9 skills found
himanshub1007 / Alzhimers Disease Prediction Using Deep Learning# AD-Prediction Convolutional Neural Networks for Alzheimer's Disease Prediction Using Brain MRI Image ## Abstract Alzheimers disease (AD) is characterized by severe memory loss and cognitive impairment. It associates with significant brain structure changes, which can be measured by magnetic resonance imaging (MRI) scan. The observable preclinical structure changes provides an opportunity for AD early detection using image classification tools, like convolutional neural network (CNN). However, currently most AD related studies were limited by sample size. Finding an efficient way to train image classifier on limited data is critical. In our project, we explored different transfer-learning methods based on CNN for AD prediction brain structure MRI image. We find that both pretrained 2D AlexNet with 2D-representation method and simple neural network with pretrained 3D autoencoder improved the prediction performance comparing to a deep CNN trained from scratch. The pretrained 2D AlexNet performed even better (**86%**) than the 3D CNN with autoencoder (**77%**). ## Method #### 1. Data In this project, we used public brain MRI data from **Alzheimers Disease Neuroimaging Initiative (ADNI)** Study. ADNI is an ongoing, multicenter cohort study, started from 2004. It focuses on understanding the diagnostic and predictive value of Alzheimers disease specific biomarkers. The ADNI study has three phases: ADNI1, ADNI-GO, and ADNI2. Both ADNI1 and ADNI2 recruited new AD patients and normal control as research participants. Our data included a total of 686 structure MRI scans from both ADNI1 and ADNI2 phases, with 310 AD cases and 376 normal controls. We randomly derived the total sample into training dataset (n = 519), validation dataset (n = 100), and testing dataset (n = 67). #### 2. Image preprocessing Image preprocessing were conducted using Statistical Parametric Mapping (SPM) software, version 12. The original MRI scans were first skull-stripped and segmented using segmentation algorithm based on 6-tissue probability mapping and then normalized to the International Consortium for Brain Mapping template of European brains using affine registration. Other configuration includes: bias, noise, and global intensity normalization. The standard preprocessing process output 3D image files with an uniform size of 121x145x121. Skull-stripping and normalization ensured the comparability between images by transforming the original brain image into a standard image space, so that same brain substructures can be aligned at same image coordinates for different participants. Diluted or enhanced intensity was used to compensate the structure changes. the In our project, we used both whole brain (including both grey matter and white matter) and grey matter only. #### 3. AlexNet and Transfer Learning Convolutional Neural Networks (CNN) are very similar to ordinary Neural Networks. A CNN consists of an input and an output layer, as well as multiple hidden layers. The hidden layers are either convolutional, pooling or fully connected. ConvNet architectures make the explicit assumption that the inputs are images, which allows us to encode certain properties into the architecture. These then make the forward function more efficient to implement and vastly reduce the amount of parameters in the network. #### 3.1. AlexNet The net contains eight layers with weights; the first five are convolutional and the remaining three are fully connected. The overall architecture is shown in Figure 1. The output of the last fully-connected layer is fed to a 1000-way softmax which produces a distribution over the 1000 class labels. AlexNet maximizes the multinomial logistic regression objective, which is equivalent to maximizing the average across training cases of the log-probability of the correct label under the prediction distribution. The kernels of the second, fourth, and fifth convolutional layers are connected only to those kernel maps in the previous layer which reside on the same GPU (as shown in Figure1). The kernels of the third convolutional layer are connected to all kernel maps in the second layer. The neurons in the fully connected layers are connected to all neurons in the previous layer. Response-normalization layers follow the first and second convolutional layers. Max-pooling layers follow both response-normalization layers as well as the fifth convolutional layer. The ReLU non-linearity is applied to the output of every convolutional and fully-connected layer.  The first convolutional layer filters the 224x224x3 input image with 96 kernels of size 11x11x3 with a stride of 4 pixels (this is the distance between the receptive field centers of neighboring neurons in a kernel map). The second convolutional layer takes as input the (response-normalized and pooled) output of the first convolutional layer and filters it with 256 kernels of size 5x5x48. The third, fourth, and fifth convolutional layers are connected to one another without any intervening pooling or normalization layers. The third convolutional layer has 384 kernels of size 3x3x256 connected to the (normalized, pooled) outputs of the second convolutional layer. The fourth convolutional layer has 384 kernels of size 3x3x192 , and the fifth convolutional layer has 256 kernels of size 3x3x192. The fully-connected layers have 4096 neurons each. #### 3.2. Transfer Learning Training an entire Convolutional Network from scratch (with random initialization) is impractical[14] because it is relatively rare to have a dataset of sufficient size. An alternative is to pretrain a Conv-Net on a very large dataset (e.g. ImageNet), and then use the ConvNet either as an initialization or a fixed feature extractor for the task of interest. Typically, there are three major transfer learning scenarios: **ConvNet as fixed feature extractor:** We can take a ConvNet pretrained on ImageNet, and remove the last fully-connected layer, then treat the rest structure as a fixed feature extractor for the target dataset. In AlexNet, this would be a 4096-D vector. Usually, we call these features as CNN codes. Once we get these features, we can train a linear classifier (e.g. linear SVM or Softmax classifier) for our target dataset. **Fine-tuning the ConvNet:** Another idea is not only replace the last fully-connected layer in the classifier, but to also fine-tune the parameters of the pretrained network. Due to overfitting concerns, we can only fine-tune some higher-level part of the network. This suggestion is motivated by the observation that earlier features in a ConvNet contains more generic features (e.g. edge detectors or color blob detectors) that can be useful for many kind of tasks. But the later layer of the network becomes progressively more specific to the details of the classes contained in the original dataset. **Pretrained models:** The released pretrained model is usually the final ConvNet checkpoint. So it is common to see people use the network for fine-tuning. #### 4. 3D Autoencoder and Convolutional Neural Network We take a two-stage approach where we first train a 3D sparse autoencoder to learn filters for convolution operations, and then build a convolutional neural network whose first layer uses the filters learned with the autoencoder.  #### 4.1. Sparse Autoencoder An autoencoder is a 3-layer neural network that is used to extract features from an input such as an image. Sparse representations can provide a simple interpretation of the input data in terms of a small number of \parts by extracting the structure hidden in the data. The autoencoder has an input layer, a hidden layer and an output layer, and the input and output layers have same number of units, while the hidden layer contains more units for a sparse and overcomplete representation. The encoder function maps input x to representation h, and the decoder function maps the representation h to the output x. In our problem, we extract 3D patches from scans as the input to the network. The decoder function aims to reconstruct the input form the hidden representation h. #### 4.2. 3D Convolutional Neural Network Training the 3D convolutional neural network(CNN) is the second stage. The CNN we use in this project has one convolutional layer, one pooling layer, two linear layers, and finally a log softmax layer. After training the sparse autoencoder, we take the weights and biases of the encoder from trained model, and use them a 3D filter of a 3D convolutional layer of the 1-layer convolutional neural network. Figure 2 shows the architecture of the network. #### 5. Tools In this project, we used Nibabel for MRI image processing and PyTorch Neural Networks implementation.
SnehaPathrose / DNSSpoofAndDetectdevelop 1) an on-path DNS packet injector, and 2) a passive DNS poisoning attack detector. Part 1: The DNS packet injector you are going to develop, named 'dnsinject', will capture the traffic from a network interface in promiscuous mode, and attempt to inject forged responses to selected DNS A requests with the goal to poison the resolver's cache. Your program should conform to the following specification: dnsinject [-i interface] [-h hostnames] expression -i Listen on network device <interface> (e.g., eth0). If not specified, dnsinject should select a default interface to listen on. The same interface should be used for packet injection. -h Read a list of IP address and hostname pairs specifying the hostnames to be hijacked. If '-h' is not specified, dnsinject should forge replies for all observed requests with the local machine's IP address as an answer. <expression> is a BPF filter that specifies a subset of the traffic to be monitored. This option is useful for targeting a single or a set of particular victims. The <hostnames> file should contain one IP and hostname pair per line, separated by whitespace, in the following format: 10.6.6.6 foo.example.com 10.6.6.6 bar.example.com 192.168.66.6 www.cs.stonybrook.edu Pay attention to the time needed for generating the spoofed response! Your code should be fast enough so that the injected reply reaches the victim sooner than the server's actual response. The spoofed packet and content should also be valid according to the initial DNS request, and the forged response should be accepted and processed normally by the victim. Part 2: The DNS poisoning attack detector you are going to develop, named 'dnsdetect', will capture the traffic from a network interface in promiscuous mode and detect DNS poisoning attack attempts, such as those generated by dnsinject. Detection will be based on identifying duplicate responses towards the same destination that contain different answers for the same A request, i.e., the observation of the attacker's spoofed response followed by the server's actual response. You should make every effort to avoid false positives, e.g., due to legitimate consecutive responses with different IP addresses for the same hostname due to round robin DNS load balancing. Your program should conform to the following specification: dnsdetect [-i interface] [-r tracefile] expression -i Listen on network device <interface> (e.g., eth0). If not specified, the program should select a default interface to listen on. -r Read packets from <tracefile> (tcpdump format). Useful for detecting DNS poisoning attacks in existing network traces. <expression> is a BPF filter that specifies a subset of the traffic to be monitored. Once an attack is detected, dnsdetect should print to stdout a detailed alert containing a printout of both the spoofed and legitimate responses. You can format the output in any way you like. Output must contain the detected DNS transaction ID, attacked domain name, and the original and malicious IP addresses - for example: 20160406-15:08:49.205618 DNS poisoning attempt TXID 0x5cce Request www.example.com Answer1 [List of IP addresses] Answer2 [List of IP addresses]
wmlynar / Extended Kalman FilterExtended Kalman Filter implemented in Java with easy representation of model and observation functions
AAVSO / VStarVStar is a visualisation and analysis tool for variable star data brought to you by AAVSO
burkh4rt / Discriminative Kalman FilterCode supplement for "The Discriminative Kalman Filter for Bayesian Filtering with Nonlinear and Nongaussian Observation Models"
adrianodemarino / Detect And Remove OutliersIn statistics, an outlier is an observation point that is distant from other observations. How we can filter out these values using python?
fholzm / Deep Observation FilterNeural network-based observation filter estimation for virutal sensing in local active noise control
pankaj614 / Gdp Analysis India 2014 15India GDP Analysis Problem Description - I NITI Aayog: Background NITI Aayog (National Institution for Transforming India) is a policy think tank of the Government of India; it provides strategic inputs to the central and the state governments to achieve various development goals. In the past, NITI Aayog has played an important role in initiatives such as Digital India, Atal Innovation Mission and various agricultural reforms and have designed various policies in education, skill development, water management, healthcare, etc. NITI Aayog was established to replace the Planning Commission of India, which used to follow a top-down model for policy making, i.e., it typically designed policies at the central level (such as the 5-year plans). On the other hand, NITI Aayog designs policies specific to the different states or segments of the economy. Finance Minister, Arun Jaitley, made the following observation on the necessity of creating NITI Aayog, "The 65-year-old Planning Commission had become a redundant organisation. It was relevant in a command economy structure, but not any longer. India is a diversified country and its states are in various phases of economic development along with their own strengths and weaknesses. In this context, a ‘one size fits all’ approach to economic planning is obsolete...". Project Brief We are working as the chief data scientist at NITI Aayog, reporting to the CEO. The CEO has initiated a project wherein the NITI Aayog will provide top-level recommendations to the Chief Ministers (CMs) of various states, which will help them prioritise areas of development for their respective states. Since different states are in different phases of development, the recommendations should be specific to the states. The overall goal of this project is to help the CMs focus on areas that will foster economic development for their respective states. Since the most common measure of economic development is the GDP, we will analyse the GDP of the various states of India and suggest ways to improve it. Understanding GDP Gross domestic product (GDP) at current prices is the GDP at the market value of goods and services produced in a country during a year. In other words, GDP measures the 'monetary value of final goods and services produced by a country/state in a given period of time'. GDP can be broadly divided into goods and services produced by three sectors: the primary sector (agriculture), the secondary sector (industry), and the tertiary sector (services). It is also known as nominal GDP. More technically, (real) GDP takes into account the price change that may have occurred due to inflation. This means that the real GDP is nominal GDP adjusted for inflation. We will use the nominal GDP for this exercise. Also, we will consider the financial year 2015-16 as the base year, as most of the data required for this exercise is available for the aforementioned period. Per Capita GDP and Income Total GDP divided by the population gives the per capita GDP, which roughly measures the average value of goods and services produced per person. The per capita income is closely related to the per capita GDP (though they are not the same). In general, the per capita income increases when the per capita GDP increases, and vice-versa. For instance, in the financial year 2015-16, the per capita income of India was ₹93,293, whereas the per capita GDP of India was $1717, which roughly amounts to ₹1,11,605. Problem Description - II Data The data is sourced from https://data.gov.in/, an Open Government Data (OGD) platform of India. The download instructions are provided in the next segment. The data for GDP analysis of the Indian states is divided into two parts: Data I-A: This dataset consists of the GSDP (Gross State Domestic Product) data for the states and union territories. Data I-B: This dataset contains the distribution of GSDP among three sectors: the primary sector (agriculture), the secondary sector (industry) and the tertiary sector (services) along with taxes and subsidies. There is separate dataset for each of the states. We are expected to read the dataset for the available states and join these (in Python) if needed. There are two parts to this project. In the first part, we will analyse and compare the GDPs of various Indian states (both total and per capita). The GDP of a state is referred to as the GSDP (Gross State Domestic Product). Then, we will divide the states into four categories based on the GDP per capita, and for each of these four categories, we will analyse the sectors that contribute the most to the GDP (such as agriculture, real estate, manufacturing, etc.). In the second part, we will analyse whether GDP per capita is related to dropout rates in schools and colleges. Part-I: GDP Analysis of the Indian States For each of the following steps of analysis, choose an appropriate type of plot for comparing the data. Also, ensure that the plots are in increasing or decreasing order for better comparison. For example, if we make a bar plot to compare the GDPs of the states, ensure that the bars are in either increasing or decreasing order of GDP. Part I-A: For the analysis below, use the Data I-A. First, we need to load the data in Python properly and then clean it. This also involves the treatment of missing values, we can choose to drop the row or column as well. Remember this will affect our next analysis and results drastically. Plot a graph for rows " % Growth over previous year" for all the states (not union territories) whose data is available, use as much data as possible for this exercise. Use the best fit line to represent the growth for each state. Draw a similar line graph for the nation as well. How will we compare the growth rates of any two states? Which states have been growing consistently fast, and which ones have been struggling? Rank top 3 fastest and 3 slowest-growing states. What is the Nation's growth rate? What has been the growth rate of my home state, and how does it compare to the national growth rate? Plot the total GDP of the states for the year 2015-16: Which Plot will we use for this? Why? (Remeber to plot the graph in a way such as it is easier to read and compare) Identify the top 5 and the bottom 5 states based on total GDP. What insights can we draw from this graph? What states are performing poorly? (Remember: this will not be solely based on total GDP) Part I-B: For the analysis below, use Data I-B. We can also use Data I-B along with Data I-A if required. Also, perform the analysis only for the duration 2014-15. Filter out the union territories (Delhi, Chandigarh, Andaman and Nicobar Islands, etc.) for further analysis, as they are governed directly by the central, not state governments. Plot the GDP per capita for all the states. Identify the top 5 and the bottom 5 states based on the GDP per capita. Find the ratio of the highest per capita GDP to the lowest per capita GDP. Plot the percentage contribution of the primary, secondary and tertiary sectors as a percentage of the total GDP for all the states. Which plot will we use here? Why? Why is (Primary + Secondary + Tertiary) not equal to total GDP? Can we draw any insight from this? Find correlation of percentile of the state (% of states with lower per capita GDP) and %contribution of Primary sector to total GDP. Categorise the states into four groups based on the GDP per capita (C1, C2, C3, C4, where C1 would have the highest per capita GDP and C4, the lowest). The quantile values are (0.20,0.5, 0.85, 1), i.e., the states lying between the 85th and the 100th percentile are in C1; those between the 50th and the 85th percentiles are in C2, and so on. Note: Categorisation into four groups will simplify the subsequent analysis, as otherwise, comparing the data of all the states would become quite exhaustive. For each category (C1, C2, C3, C4): Find the top 3/4/5 sub-sectors (such as agriculture, forestry and fishing, crops, manufacturing etc., not primary, secondary and tertiary) that contribute to approximately 80% of the GSDP of each category. Note-I: The nomenclature for this project is as follows: primary, secondary and tertiary are named 'sectors', while agriculture, manufacturing etc. are named 'sub-sectors'. Note-II: If the top 3 sub-sectors contribute to, say, 79% of the GDP of some category, we can report "These top 3 sub-sectors contribute to approximately 80% of the GDP". This is to simplify the analysis and make the results consumable. (Remember, the CEO has to present the report to the CMs, and CMs have limited time; so, the analysis needs to be sharp and concise.) Plot the contribution of the sub-sectors as a percentage of the GSDP of each category. Now that we have summarised the data in the form of plots, tables, etc., try to draw non-obvious insights from it. Think about questions such as: How does the GDP distribution of the top states (C1) differ from the others? Which sub-sectors seem to be correlated with high GDP? Which sub-sectors do the various categories need to focus on? Ask other such relevant questions, which we think are important, and note we insights for category separately. More insights are welcome and will be awarded accordingly. Finally, provide at least two recommendations for each category to improve the per capita GDP. Part-II: GDP and Education Dropout Rates In Part-I, we would have noticed that (one) way to increase per capita GDP is by shifting the distribution of GDP towards the secondary and tertiary sectors, i.e., the manufacturing and services industries. But these industries can thrive only when there is an availability of educated and skilled labour. In this part of the analysis, we will investigate whether there is any relationship between per capita GDP with dropout rates in education. Data Data II: This section will require the dropout rate dataset apart from the dataset that we used in Part-1 of the case study. Download instructions are provided in the next segment. Part-II: GDP and Education Analyse if there is any correlation of GDP per capita with dropout rates in education (primary, upper primary and secondary) for the year 2014-2015 for each state. Choose an appropriate plot to conduct this analysis. Is there any correlation between dropout rate and %contribution of each sector (Primary, Secondary and Tertiary) to the total GDP? We have the total population of each state from the data in part I. Is there any correlation between dropout rates and population? What is the expected trend and what is the observation? Write down the key insights we draw from this data: Form at least one reasonable hypothesis for the observations from the data About GDP analysis for India in the year for 2015-16 and recommendation for the individual states for increasing the GDP by focusing on various factor. Topics python statistical-analysis data-analysis gdp-analysis Resources Readme Stars 0 stars Watchers 1 watching Forks 0 forks Releases No releases published Packages No packages published Languages Jupyter Notebook 100.0% Footer © 2022 GitHub, Inc. Footer navigation Terms Privacy Security Status Docs Contact GitHub Pricing API Training Blog About
TempleRAIL / Sphd Sensor ModelsThree sensor models of the Semantic PHD Filter formultiple target tracking: observation model, detection model, and clutter model.
