 
        
        SORN is a class of neuro-inspired artificial network build based on plasticity mechanisms in biological brain and mimic neocortical circuits ability of learning and adaptation through neuroplasticity mechanisms.
        
        For ease of maintanance, example use cases and the API(under developement) are moved to https://github.com/Saran-nns/PySORN_0.1 
        
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        <h4 align="Left">SORN Reservoir and the evolution of synaptic efficacies</h4> 
        <a href="url"><img src="https://raw.githubusercontent.com/Saran-nns/PySORN_0.1/master/v0.1.0/doc/images/SORNCartcropped.png" height="320" width="430" ></a> <a href="url"><img src="https://raw.githubusercontent.com/Saran-nns/PySORN_0.1/blob/master/v0.1.0/doc/images/weights.png" height="375" width="425" ></a>	
        
        <h4 align="center">Neural Connectome</h4> 
        <p align="center">
        <a href="url"><img src="https://raw.githubusercontent.com/Saran-nns/PySORN_0.1/blob/master/v0.1.0/doc/images/neuralcorrelationall.png" height="450" width="450" ></a>
        </p>
        
        #### To install the latest release:
        
        ```python
        pip install sorn
        ```
        
        The library is still in alpha stage, so you may also want to install the latest version from the development branch:
        
        ```python
        pip install git+https://github.com/Saran-nns/sorn
        ```
        
        #### Dependencies
        SORN supports Python 3.5+ ONLY. For older Python versions please use the official Python client
        
        
        #### Usage:
        
        ##### Update Network configurations
        
        Navigate to home/conda/envs/ENVNAME/Lib/site-packages/sorn
        
        or if you are unsure about the directory of sorn
        
        Run
        
        ```python
        import sorn
        
        sorn.__file__
        ```
        to find the location of the sorn package
        
        Then, update/edit the configuration.ini
        
        
        ##### Plasticity Phase
        
        ```Python
        # Import 
        from sorn.sorn import RunSorn
        
        # Sample input 
        inputs = [0.]
        
        # To simulate the network; 
        matrices_dict, Exc_activity, Inh_activity, Rec_activity, num_active_connections = RunSorn(phase='Plasticity', matrices=None,
                                                                                  time_steps=100).run_sorn(inputs)
        
        # To resume the simulation, load the matrices_dict from previous simulation;
        matrices_dict, Exc_activity, Inh_activity, Rec_activity, num_active_connections = RunSorn(phase='Plasticity', matrices=matrices_dict,
                                                                                  time_steps=100).run_sorn(inputs)
        ```
        
        ##### Training phase:
        
        ```Python
        matrices_dict, Exc_activity, Inh_activity, Rec_activity, num_active_connections = RunSorn(phase='Training', matrices=matrices_dict,
                                                                                  time_steps=100).run_sorn(inputs)
        ```
        
        #### Network Output Descriptions:
            matrices_dict  - Dictionary of connection weights ('Wee','Wei','Wie') , Excitatory network activity ('X'), Inhibitory network activities('Y'), Threshold values ('Te','Ti')
        
            Exc_activity - Collection of Excitatory network activity of entire simulation period
        
            Inh_activitsy - Collection of Inhibitory network activity of entire simulation period
        
            Rec_activity - Collection of Recurrent network activity of entire simulation period
        
            num_active_connections - List of number of active connections in the Excitatory pool at each time step 
        
        
        #### Sample use with OpenAI gym :
        ##### Cartpole balance problem
        ```python
        # Imports
        import utils.InitHelper as initializer
        from sorn.sorn import Sorn, Plasticity, TrainSorn, TrainSornPlasticity
        import gym
        
        # Load the simulated network matrices
        # Note these matrices are obtained after the network achieved convergence under random inputs and noise
        
        with open('simulation_matrices.pkl','rb') as f:  
            sim_matrices,excit_states,inhib_states,recur_states,num_reservoir_conn = pickle.load(f)
        
        # Training parameters
        NUM_EPISODES = 2e6
        NUM_PLASTICITY_EPISODES = 20000
        
        env = gym.make('CartPole-v0')
        
        for EPISODE in range(NUM_EPISODES):
            
            # Environment observation
            state = env.reset()[None,:]
            
            # Play the episode
            
            while True:
              
              if EPISODE < NUM_PLASTICITY_EPISODE:
              
                # Plasticity phase
                sim_matrices,excit_states,inhib_states,recur_states,num_reservoir_conn = TrainSornPlasticity.train_sorn(phase = 'Plasticity',
                                                                                                                    matrices = sim_matrices,
                                                                                                                    inputs = state)
        
              else:
                # Training phase with frozen reservoir connectivity
                sim_matrices,excit_states,inhib_states,recur_states,num_reservoir_conn = TrainSorn.train_sorn(phase = 'Training',
                                                                                                                    matrices = sim_matrices,
                                                                                                                    inputs = state)
              
              # Feed excit_states as input states to your RL algorithm, below goes for simple policy gradient algorithm
              # Sample policy w.r.t excitatory states and take action in the environment
               
              probs = policy(np.asarray(excit_states),output_layer_weights))
              action = np.random.choice(action_space,probs)
              state,reward,done,_ = env.step(action) 
              
              if done:
                break
        ```
        
        #### Sample Plotting functions 
        
        ```Python
        from sorn.utils import Plotter
        # Plot weight distribution in the network
        Plotter.weight_distribution(weights= matrices_dict['Wee'], bin_size = 5, savefig = False)
        
        # Plot Spike train of all neurons in the network
        Plotter.scatter_plot(spike_train = np.asarray(Exc_activity), savefig=False)
        
        
        Plotter.raster_plot(spike_train = np.asarray(Exc_activity), savefig=False)
        ```
        
        #### Sample Statistical analysis functions
        
        ```Python
        from sorn.utils import Statistics
        #t-lagged auto correlation between neural activity
        Statistics.autocorr(firing_rates = [1,1,5,6,3,7],t= 2)
        
        # Fano factor: To verify poissonian process in spike generation of neuron 10
        Statistics.fanofactor(spike_train= np.asarray(Exc_activity),neuron = 10,window_size = 10)
        ```
        
        #### The network is inspired by folowing articles:
        
        Lazar, A. (2009). SORN: a Self-organizing Recurrent Neural Network. Frontiers in Computational Neuroscience, 3. https://doi.org/10.3389/neuro.10.023.2009
        
        Hartmann, C., Lazar, A., Nessler, B., & Triesch, J. (2015). Whereâ€™s the Noise? Key Features of Spontaneous Activity and Neural Variability Arise through Learning in a Deterministic Network. PLoS Computational Biology, 11(12). https://doi.org/10.1371/journal.pcbi.1004640 
        
        Del Papa, B., Priesemann, V., & Triesch, J. (2017). Criticality meets learning: Criticality signatures in a self-organizing recurrent neural network. PLoS ONE, 12(5). https://doi.org/10.1371/journal.pone.0178683 
        
        Zheng, P., Dimitrakakis, C., & Triesch, J. (2013). Network Self-Organization Explains the Statistics and Dynamics of Synaptic Connection Strengths in Cortex. PLoS Computational Biology, 9(1). https://doi.org/10.1371/journal.pcbi.1002848  
        
        
Keywords: Brain-Inspired Computing,Artificial Neural Networks,Neuro Informatics,Spiking Cortical Networks,Neural Connectomics,Neuroscience,Artificial General Intelligence,Neural Information Processing
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
