Analyzing the state of the Basic Health Units of Brazil (UBS) using Python for Data Science

This work was developed during the “Python IMD challenge” happened on 10/21/2017 with Igor, Ricardo, Luiza and me. The competition purpose was to develop a project involving Data Science during 5 hours. Our goal focused on choosing something impactful and at the same time simple to be developed in the short given time. We were very happy to know that we won the first position in the competition at the end! The prize is a free ticket to the national Python event that is going to happen next year.

eqp.jpg

Without further ado, let’s talk about the project itself!

During our searches for datasets about various topics, we found the national website which contains numerous pre-formatted data about national interests:   http://dados.gov.br/

The subject that called our attention was about the Basic Health Units of Brazil (Unidade básica de saúde), which are small public hospitals basically. The dataset had some interesting columns that we thought could bring an important conclusion, for example, the hospitals coordinates and their evaluation about different aspects like the hospital structure and medical supplies.

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A Fan control system with ATmega2560 Microcontroller

The following project was developed during a class taken at Federal University of Rio Grande do Norte with professor Marcelo. The group was composed by GiovannaJoãoRaí and me.

The group goal was to implement a drying grain system. The process of drying should start with the press of a button, after that, a fan speed is controlled based on a “dry curve” and the reading of a luminosity and temperature sensor. With 3 minutes the routine is finished, and the machine should wait for another button press to start the system again.

agoravai.png

The hardware of the control system consists of:

  • An ATmega2560 Microcontroller
  • An LDR to sense the luminosity
  • An NTC sensor for the temperature
  • A Push-Button to start the system
  • LEDs for behavior visualization
  • A “4N25” Photocoupler to protect the Microcontroller from the load
  • An NPN transistor with a diode for circuit protection
  • Power supply to the Fan
  • Some resistors

The last picture represents the components, an Arduino Mega board is used to facilitate communication with the microprocessor, the DC motor illustrates the fan. Since the LDR and NTC sensors are a variable resistance for the desired domain, a voltage divider is applied to convert the input voltage to a measured voltage. An operational range should be specified in this type of configuration, in the example of the NTC temperature sensor, the fixed resistor was chosen based on its measured resistance at the ambient temperature which, for 25 °C is approximately 50Ω.

VoltageDividerSchematic

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Easily Using SWI-Prolog within Matlab

This post intends to show how to interact with SWI-Prolog codes inside MatLab.

The following code is an arbitrary example of a special system, which covers different situations for “control” based on various inputs.


:- dynamic upOn/0, upOff/0.

upOff.

getOn(sensor,Value) :- Value < 0.5.
getOff(sensor,Value) :- Value > 0.5. 

setOn(valve,Value) :- Value is 1.0.
setOff(valve,Value) :- Value is 0.0.

control(V_in,V_out,S0,S1,S2,SW) :- getOff(sensor,SW),getOff(sensor,S0),getOff(sensor,S1),getOff(sensor,S2),upOff,setOff(valve,V_in),setOff(valve,V_out).
control(V_in,V_out,S0,S1,S2,SW) :- getOn(sensor,SW),getOff(sensor,S0),getOff(sensor,S1),getOff(sensor,S2),upOff,setOn(valve,V_in),setOff(valve,V_out),retract(upOff),asserta(upOn).
control(V_in,V_out,S0,S1,S2,SW) :- getOn(sensor,SW),getOn(sensor,S0),getOff(sensor,S1),getOff(sensor,S2),upOn,setOn(valve,V_in),setOff(valve,V_out).
control(V_in,V_out,S0,S1,S2,SW) :- getOn(sensor,SW),getOn(sensor,S0),getOn(sensor,S1),getOff(sensor,S2),upOn,setOn(valve,V_in),setOff(valve,V_out).
control(V_in,V_out,S0,S1,S2,SW) :- getOn(sensor,SW),getOn(sensor,S0),getOn(sensor,S1),getOn(sensor,S2),upOn,setOff(valve,V_in),setOn(valve,V_out),retract(upOn),asserta(upOff).
control(V_in,V_out,S0,S1,S2,SW) :- getOn(sensor,SW),getOn(sensor,S0),getOn(sensor,S1),getOn(sensor,S2),upOff,setOff(valve,V_in),setOn(valve,V_out).
control(V_in,V_out,S0,S1,S2,SW) :- getOn(sensor,SW),getOn(sensor,S0),getOn(sensor,S1),getOff(sensor,S2),upOff,setOff(valve,V_in),setOn(valve,V_out).
control(V_in,V_out,S0,S1,S2,SW) :- getOn(sensor,SW),getOn(sensor,S0),getOff(sensor,S1),getOff(sensor,S2),upOff,setOn(valve,V_in),setOff(valve,V_out),retract(upOff),asserta(upOn).
control(V_in,V_out,S0,S1,S2,SW) :- getOff(sensor,SW),getOn(sensor,S0),getOn(sensor,S1),getOn(sensor,S2),setOff(valve,V_in),setOn(valve,V_out).
control(V_in,V_out,S0,S1,S2,SW) :- getOff(sensor,SW),getOn(sensor,S0),getOn(sensor,S1),getOff(sensor,S2),upOff,setOff(valve,V_in),setOn(valve,V_out).
control(V_in,V_out,S0,S1,S2,SW) :- getOff(sensor,SW),getOn(sensor,S0),getOn(sensor,S1),getOff(sensor,S2),upOn,setOff(valve,V_in),setOn(valve,V_out),retract(upOn),asserta(upOff).
control(V_in,V_out,S0,S1,S2,SW) :- getOff(sensor,SW),getOn(sensor,S0),getOff(sensor,S1),getOff(sensor,S2),upOff,setOff(valve,V_in),setOn(valve,V_out).
control(V_in,V_out,S0,S1,S2,SW) :- getOff(sensor,SW),getOn(sensor,S0),getOff(sensor,S1),getOff(sensor,S2),upOn,setOff(valve,V_in),setOn(valve,V_out),retract(upOn),asserta(upOff).

The above code can be called by another Prolog script as follows:

#!/usr/bin/env swipl

:- initialization main. 

main:-  current_prolog_flag(argv,Argv),
        nth0(0, Argv, A), % get first argument
		nth0(1, Argv, B), % get second argument
		nth0(2, Argv, C), % get third argument
		nth0(3, Argv, D), % get fourth argument
		format("~w ~w ~w ~w \n",[A,B,C,D]), % Print inputs
        consult('example1Prolog'), % Load main Prolog code
		atom_number(A,E), % Transform inputs into Prolog integers
		atom_number(B,F),
		atom_number(C,G),
		atom_number(D,H),
		control(X,Y,E,F,G,H), % Query control function with inputs
		format("X= ~w Y= ~w \n",[X,Y]),	% Prints output variables
		halt. % Finishes execution

The script is executed with the bash shell command:


swipl -s plscript.pl 1 1 1 1

Where the last 4 numbers stand for the Prolog code inputs. The following output with the above command is:


1 1 1 1
X= 0.0 Y= 1.0

Most of the work is already done! (WOW). The last step is executing the same bash command within Matlab using the “system” function:


[status,term_out] = system('swipl -s plscript.pl 1 1 1 1')

“term_out” variable will hold the script output for the inputs given. The following picture shows the previous call output on the main console with the described method.

matlab_run_prolog

Note: It is important to check if a set of inputs will return valid outputs for the system (if they are covered). Also, make sure to test if the script is reaching the last line “halt.”, otherwise the SWI-Prolog will open without closing and the Matlab will wait until the application finishes (never) and crash.

The following Prolog command is helpful if the developed Prolog code depends on dynamic variables like the one shown in this tutorial:


qsave_program(runtime_data).

The problem is that the saved data can not be loaded into a running environment, making this post approach not to work for dynamic variables (for now).

Files can be accessed at:

https://github.com/YangTavares/Deep_learning/tree/master/Prolog_to_Matlab

Robot navigation using a Multilayer Perceptron Neural Network

The Single-Layer Perceptron (SLP) was one of the first artificial neural networks to be developed. It consists of a system that can classify a series of inputs based on their weights, and distinguish two different type of classes linearly. The activation function, in the case of the picture below, is a step function, meaning the resulting output can assume only two values. An input constant, also known as bias, determines the system threshold to define the output.perceptron-picture

Image source: http://abhay.harpale.net/blog/machine-learning/a-hands-on-tutorial-on-the-perceptron-learning-algorithm/

The limitation of the SLP consists of only separating two classes with a single line, in the example below, if one blue dot were in the middle of the red dots, the training algorithm would not converge to an acceptable solution.

perceptron

Image source: https://glowingpython.blogspot.com.br/2011/10/perceptron.html

xor2

Image source: http://ecee.colorado.edu/

The Multilayer Perceptron solves the problem of the SLP linearity, which can address a wider range of applications.  In the picture above, the MLP is able to learn all three logic gates including the “XOR”, the two dots classes can’t be separated by one line. Professor Marcelo implemented an MLP code with a single hidden layer, available on Matlab repository, which has an example of an MLP learning the behavior of a XOR gate.

mlp

Image source: http://www.mdpi.com/

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PYNQ-Z1 peripherals control with an Overlay created from Vivado

This post is an extension of “Creating a simple overlay for PYNQ-Z1 board from Vivado HLx“, which presented an Overlay creation methodology for an accelerator block. The implemented block only communicates with Zynq Processing System (PS) and does not explain the PYNQ peripherals management. This work was developed with the help of Wagner Wesner.

The “base” Overlay found inside the PYNQ package is composed of the basic structures needed to handle PYNQ functionalities. The Vivado project (built on Vivado 2016.1) used to develop the “base” Overlay can be reconstructed from the Tcl file and observed:

base_blockd

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Creating a simple Overlay for PYNQ-Z1 board from Vivado HLx

The content presented in this post was developed during the winter class given at Federal University of Rio Grande do Norte, with professors Carlos Valderrama and Samuel Xavier. My group was composed by Wagner Wesner and me.

Our group task was targeting Vivado HLS to implement accelerator blocks for the PYNQ-Z1 board. The PYNQ consists of a board with some peripherals and a ZYNQ chip, the ZYNQ has a cluster with a Central Processing Unit (CPU) and a Field-Programmable Gate Array (FPGA) which enables the test of the synthesized blocks on Vivado. Vivado outputs such as a bitstream and a Tcl file are used to create a PYNQ overlay. The overlay is further used to communicate the generated blocks with the PYNQ python interface.

The High-Level Synthesis (HLS) is very useful to transform complex algorithms into Hardware Description Language (HDL) code. There is a variety of algorithms which takes considerable CPU processing time, those algorithms can be translated to a hardware description which can be implemented on an FPGA. Once the circuit is configured on the FPGA, the algorithm time demanding tasks are parallelized (summing up), which increases performance and brings other potential benefits.

The Vivavo HLS software starts the PYNQ overlay creation with a custom block.

vivado_hls_wel.png

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A Viterbi Decoder Python implementation

A Viterbi decoder uses the Viterbi algorithm for decoding a bitstream that was generated by a convolutional encoder, finding the most-likely sequence of hidden states from a sequence of observed events, in the context of hidden Markov models. In other words, in a communication system, for example, the transceiver encodes the desired bits to be transferred, encrypting and at the same time preparing the encoded bitstream for an unfortunate data change caused by the channel noise. The receiver decoder knows the state machine created by the encoder hardware, which can find the most-likely transmitted bits based on the most-likely path.

A convolutional encoder is built the same as presented in the video: https://www.youtube.com/watch?v=oI0MwwXJ8dE&t=640s

viterbi_encoder

The input bits shifts at different times (clocks) on the three registers shown in the figure above. Depending on the bits available inside those registers, the system will deliver a pair of bits produced (in this case) by two xor gates connected like so. The constraint length (k) is the number of registers an input bit can influence on the encoded bits, in the presented case k=3. The code rate (R) is a relation upon the number of bits that enter the system and the number of bits leaving, leading to R=1/2.

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