dependabot /
gem-vulnerability-analysis
Jupyter notebook for a blog post on gem vulnerabilities and version updates.
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scikit_ML_Pipeline_Binary_Notebook
An (updated and expanded) rigorous, well documented machine learning analysis pipeline for binary classification datasets assembled as a Jupyter Notebook. Includes exploratory analysis, data processing, feature processing, ML modeling (13 algorithms) with hyperparameter sweeps, visualizations, and statistical analysis. A comprehensive starting point to adapt to your own dataset.
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Introduction
This respository includes the code (including a Jupyter Notebook) to run the machine learning analysis pipeline (for binary classification) that simplifies and extends a previous one that pairs with our paper titled "A Rigorous Machine Learning Analysis Pipeline for Biomedical Binary Classification: Application in Pancreatic Cancer Nested Case-control Studies with Implications for Bias Assessments". This notebook presents an example of a 'rigorous' and well annotated machine learning (ML) analysis pipeline that could be reasonablly applied to various supervised learning classification tasks, but was developed here specifically for biomedical data mining/modeling. This pipeline could be used as follows:
- Apply/run pipeline (as is) on other binary classification datasets
- Utilize this pipeline as a blueprint to implement your own expanded or simplified anlaysis pipeline
- Utilize as an educational tool/example of how to run python-based data handling, preprocessing, feature selection, machine learning modeling, generating relevant visualizations, and running non-parametric statistical comparisons. Packages such as pandas, scikit-learn and scipy are used.
- Obtain the code to generate our porposed 'compound feature importance barplots'.
Schematic of ML Analysis Pipeline
Prerequisites for Use
Environment Requirements
In order to run this pipeline as a Jupyter Notebook you must have the proper environment set up on your computer. Python 3 as well as a number of Python packages are required. Most of these requirements are satisfied by installing the most recent version of anaconda (https://docs.anaconda.com/anaconda/install/). We used Anaconda3 with python version 3.7.7 during this pipeline development. In addition to the packages included in anaconda, the following packages will need to be installed separately (or possibly updated, if you have an older version installed). We recommend installing them within the 'anaconda prompt' that installs with anaconda:
- scikit-rebate (To install: pip install skrebate)
- xgboost (To install: pip install xgboost)
- lightgbm (To install: pip install lightgbm)
- optuna (To install: pip install optuna)
- eLCS (To install: pip install scikit-elcs)
- XCS (To install: pip install scikit-XCS)
- ExSTraCS (To install: pip install scikit-ExSTraCS)
Additionally, while currently commented out in the file (modeling_methods.py) if you want the optuna hypterparameter sweep figures to appear within the jupyter notebook (via the command 'fig.show()' ) you will need to run the following installation commands. This should only be required if you edit the python file to uncomment this line for any or all of the ML modeling algorithms.
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etherceo1x1 /
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BUILD YOUR OWN BLOCKCHAIN: A PYTHON TUTORIAL Download the full Jupyter/iPython notebook from Github here Build Your Own Blockchain – The Basics¶ This tutorial will walk you through the basics of how to build a blockchain from scratch. Focusing on the details of a concrete example will provide a deeper understanding of the strengths and limitations of blockchains. For a higher-level overview, I’d recommend this excellent article from BitsOnBlocks. Transactions, Validation, and updating system state¶ At its core, a blockchain is a distributed database with a set of rules for verifying new additions to the database. We’ll start off by tracking the accounts of two imaginary people: Alice and Bob, who will trade virtual money with each other. We’ll need to create a transaction pool of incoming transactions, validate those transactions, and make them into a block. We’ll be using a hash function to create a ‘fingerprint’ for each of our transactions- this hash function links each of our blocks to each other. To make this easier to use, we’ll define a helper function to wrap the python hash function that we’re using. In [1]: import hashlib, json, sys def hashMe(msg=""): # For convenience, this is a helper function that wraps our hashing algorithm if type(msg)!=str: msg = json.dumps(msg,sort_keys=True) # If we don't sort keys, we can't guarantee repeatability! if sys.version_info.major == 2: return unicode(hashlib.sha256(msg).hexdigest(),'utf-8') else: return hashlib.sha256(str(msg).encode('utf-8')).hexdigest() Next, we want to create a function to generate exchanges between Alice and Bob. We’ll indicate withdrawals with negative numbers, and deposits with positive numbers. We’ll construct our transactions to always be between the two users of our system, and make sure that the deposit is the same magnitude as the withdrawal- i.e. that we’re neither creating nor destroying money. In [2]: import random random.seed(0) def makeTransaction(maxValue=3): # This will create valid transactions in the range of (1,maxValue) sign = int(random.getrandbits(1))*2 - 1 # This will randomly choose -1 or 1 amount = random.randint(1,maxValue) alicePays = sign * amount bobPays = -1 * alicePays # By construction, this will always return transactions that respect the conservation of tokens. # However, note that we have not done anything to check whether these overdraft an account return {u'Alice':alicePays,u'Bob':bobPays} Now let’s create a large set of transactions, then chunk them into blocks. In [3]: txnBuffer = [makeTransaction() for i in range(30)] Next step: making our very own blocks! We’ll take the first k transactions from the transaction buffer, and turn them into a block. Before we do that, we need to define a method for checking the valididty of the transactions we’ve pulled into the block. For bitcoin, the validation function checks that the input values are valid unspent transaction outputs (UTXOs), that the outputs of the transaction are no greater than the input, and that the keys used for the signatures are valid. In Ethereum, the validation function checks that the smart contracts were faithfully executed and respect gas limits. No worries, though- we don’t have to build a system that complicated. We’ll define our own, very simple set of rules which make sense for a basic token system: The sum of deposits and withdrawals must be 0 (tokens are neither created nor destroyed) A user’s account must have sufficient funds to cover any withdrawals If either of these conditions are violated, we’ll reject the transaction. In [4]: def updateState(txn, state): # Inputs: txn, state: dictionaries keyed with account names, holding numeric values for transfer amount (txn) or account balance (state) # Returns: Updated state, with additional users added to state if necessary # NOTE: This does not not validate the transaction- just updates the state! # If the transaction is valid, then update the state state = state.copy() # As dictionaries are mutable, let's avoid any confusion by creating a working copy of the data. for key in txn: if key in state.keys(): state[key] += txn[key] else: state[key] = txn[key] return state In [5]: def isValidTxn(txn,state): # Assume that the transaction is a dictionary keyed by account names # Check that the sum of the deposits and withdrawals is 0 if sum(txn.values()) is not 0: return False # Check that the transaction does not cause an overdraft for key in txn.keys(): if key in state.keys(): acctBalance = state[key] else: acctBalance = 0 if (acctBalance + txn[key]) < 0: return False return True Here are a set of sample transactions, some of which are fraudulent- but we can now check their validity! In [6]: state = {u'Alice':5,u'Bob':5} print(isValidTxn({u'Alice': -3, u'Bob': 3},state)) # Basic transaction- this works great! print(isValidTxn({u'Alice': -4, u'Bob': 3},state)) # But we can't create or destroy tokens! print(isValidTxn({u'Alice': -6, u'Bob': 6},state)) # We also can't overdraft our account. print(isValidTxn({u'Alice': -4, u'Bob': 2,'Lisa':2},state)) # Creating new users is valid print(isValidTxn({u'Alice': -4, u'Bob': 3,'Lisa':2},state)) # But the same rules still apply! True False False True False Each block contains a batch of transactions, a reference to the hash of the previous block (if block number is greater than 1), and a hash of its contents and the header Building the Blockchain: From Transactions to Blocks¶ We’re ready to start making our blockchain! Right now, there’s nothing on the blockchain, but we can get things started by defining the ‘genesis block’ (the first block in the system). Because the genesis block isn’t linked to any prior block, it gets treated a bit differently, and we can arbitrarily set the system state. In our case, we’ll create accounts for our two users (Alice and Bob) and give them 50 coins each. In [7]: state = {u'Alice':50, u'Bob':50} # Define the initial state genesisBlockTxns = [state] genesisBlockContents = {u'blockNumber':0,u'parentHash':None,u'txnCount':1,u'txns':genesisBlockTxns} genesisHash = hashMe( genesisBlockContents ) genesisBlock = {u'hash':genesisHash,u'contents':genesisBlockContents} genesisBlockStr = json.dumps(genesisBlock, sort_keys=True) Great! This becomes the first element from which everything else will be linked. In [8]: chain = [genesisBlock] For each block, we want to collect a set of transactions, create a header, hash it, and add it to the chain In [9]: def makeBlock(txns,chain): parentBlock = chain[-1] parentHash = parentBlock[u'hash'] blockNumber = parentBlock[u'contents'][u'blockNumber'] + 1 txnCount = len(txns) blockContents = {u'blockNumber':blockNumber,u'parentHash':parentHash, u'txnCount':len(txns),'txns':txns} blockHash = hashMe( blockContents ) block = {u'hash':blockHash,u'contents':blockContents} return block Let’s use this to process our transaction buffer into a set of blocks: In [10]: blockSizeLimit = 5 # Arbitrary number of transactions per block- # this is chosen by the block miner, and can vary between blocks! while len(txnBuffer) > 0: bufferStartSize = len(txnBuffer) ## Gather a set of valid transactions for inclusion txnList = [] while (len(txnBuffer) > 0) & (len(txnList) < blockSizeLimit): newTxn = txnBuffer.pop() validTxn = isValidTxn(newTxn,state) # This will return False if txn is invalid if validTxn: # If we got a valid state, not 'False' txnList.append(newTxn) state = updateState(newTxn,state) else: print("ignored transaction") sys.stdout.flush() continue # This was an invalid transaction; ignore it and move on ## Make a block myBlock = makeBlock(txnList,chain) chain.append(myBlock) In [11]: chain[0] Out[11]: {'contents': {'blockNumber': 0, 'parentHash': None, 'txnCount': 1, 'txns': [{'Alice': 50, 'Bob': 50}]}, 'hash': '7c88a4312054f89a2b73b04989cd9b9e1ae437e1048f89fbb4e18a08479de507'} In [12]: chain[1] Out[12]: {'contents': {'blockNumber': 1, 'parentHash': '7c88a4312054f89a2b73b04989cd9b9e1ae437e1048f89fbb4e18a08479de507', 'txnCount': 5, 'txns': [{'Alice': 3, 'Bob': -3}, {'Alice': -1, 'Bob': 1}, {'Alice': 3, 'Bob': -3}, {'Alice': -2, 'Bob': 2}, {'Alice': 3, 'Bob': -3}]}, 'hash': '7a91fc8206c5351293fd11200b33b7192e87fad6545504068a51aba868bc6f72'} As expected, the genesis block includes an invalid transaction which initiates account balances (creating tokens out of thin air). The hash of the parent block is referenced in the child block, which contains a set of new transactions which affect system state. We can now see the state of the system, updated to include the transactions: In [13]: state Out[13]: {'Alice': 72, 'Bob': 28} Checking Chain Validity¶ Now that we know how to create new blocks and link them together into a chain, let’s define functions to check that new blocks are valid- and that the whole chain is valid. On a blockchain network, this becomes important in two ways: When we initially set up our node, we will download the full blockchain history. After downloading the chain, we would need to run through the blockchain to compute the state of the system. To protect against somebody inserting invalid transactions in the initial chain, we need to check the validity of the entire chain in this initial download. Once our node is synced with the network (has an up-to-date copy of the blockchain and a representation of system state) it will need to check the validity of new blocks that are broadcast to the network. We will need three functions to facilitate in this: checkBlockHash: A simple helper function that makes sure that the block contents match the hash checkBlockValidity: Checks the validity of a block, given its parent and the current system state. We want this to return the updated state if the block is valid, and raise an error otherwise. checkChain: Check the validity of the entire chain, and compute the system state beginning at the genesis block. This will return the system state if the chain is valid, and raise an error otherwise. In [14]: def checkBlockHash(block): # Raise an exception if the hash does not match the block contents expectedHash = hashMe( block['contents'] ) if block['hash']!=expectedHash: raise Exception('Hash does not match contents of block %s'% block['contents']['blockNumber']) return In [15]: def checkBlockValidity(block,parent,state): # We want to check the following conditions: # - Each of the transactions are valid updates to the system state # - Block hash is valid for the block contents # - Block number increments the parent block number by 1 # - Accurately references the parent block's hash parentNumber = parent['contents']['blockNumber'] parentHash = parent['hash'] blockNumber = block['contents']['blockNumber'] # Check transaction validity; throw an error if an invalid transaction was found. for txn in block['contents']['txns']: if isValidTxn(txn,state): state = updateState(txn,state) else: raise Exception('Invalid transaction in block %s: %s'%(blockNumber,txn)) checkBlockHash(block) # Check hash integrity; raises error if inaccurate if blockNumber!=(parentNumber+1): raise Exception('Hash does not match contents of block %s'%blockNumber) if block['contents']['parentHash'] != parentHash: raise Exception('Parent hash not accurate at block %s'%blockNumber) return state In [16]: def checkChain(chain): # Work through the chain from the genesis block (which gets special treatment), # checking that all transactions are internally valid, # that the transactions do not cause an overdraft, # and that the blocks are linked by their hashes. # This returns the state as a dictionary of accounts and balances, # or returns False if an error was detected ## Data input processing: Make sure that our chain is a list of dicts if type(chain)==str: try: chain = json.loads(chain) assert( type(chain)==list) except: # This is a catch-all, admittedly crude return False elif type(chain)!=list: return False state = {} ## Prime the pump by checking the genesis block # We want to check the following conditions: # - Each of the transactions are valid updates to the system state # - Block hash is valid for the block contents for txn in chain[0]['contents']['txns']: state = updateState(txn,state) checkBlockHash(chain[0]) parent = chain[0] ## Checking subsequent blocks: These additionally need to check # - the reference to the parent block's hash # - the validity of the block number for block in chain[1:]: state = checkBlockValidity(block,parent,state) parent = block return state We can now check the validity of the state: In [17]: checkChain(chain) Out[17]: {'Alice': 72, 'Bob': 28} And even if we are loading the chain from a text file, e.g. from backup or loading it for the first time, we can check the integrity of the chain and create the current state: In [18]: chainAsText = json.dumps(chain,sort_keys=True) checkChain(chainAsText) Out[18]: {'Alice': 72, 'Bob': 28} Putting it together: The final Blockchain Architecture¶ In an actual blockchain network, new nodes would download a copy of the blockchain and verify it (as we just did above), then announce their presence on the peer-to-peer network and start listening for transactions. Bundling transactions into a block, they then pass their proposed block on to other nodes. We’ve seen how to verify a copy of the blockchain, and how to bundle transactions into a block. If we recieve a block from somewhere else, verifying it and adding it to our blockchain is easy. Let’s say that the following code runs on Node A, which mines the block: In [19]: import copy nodeBchain = copy.copy(chain) nodeBtxns = [makeTransaction() for i in range(5)] newBlock = makeBlock(nodeBtxns,nodeBchain) Now assume that the newBlock is transmitted to our node, and we want to check it and update our state if it is a valid block: In [20]: print("Blockchain on Node A is currently %s blocks long"%len(chain)) try: print("New Block Received; checking validity...") state = checkBlockValidity(newBlock,chain[-1],state) # Update the state- this will throw an error if the block is invalid! chain.append(newBlock) except: print("Invalid block; ignoring and waiting for the next block...") print("Blockchain on Node A is now %s blocks long"%len(chain)) Blockchain on Node A is currently 7 blocks long New Block Received; checking validity... Blockchain on Node A is now 8 blocks long