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Deep Learning and Human Intelligence – Part 1 of 2

Many people are under the impression that the new wave of data science, machine learning and/or digitalization is new, that it did not exist before. But its history is as long as the history of humanity and/or science itself.  The scientific discovery could hardly take place without the necessary data. Even the process of discovering the numbers included elements of machine learning: pattern recognition, comparison between different groups (ranking), clustering, etc. So what differentiates mathematical formulas from machine learning and how does it relate to artificial intelligence?

There is no difference between the two if seen from the perspective of formulas however, such a perspective limits the type of data to which they can be applied. Data stored via tables consist of structured data and are stored in so-called relational databases. The reason for such a data storage is the connection between different fields that assume a well-established structure in advance, such as a company’s sales or balance sheet. However, with the emergence of personal computers, many of the daily activities have been digitalized: music, pictures, movies, and so on. All this information is stored unrelated to other data and therefore called unstructured data.

IEEE International Conference on Computer Vision (ICCV), 2015, DOI: 10.1109/ICCV.2015.428

Copyright: IEEE International Conference on Computer Vision (ICCV), 2015, DOI: 10.1109/ICCV.2015.428

The essence of scientific discoveries was and will be structure. Not surprisingly, the mathematical formulas revolve around relations between variables – information, in general. For example, Galileo derived the law of falling balls from measuring the successive hight of a falling ball. The main difficulty was to obtain measurements at regular time intervals. What about if the data is not structured, which mathematical formula should be applied then? There is a distribution of people’s height, but no distribution for the pictures taken in all holidays for the last year, there is an amplitude for acoustic signals, but no function that detects the similarity between two songs. This is one of the reasons why machine learning focuses heavily on clustering and classification.

Roughly speaking, these simple examples are enough to categorize the difference between scientific discovery and machine learning. Science is about discovering relationships between different variables, Machine Learning tries to automatize processes. Every technical improvement is part of the automation, so why is everything different in this case? Because the current automation deals with human intelligence. The car automates the walking, the kitchen stove the fire, but Machine Learning parts of the human intelligence. There is a difference between the previous automation steps and those of human intelligence. All the previous ones are either outside the human body – such as Fire – or unconsciously executed (once learned) – walking, spinning, etc. The automation induced by Machine Learning affects a part of the human intelligence that we consciously perceive. Of course, today’s machine learning tools are unable to automate all human intelligence, but it is a fascinating step in that direction.

A breakthrough in Machine Learning tasks was achieved in 2012 when the first Deep Learning algorithm for detecting types of images, reached near-human accuracy. It could appreciate the likelihood that the image is a human face, a train, a ball or a fish without having “seen” the picture before. Such an algorithm can be used in various areas:  personally – facial recognition in pictures and/or social media – as tagging of images or videos, medicine – cancer detection, etc. For understanding such cutting-edge issues of classification, one cannot avoid understanding how Deep Learning works. To see the beauty of such algorithms and, at the same time, to be able to comprehend the difficulty of working with them, an example will be the best guide.

The building blocks of Deep Learning are neurons, operational units, which perform mathematical operations or logical operations like AND, OR, etc., and are modelled after the neurons in the brain. Already in the 1950’s two neuroscientist, Hubel and Wiesel, observed that not all neurons in the brain are responding in the same fashion to visual stimuli. Some responded only to horizontal lines, whereas others to vertical lines, with other words, the brain is constructed with specialized neurons. Groups of such neurons are called, in the Machine Learning community, layers. Like in the brain, neurons with different properties are clustered in different layers. This implies that layers have also specific properties and have to be arranged in a specific way, called architecture. It is this architecture which differentiates Deep Learning from Artificial Neuronal Networks (ANN are similar to a layer).

Unfortunately, scientists still haven’t figured out how the brain works, thus to discover how to train Deep Learning from data was not an easy task, and is also the reason why another example is used to explain the training of Deep Learning: the eye. One has always to remember: once it is known how Deep Learning works, it is simple to find example which illustrates the working mechanism.  For such an analogy, it is sufficient for someone without any knowledge about Deep Learning, to keep in mind only the elements that compose such architectures: input data, different layers of neurons, output layers, ReLu’s.

Input data are any type of information, in our example it is light. Of course, that Deep Learning is not limited only to images or videos, but also to sound and/or time series, which would imply that the example would be the ear and sound waves, or the brain and numbers.

Layers can be seen as cells in the eye. It is well known that the eye is formed of different layers connected to each other with each of them having different properties, functionalities. The same is true also for the layers of a Deep Learning architecture: one can see the neurons as cells of the layer as the tissue. While, mathematically, the neurons are nothing more than simple operations, usually linear weight functions, they can be seen as the properties of individual cells. Each layer has one weight matrix, which gives the neuron (and layer) specific properties depending on the data and the task at hand.

It is here that the architecture becomes very important. What Deep Learning offers is a default setting of the layers with unknown weights. One can see this as trying to build an eye knowing that there are different types of cells and different ways how tissues of such cells can be arranged, but not which cell exactly is needed (with what properties) and which arrangement of layers works best. Such an approach has the advantage that one is capable of building any type of organ desired, but the disadvantage is also very obvious: it is time consuming to find the appropriate cell properties and layers arrangements.

Still, the strategy of Deep Learning is a significant departure from the Machine Learning approaches. The performance of Machine Learning methods is as good as the features engineering performed by Data Scientists, and thus depending on the creativity of the Data Scientist. In the case of Deep Learning the engineers of the features is performed automatically as part of the model building. This is a huge improvement, as the only difficult task is to have enough data and computer power to find the right weights matrices. Such an endeavor was performed also by nature for the eye — and is also the reason why one can choose it as an example for Deep Learning — evolution. It is not surprising that Deep Learning is one of the best direction scientists have of Artificial Intelligence today.

The evolution of the eye can be seen, from the perspective of Data Scientists, as the continuous training of a Deep Learning architecture which enables to recognize and track one or more objects. The performance of the evolutional process can be summed up as the fine tuning of the cells which are getting more and more susceptible to light and the adaptation of layers to enable a better vision. Different animals in different environments and different targets — as the hawk and the fly — developed different eyes than humans, but they all work according to the same principle. The tasks that Deep Learning is performing today are similar, for example it can be used to drive cars but there is still a difference:  there is no connection to other organs. Deep Learning is not the approximation of an Artificial Organism, like an android, but a simplified Artificial Organ that can work on its own.

Returning to the working mechanism of the Deep Learning architecture, we can already follow the analogy of what happens if a ray of light is hitting the eye. Once the eye is fully adapted to the task, one can followed how the information enters the Deep Learning architecture (Artificial Eye) by penetrating the input layer. already here arises the question, what kind of eye is the best? One where a small source of light can reach as many neurons as possible, or the one where the light sources reaches only few neurons? In order to take such a decision, a last piece of the puzzle is required: ReLu. One can see them as synapses between neurons (cells) and/or similarly for tissue. By using continuous functions, such as the shape of the latter ‘S’ (called sigmoid), the information from one neuron will be distributed over a large number of other neurons. If one uses the maximum function, then only few neurons are updated with processed information from earlier layers.

Such sparse structures between neurons, was a major improvement in the development of the technique of training Deep Learning architectures. Again, it has a strong evolutionary analogy: energy efficiency. By needing less neurons, the tissues and architecture are both kept to a minimal size which enables flexibility in development and less energy. As the information is process by the different layers, the Artificial Eye is gathering more and more complex (non-linear) structures — the adapted features –, which help to decide, from past experience, what kind of object is detected.

This was part 1 of 2 of the article series. Continue with Part 2.

Interview – Python as productive data science environment

Miroslav Šedivý is a Senior Software Architect at UBIMET GmbH, using Python to make the sun shine and the wind blow. He is an enthusiast of both human and programming languages and found Python as his language of choice to setup very productive environments. Mr. Šedivý was born in Czechoslovakia, studied in France and is now living in Germany. Furthermore, he helps in the organization of the events PyCon.DE and Polyglot Gathering.


On 26th June 2018 he will explain at the Python@DWX conference why “Lifelong Text Hackers Use Vim and Python”. Insert the promotion code PY18science to unlock your 10% discount on all tickets. More info and tickets on python-con.com.


Data Science Blog: Mr. Šedivý, how did you find the way to Python as your favorite programming language?

Apart from traditional languages taught at school (Basic, Pascal, C, Java), some twenty years ago I learned Perl to hack a dynamic web site and used it to automate my daily tasks. Later I used it professionally for scientific calculations in the production. This was later replaced by Python, its newer versions and more advanced libraries. Nowadays Python has almost completely replaced Perl as my principal language and I use Perl just to hack some command line filters and to impress colleagues.

Data Science Blog: Python is one of the most popular programming language for data scientists. This is remarkable as it is originally not designed for doing data science with it. What made it a competitor to languages like R or Julia?

Python is the most powerful programming language that is still legible. This appeals to data scientists who can enter each line interactively, and immediately see what happens, because each line actually does something. They can inspect their data easily and build automating systems to process their data transparently.

Data Science Blog: Is there anything you could do better with another programming language?

Sometimes I’m playing with some functional languages that would allow me to write code that is easier to test and parallelize.

Data Science Blog: Which libraries are the most important ones for your daily business?

The whole Pandas ecosystem with Numpy and Scipy. Matplotlib for plots, PyTables and Psycopg2 for storage. I’m also importing a few async libs for webservices and similar network-based software.

I also enjoy discovering the world of Unicode and Timezones – both of them are the spots where the programmers absolutely have to obey the chaotic reality of the outside world.

Data Science Blog: Which editor do you use? And how to set it up as a productive environment?

I tried several editors and IDEs, but always came back to Vi or Vim. This is an extremely powerful editor that is around since over forty years, which was probably before most of today’s active developers learned to type. I’m using it for all text editing tasks, which I’m actually going to show in my talk at DWX [Lifelong Text Hackers Use Vim and Python]. Steep learning curve is not an argument against a tool you can grok during your entire career.

Data Science Blog: In your opinion: For all developers and data scientists, who are used to Java, Scala, R oder Perl, is Python easy to learn? Could it be too late to switch for somebody?

Python is a great general language that can be learned rapidly to a usable level. It’s different from the aforementioned languages. I remember my switching process from Perl to Python over ten years ago with a book “Perl to Python Migration”, which forced me to switch my way of thinking. From the question “Why do I have to import ‘re’ for regular expressions if Perl uses them natively?” to “Actually, I can solve this problem without regular expressions.”.

Applying Data Science Techniques in Python to Evaluate Ionospheric Perturbations from Earthquakes

Multi-GNSS (Galileo, GPS, and GLONASS) Vertical Total Electron Content Estimates: Applying Data Science techniques in Python to Evaluate Ionospheric Perturbations from Earthquakes

1 Introduction

Today, Global Navigation Satellite System (GNSS) observations are routinely used to study the physical processes that occur within the Earth’s upper atmosphere. Due to the experienced satellite signal propagation effects the total electron content (TEC) in the ionosphere can be estimated and the derived Global Ionosphere Maps (GIMs) provide an important contribution to monitoring space weather. While large TEC variations are mainly associated with solar activity, small ionospheric perturbations can also be induced by physical processes such as acoustic, gravity and Rayleigh waves, often generated by large earthquakes.

In this study Ionospheric perturbations caused by four earthquake events have been observed and are subsequently used as case studies in order to validate an in-house software developed using the Python programming language. The Python libraries primarily utlised are Pandas, Scikit-Learn, Matplotlib, SciPy, NumPy, Basemap, and ObsPy. A combination of Machine Learning and Data Analysis techniques have been applied. This in-house software can parse both receiver independent exchange format (RINEX) versions 2 and 3 raw data, with particular emphasis on multi-GNSS observables from GPS, GLONASS and Galileo. BDS (BeiDou) compatibility is to be added in the near future.

Several case studies focus on four recent earthquakes measuring above a moment magnitude (MW) of 7.0 and include: the 11 March 2011 MW 9.1 Tohoku, Japan, earthquake that also generated a tsunami; the 17 November 2013 MW 7.8 South Scotia Ridge Transform (SSRT), Scotia Sea earthquake; the 19 August 2016 MW 7.4 North Scotia Ridge Transform (NSRT) earthquake; and the 13 November 2016 MW 7.8 Kaikoura, New Zealand, earthquake.

Ionospheric disturbances generated by all four earthquakes have been observed by looking at the estimated vertical TEC (VTEC) and residual VTEC values. The results generated from these case studies are similar to those of published studies and validate the integrity of the in-house software.

2 Data Cleaning and Data Processing Methodology

Determining the absolute VTEC values are useful in order to understand the background ionospheric conditions when looking at the TEC perturbations, however small-scale variations in electron density are of primary interest. Quality checking processed GNSS data, applying carrier phase leveling to the measurements, and comparing the TEC perturbations with a polynomial fit creating residual plots are discussed in this section.

Time delay and phase advance observables can be measured from dual-frequency GNSS receivers to produce TEC data. Using data retrieved from the Center of Orbit Determination in Europe (CODE) site (ftp://ftp.unibe.ch/aiub/CODE), the differential code biases are subtracted from the ionospheric observables.

2.1 Determining VTEC: Thin Shell Mapping Function

The ionospheric shell height, H, used in ionosphere modeling has been open to debate for many years and typically ranges from 300 – 400 km, which corresponds to the maximum electron density within the ionosphere. The mapping function compensates for the increased path length traversed by the signal within the ionosphere. Figure 1 demonstrates the impact of varying the IPP height on the TEC values.

Figure 1 Impact on TEC values from varying IPP heights. The height of the thin shell, H, is increased in 50km increments from 300 to 500 km.

2.2 Phase Smoothing

For dual-frequency GNSS users TEC values can be retrieved with the use of dual-frequency measurements by applying calculations. Calculation of TEC for pseudorange measurements in practice produces a noisy outcome and so the relative phase delay between two carrier frequencies – which produces a more precise representation of TEC fluctuations – is preferred. To circumvent the effect of pseudorange noise on TEC data, GNSS pseudorange measurements can be smoothed by carrier phase measurements, with the use of the carrier phase smoothing technique, which is often referred to as carrier phase leveling.

Figure 2 Phase smoothed code differential delay

2.3 Residual Determination

For the purpose of this study the monitoring of small-scale variations in ionospheric electron density from the ionospheric observables are of particular interest. Longer period variations can be associated with diurnal alterations, and changes in the receiver- satellite elevation angles. In order to remove these longer period variations in the TEC time series as well as to monitor more closely the small-scale variations in ionospheric electron density, a higher-order polynomial is fitted to the TEC time series. This higher-order polynomial fit is then subtracted from the observed TEC values resulting in the residuals. The variation of TEC due to the TID perturbation are thus represented by the residuals. For this report the polynomial order applied was typically greater than 4, and was chosen to emulate the nature of the arc for that particular time series. The order number selected is dependent on the nature of arcs displayed upon calculating the VTEC values after an initial inspection of the VTEC plots.

3 Results

3.1 Tohoku Earthquake

For this particular report, the sampled data focused on what was retrieved from the IGS station, MIZU, located at Mizusawa, Japan. The MIZU site is 39N 08′ 06.61″ and 141E 07′ 58.18″. The location of the data collection site, MIZU, and the earthquake epicenter can be seen in Figure 3.

Figure 3 MIZU IGS station and Tohoku earthquake epicenter [generated using the Python library, Basemap]

Figure 4 displays the ionospheric delay in terms of vertical TEC (VTEC), in units of TECU (1 TECU = 1016 el m-2). The plot is split into two smaller subplots, the upper section displaying the ionospheric delay (VTEC) in units of TECU, the lower displaying the residuals. The vertical grey-dashed lined corresponds to the epoch of the earthquake at 05:46:23 UT (2:46:23 PM local time) on March 11 2011. In the upper section of the plot, the blue line corresponds to the absolute VTEC value calculated from the observations, in this case L1 and L2 on GPS, whereby the carrier phase leveling technique was applied to the data set. The VTEC values are mapped from the STEC values which are calculated from the LOS between MIZU and the GPS satellite PRN18 (on Figure 4 denoted G18). For this particular data set as seen in Figure 4, a polynomial fit of  five degrees was applied, which corresponds to the red-dashed line. As an alternative to polynomial fitting, band-pass filtering can be employed when TEC perturbations are desired. However for the scope of this report polynomial fitting to the time series of TEC data was the only method used. In the lower section of Figure 4 the residuals are plotted. The residuals are simply the phase smoothed delay values (the blue line) minus the polynomial fit line (the red-dashed line). All ionosphere delay plots follow the same layout pattern and all time data is represented in UT (UT = GPS – 15 leap seconds, whereby 15 leap seconds correspond to the amount of leap seconds at the time of the seismic event). The time series shown for the ionosphere delay plots are given in terms of decimal of the hour, so that the format follows hh.hh.

Figure 4 VTEC and residual plot for G18 at MIZU on March 11 2011

3.2 South Georgia Earthquake

In the South Georgia Island region located in the North Scotia Ridge Transform (NSRT) plate boundary between the South American and Scotia plates on 19 August 2016, a magnitude of 7.4 MW earthquake struck at 7:32:22 UT. This subsection analyses the data retrieved from KEPA and KRSA. As well as computing the GPS and GLONASS TEC values, four Galileo satellites (E08, E14, E26, E28) are also analysed. Figure 5 demonstrates the TEC perturbations as computed for the Galileo L1 and L5 carrier frequencies.

Figure 5 VTEC and residual plots at KRSA on 19 August 2016. The plots are from the perspective of the GNSS receiver at KRSA, for four Galileo satellites (a) E08; (b) E14; (c) E24; (d) E26. The y-axes and x-axes in all plots do not conform with one another but are adjusted to fit the data. The y-axes for the residual section of each plot is consistent with one another.

Figure 6 Geometry of the Galileo (E08, E14, E24 and E26) satellites’ projected ground track whereby the IPP is set to 300km altitude. The orange lines correspond to tectonic plate boundaries.

4 Conclusion

The proximity of the MIZU site and magnitude of the Tohoku event has provided a remarkable – albeit a poignant – opportunity to analyse the ocean-ionospheric coupling aftermath of a deep submarine seismic event. The Tohoku event has also enabled the observation of the origin and nature of the TIDs generated by both a major earthquake and tsunami in close proximity to the epicenter. Further, the Python software developed is more than capable of providing this functionality, by drawing on its mathematical packages, such as NumPy, Pandas, SciPy, and Matplotlib, as well as employing the cartographic toolkit provided from the Basemap package, and finally by utilizing the focal mechanism generation library, Obspy.

Pre-seismic cursors have been investigated in the past and strongly advocated in particular by Kosuke Heki. The topic of pre-seismic ionospheric disturbances remains somewhat controversial. A potential future study area could be the utilization of the Python program – along with algorithmic amendments – to verify the existence of this phenomenon. Such work would heavily involve the use of Scikit-Learn in order to ascertain the existence of any pre-cursors.

Finally, the code developed is still retained privately and as of yet not launched to any particular platform, such as GitHub. More detailed information on this report can be obtained here:

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Data Science Modeling and Featurization

Overview

Data modeling is an essential part of the data science pipeline. This, combined with the fact that it is a very rewarding process, makes it the one that often receives the most attention among data science learners. However, things are not as simple as they may seem, since there is much more to it than applying a function from a particular class of a package and applying it on the data available.

A big part of data science modeling involves evaluating a model, for example, making sure that it is robust and therefore reliable. Also, data science modeling is closely linked to creating an information rich feature set. Moreover, it entails a variety of other processes that ensure that the data at hand is harnessed as much as possible.

What Is a Robust Data Model?

When it comes to robust models, worthy of making it to production, these need to tick several boxes. First of all, they need to have a good performance, based on various metrics. Oftentimes a single metric can be misleading, as how well a model performs has many aspects, especially for classification problems.

In addition, a robust model has good generalization. This means that the model performs well for various datasets, not just the one it has been trained on.

Sensitivity analysis is another aspect of a data science modeling, something essential for thoroughly testing a model to ensure it is robust enough. Sensitivity is a condition whereby a model’s output is bound to change significantly if the inputs change even slightly. This is quite undesirable and needs to be checked since a robust model ought to be stable.

Finally, interpretability is an important aspect too, though it’s not always possible. This has to do with how easy it is to interpret a model’s results. Many modern models, however, are more like black boxes, making it particularly difficult to interpret them. Nevertheless, it is often preferable to opt for an interpretable model, especially if we need to defend its outputs to others.

How Is Featurization Accomplished?

In order for a model to maximize its potential, it needs an information rich set of features. The latter can be created in various ways. Whatever the case, cleaning up the data is a prerequisite. This involves removing or correcting problematic data points, filling in missing values wherever possible, and in some cases removing noisy variables.

Before you can use variables in a model, you need to perform normalization on them. This is usually accomplished through a linear transformation ensuring that the variable’s values are around a certain range. Oftentimes, normalization is sufficient for turning your variables into features, once they are cleaned.

Binning is another process that can aid in featurization. This entails creating nominal (discreet) variables, which can in turn be broken down into binary features, to be used in a data model.

Finally, some dimensionality reduction method (e.g. PCA) can be instrumental in shaping up your feature-set. This has to do with creating linear combinations of features, aka meta-features, which express the same information in fewer dimensions.

Some Useful Considerations

Beyond these basic attributes of data science modeling there several more that every data scientist has in mind in order to create something of value from the available data. Things like in-depth testing using sensitivity analysis, specialized sampling, and various aspects of model performance (as well as tweaking the model to optimize for a particular performance metric) are parts of data science modeling that require meticulous study and ample practice. After all, even though this part of data science is fairly easy to pick up, it takes a while to master, while performing well in it is something that every organization can benefit from.

Resources

To delve more into all this, there are various relevant resources you can leverage, helping you in not just the methodologies involved but also in the mindset behind them. Here are two of the most useful ones.

  1. Data Science Modeling Tutorial on the Safari platform
  2. Data Science Mindset, Methodologies and Misconceptions book (Technics Publications)

Show your Data Science Workplace!

The job of a data scientist is often a mystery to outsiders. Of course, you do not really need much more than a medium-sized notebook to use data science methods for finding value in data. Nevertheless, data science workplaces can look so different and, let’s say, interesting. And that’s why I want to launch a blog parade – which I want to start with this article – where you as a Data Scientist or Data Engineer can show your workplace and explain what tools a data scientist in your opinion really needs.

I am very curious how many monitors you prefer, whether you use Apple, Dell, HP or Lenovo, MacOS, Linux or Windows, etc., etc. And of course, do you like a clean or messy desk?

What is a Blog Parade?

A blog parade is a call to blog owners to report on a specific topic. Everyone who participates in the blog parade, write on their blog a contribution to the topic. The organizer of the blog parade collects all the articles and will recap those articles in a short form together, of course with links to the articles.

How can I participate?

Write an article on your blog! Mention this blog parade here, show and explain your workplace (your desk with your technical equipment) in an article. If you’re missing your own blog, articles can also be posted directly to LinkedIn (LinkedIn has its own blogging feature that every LinkedIn member can use). Alternative – as a last resort – it would also be possible to send me your article with a photo about your workplace directly to: redaktion@data-science-blog.com.
Please make me aware of an article, via e-mail or with a comment (below) on this article.

Who can participate?

Any data scientist or anyone close to Data Science: Everyone concerned with topics such as data analytics, data engineering or data security. Please do not over-define data science here, but keep it in a nutshell, so that all professionals who manage and analyze data can join in with a clear conscience.

And yes, I will participate too. I will propably be the first who write an article about my workplace (I just need a new photo of my desk).

When does the article have to be finished?

By 31/12/2017, the article must have been published on your blog (or LinkedIn or wherever) and the release has to be reported to me.
But beware: Anyone who has previously written an article will also be linked earlier. After all, reporting on your article will take place immediately after I hear about it.
If you publish an artcile tomorrow, it will be shown the day after tomorrow here on the Data Science Blog.

What is in it for me to join?

Nothing! Except perhaps the fun factor of sharing your idea of ​​a nice desk for a data expert with others, so as to share creativity or a certain belief in what a data scientist needs.
Well and for bloggers: There is a great backlink from this data science blog for you 🙂

What should I write? What are the minimum requirements of content?

The article does not have to (but may be) particularly long. Anyway, here on this data science blog only a shortened version of your article will appear (with a link, of course).

Minimum requirments:

  • Show a photo (at least one!) of your workplace desk!
  • And tell us something about:
    • How many monitors do you use (or wish to have)?
    • What hardware do you use? Apple? Dell? Lenovo? Others?
    • Which OS do you use (or prefer)? MacOS, Linux, Windows? Virtual Machines?
    • What are your favorite databases, programming languages and tools? (e.g. Python, R, SAS, Postgre, Neo4J,…)
    • Which data dou you analyze on your local hardware? Which in server clusters or clouds?
    • If you use clouds, do you prefer Azure, AWS, Google oder others?
    • Where do you make your notes/memos/sketches. On paper or digital?

Not allowed:
Of course, please do not provide any information, which could endanger your company`s IT security.

Absolutly allowed:
Bringing some joke into the matter 🙂 We are happy to vote in the comments on the best or funniest desk for election, there may be also a winner later!


The resulting Blog Posts: https://data-science-blog.com/data-science-insights/show-your-desk/


 

The importance of domain knowledge – A healthcare data science perspective

Data scientists have (and need) many skills. They are frequently either former academic researchers or software engineers, with knowledge and skills in statistics, programming, machine learning, and many other domains of mathematics and computer science. These skills are general and allow data scientists to offer valuable services to almost any field. However, data scientists in some cases find themselves in industries they have relatively little knowledge of.

This is especially true in the healthcare field. In healthcare, there is an enormous amount of important clinical knowledge that might be relevant to a data scientist. It is unreasonable to expect a data scientist to not only have all of the skills typically required of a data scientist, but to also have all of the knowledge a medical professional may have.

Why is domain knowledge necessary?

This lack of domain knowledge, while perfectly understandable, can be a major barrier to healthcare data scientists. For one thing, it’s difficult to come up with project ideas in a domain that you don’t know much about. It can also be difficult to determine the type of data that may be helpful for a project – if you want to build a model to predict a health outcome (for example, whether a patient has or is likely to develop a gastrointestinal bleed), you need to know what types of variables might be related to this outcome so you can make sure to gather the right data.

Knowing the domain is useful not only for figuring out projects and how to approach them, but also for having rules of thumb for sanity checks on the data. Knowing how data is captured (is it hand-entered? Is it from machines that can give false readings for any number of reasons?) can help a data scientist with data cleaning and from going too far down the wrong path. It can also inform what true outliers are and which values might just be due to measurement error.

Often the most challenging part of building a machine learning model is feature engineering. Understanding clinical variables and how they relate to a health outcome is extremely important for this. Is a long history of high blood pressure important for predicting heart problems, or is only very recent history? How long a time horizon is considered ‘long’ or ‘short’ in this context? What other variables might be related to this health outcome? Knowing the domain can help direct the data exploration and greatly speed (and enhance) the feature engineering process.

Once features are generated, knowing what relationships between variables are plausible helps for basic sanity checks. If you’re finding the best predictor of hospitalization is the patient’s eye color, this might indicate an issue with your code. Being able to glance at the outcome of a model and determine if they make sense goes a long way for quality assurance of any analytical work.

Finally, one of the biggest reasons a strong understanding of the data is important is because you have to interpret the results of analyses and modeling work. Knowing what results are important and which are trivial is important for the presentation and communication of results. An analysis that determines there is a strong relationship between age and mortality is probably well-known to clinicians, while weaker but more surprising associations may be of more use. It’s also important to know what results are actionable. An analysis that finds that patients who are elderly are likely to end up hospitalized is less useful for trying to determine the best way to reduce hospitalizations (at least, without further context).

How do you get domain knowledge?

In some industries, such as tech, it’s fairly easy and straightforward to see an end-user’s prospective. By simply viewing a website or piece of software from the user’s point of view, a data scientist can gain a lot of the needed context and background knowledge needed to understand where their data is coming from and how their model output is being used. In the healthcare industry, it’s more difficult. A data scientist can’t easily choose to go through med school or the experience of being treated for a chronic illness. This means there is no easy single answer to where to gain domain knowledge. However, there are many avenues available.

Reading literature and attending presentations can boost one’s domain knowledge. However, it’s often difficult to find resources that are penetrable for someone who is not already a clinician. To gain deep knowledge, one needs to be steeped in the topic. One important avenue to doing this is through the establishment of good relationships with clinicians. Clinicians can be powerful allies that can help point you in the right direction for understanding your data, and simply by chatting with them you can gain important insights. They can also help you visit the clinics or practices to interact with the people that perform the procedures or even watch the procedures being done. At Fresenius Medical Care, where I work, members of my team regularly visit clinics. I have in the last year visited one of our dialysis clinics, a nephrology practice, and a vascular care unit. These experiences have been invaluable to me in developing my knowledge of the treatment of chronic illnesses.

In conclusion, it is crucial for data scientists to acquire basic familiarity in the field they are working in and in being part of collaborative teams that include people who are technically knowledgeable in the field they work in. This said, acquiring even an essential understanding (such as “Medicine 101”) may go a long way for the data scientists in being able to become self-sufficient in essential feature selection and design.

 

Data Science vs Data Engineering

The job of the Data Scientist is actually a fairly new trend, and yet other job titles are coming to us. “Is this really necessary?”, Some will ask. But the answer is clear: yes!

There are situations, every Data Scientist know: a recruiter calls, speaks about a great new challenge for a Data Scientist as you obviously claim on your LinkedIn profile, but in the discussion of the vacancy it quickly becomes clear that you have almost none of the required skills. This mismatch is mainly due to the fact that under the job of the Data Scientist all possible activity profiles, method and tool knowledge are summarized, which a single person can hardly learn in his life. Many open jobs, which are to be called under the name Data Science, describe rather the professional image of the Data Engineer.


Read this article in German:
“Data Science vs Data Engineering – Wo liegen die Unterschiede?“


What is a Data Engineer?

Data engineering is primarily about collecting or generating data, storing, historicalizing, processing, adapting and submitting data to subsequent instances. A Data Engineer, often also named as Big Data Engineer or Big Data Architect, models scalable database and data flow architectures, develops and improves the IT infrastructure on the hardware and software side, deals with topics such as IT Security , Data Security and Data Protection. A Data Engineer is, as required, a partial administrator of the IT systems and also a software developer, since he or she extends the software landscape with his own components. In addition to the tasks in the field of ETL / Data Warehousing, he also carries out analyzes, for example, to investigate data quality or user access. A Data Engineer mainly works with databases and data warehousing tools.

A Data Engineer is talented as an educated engineer or computer scientist and rather far away from the actual core business of the company. The Data Engineer’s career stages are usually something like:

  1. (Big) Data Architect
  2. BI Architect
  3. Senior Data Engineer
  4. Data Engineer

What makes a Data Scientist?

Although there may be many intersections with the Data Engineer’s field of activity, the Data Scientist can be distinguished by using his working time as much as possible to analyze the available data in an exploratory and targeted manner, to visualize the analysis results and to convert them into a red thread (storytelling). Unlike the Data Engineer, a data scientist rarely sees into a data center, because he picks up data via interfaces provided by the Data Engineer or provides by other resources.

A Data Scientist deals with mathematical models, works mainly with statistical procedures, and applies them to the data to generate knowledge. Common methods of Data Mining, Machine Learning and Predictive Modeling should be known to a Data Scientist. Data Scientists basically work close to the department and need appropriate expertise. Data Scientists use proprietary tools (e.g. Tools by IBM, SAS or Qlik) and program their own analyzes, for example, in Scala, Java, Python, Julia, or R. Using such programming languages and data science libraries (e.g. Mahout, MLlib, Scikit-Learn or TensorFlow) is often considered as advanced data science.

Data Scientists can have diverse academic backgrounds, some are computer scientists or engineers for electrical engineering, others are physicists or mathematicians, not a few have economical backgrounds. Common career levels could be:

  1. Chief Data Scientist
  2. Senior Data Scientist
  3. Data Scientist
  4. Data Analyst oder Junior Data Scientist

Data Scientist vs Data Analyst

I am often asked what the difference between a Data Scientist and a Data Analyst would be, or whether there would be a distinction criterion at all:

In my experience, the term Data Scientist stands for the new challenges for the classical concept of Data Analysts. A Data Analyst performs data analysis like a Data Scientist. More complex topics such as predictive analytics, machine learning or artificial intelligence are topics for a Data Scientist. In other words, a Data Scientist is a Data Analyst++ (one step above the Data Analyst).

And how about being a Business Analyst?

Business Analysts can (but need not) be Data Analysts. In any case, they have a very strong relationship with the core business of the company. Business Analytics is about analyzing business models and business successes. The analysis of business success is usually carried out by IT, and many business analysts are starting a career as Data Analyst now. Dashboards, KPIs and SQL are the tools of a good business analyst, but there might be a lot business analysts, who are just analysing business models by reading the newspaper…

Data Science Knowledge Stack – Abstraction of the Data Science Skillset

What must a Data Scientist be able to do? Which skills does as Data Scientist need to have? This question has often been asked and frequently answered by several Data Science Experts. In fact, it is now quite clear what kind of problems a Data Scientist should be able to solve and which skills are necessary for that. I would like to try to bring this consensus into a visual graph: a layer model, similar to the OSI layer model (which any data scientist should know too, by the way).
I’m giving introductory seminars in Data Science for merchants and engineers and in those seminars I always start explaining what we need to work out together in theory and practice-oriented exercises. Against this background, I came up with the idea for this layer model. Because with my seminars the problem already starts: I am giving seminars for Data Science for Business Analytics with Python. So not for medical analyzes and not with R or Julia. So I do not give a general knowledge of Data Science, but a very specific direction.

A Data Scientist must deal with problems at different levels in any Data Science project, for example, the data access does not work as planned or the data has a different structure than expected. A Data Scientist can spend hours debating its own source code or learning the ropes of new DataScience packages for its chosen programming language. Also, the right algorithms for data evaluation must be selected, properly parameterized and tested, sometimes it turns out that the selected methods were not the optimal ones. Ultimately, we are not doing Data Science all day for fun, but for generating value for a department and a data scientist is also faced with special challenges at this level, at least a basic knowledge of the expertise of that department is a must have.


Read this article in German:
“Data Science Knowledge Stack – Was ein Data Scientist können muss“


Data Science Knowledge Stack

With the Data Science Knowledge Stack, I would like to provide a structured insight into the tasks and challenges a Data Scientist has to face. The layers of the stack also represent a bidirectional flow from top to bottom and from bottom to top, because Data Science as a discipline is also bidirectional: we try to answer questions with data, or we look at the potentials in the data to answer previously unsolicited questions.

The DataScience Knowledge Stack consists of six layers:

Database Technology Knowledge

A Data Scientist works with data which is rarely directly structured in a CSV file, but usually in one or more databases that are subject to their own rules. In particular, business data, for example from the ERP or CRM system, are available in relational databases, often from Microsoft, Oracle, SAP or an open source alternative. A good Data Scientist is not only familiar with Structured Query Language (SQL), but is also aware of the importance of relational linked data models, so he also knows the principle of data table normalization.

Other types of databases, so-called NoSQL databases (Not only SQL) are based on file formats, column or graph orientation, such as MongoDB, Cassandra or GraphDB. Some of these databases use their own programming languages ​​(for example JavaScript at MongoDB or the graph-oriented database Neo4J has its own language called Cypher). Some of these databases provide alternative access via SQL (such as Hive for Hadoop).

A data scientist has to cope with different database systems and has to master at least SQL – the quasi-standard for data processing.

Data Access & Transformation Knowledge

If data are given in a database, Data Scientists can perform simple (and not so simple) analyzes directly on the database. But how do we get the data into our special analysis tools? To do this, a Data Scientist must know how to export data from the database. For one-time actions, an export can be a CSV file, but which separators and text qualifiers should be used? Possibly, the export is too large, so the file must be split.
If there is a direct and synchronous data connection between the analysis tool and the database, interfaces like REST, ODBC or JDBC come into play. Sometimes a socket connection must also be established and the principle of a client-server architecture should be known. Synchronous and asynchronous encryption methods should also be familiar to a Data Scientist, as confidential data are often used, and a minimum level of security is most important for business applications.

Many datasets are not structured in a database but are so-called unstructured or semi-structured data from documents or from Internet sources. And again we have interfaces, a frequent entry point for Data Scientists is, for example, the Twitter API. Sometimes we want to stream data in near real-time, let it be machine data or social media messages. This can be quite demanding, so the data streaming is almost a discipline with which a Data Scientist can come into contact quickly.

Programming Language Knowledge

Programming languages ​​are tools for Data Scientists to process data and automate processing. Data Scientists are usually no real software developers and they do not have to worry about software security or economy. However, a certain basic knowledge about software architectures often helps because some Data Science programs can be going to be integrated into an IT landscape of the company. The understanding of object-oriented programming and the good knowledge of the syntax of the selected programming languages ​​are essential, especially since not every programming language is the most useful for all projects.

At the level of the programming language, there is already a lot of snares in the programming language that are based on the programming language itself, as each has its own faults and details determine whether an analysis is done correctly or incorrectly: for example, whether data objects are copied or linked as reference, or how NULL/NaN values ​​are treated.

Data Science Tool & Library Knowledge

Once a data scientist has loaded the data into his favorite tool, for example, one of IBM, SAS or an open source alternative such as Octave, the core work just began. However, these tools are not self-explanatory and therefore there is a wide range of certification options for various Data Science tools. Many (if not most) Data Scientists work mostly directly with a programming language, but this alone is not enough to effectively perform statistical data analysis or machine learning: We use Data Science libraries (packages) that provide data structures and methods as a groundwork and thus extend the programming language to a real Data Science toolset. Such a library, for example Scikit-Learn for Python, is a collection of methods implemented in the programming language. The use of such libraries, however, is intended to be learned and therefore requires familiarization and practical experience for reliable application.

When it comes to Big Data Analytics, the analysis of particularly large data, we enter the field of Distributed Computing. Tools (frameworks) such as Apache Hadoop, Apache Spark or Apache Flink allows us to process and analyze data in parallel on multiple servers. These tools also provide their own libraries for machine learning, such as Mahout, MLlib and FlinkML.

Data Science Method Knowledge

A Data Scientist is not simply an operator of tools, he uses the tools to apply his analysis methods to data he has selected for to reach the project targets. These analysis methods are, for example, descriptive statistics, estimation methods or hypothesis tests. Somewhat more mathematical are methods of machine learning for data mining, such as clustering or dimensional reduction, or more toward automated decision making through classification or regression.

Machine learning methods generally do not work immediately, they have to be improved using optimization methods like the gradient method. A Data Scientist must be able to detect under- and overfitting, and he must prove that the prediction results for the planned deployment are accurate enough.

Special applications require special knowledge, which applies, for example, to the fields of image recognition (Visual Computing) or the processing of human language (Natural Language Processiong). At this point, we open the door to deep learning.

Expertise

Data Science is not an end in itself, but a discipline that would like to answer questions from other expertise fields with data. For this reason, Data Science is very diverse. Business economists need data scientists to analyze financial transactions, for example, to identify fraud scenarios or to better understand customer needs, or to optimize supply chains. Natural scientists such as geologists, biologists or experimental physicists also use Data Science to make their observations with the aim of gaining knowledge. Engineers want to better understand the situation and relationships between machinery or vehicles, and medical professionals are interested in better diagnostics and medication for their patients.

In order to support a specific department with his / her knowledge of data, tools and analysis methods, every data scientist needs a minimum of the appropriate skills. Anyone who wants to make analyzes for buyers, engineers, natural scientists, physicians, lawyers or other interested parties must also be able to understand the people’s profession.

Engere Data Science Definition

While the Data Science pioneers have long established and highly specialized teams, smaller companies are still looking for the Data Science Allrounder, which can take over the full range of tasks from the access to the database to the implementation of the analytical application. However, companies with specialized data experts have long since distinguished Data Scientists, Data Engineers and Business Analysts. Therefore, the definition of Data Science and the delineation of the abilities that a data scientist should have, varies between a broader and a more narrow demarcation.


A closer look at the more narrow definition shows, that a Data Engineer takes over the data allocation, the Data Scientist loads it into his tools and runs the data analysis together with the colleagues from the department. According to this, a Data Scientist would need no knowledge of databases or APIs, neither an expertise would be necessary …

In my experience, DataScience is not that narrow, the task spectrum covers more than just the core area. This misunderstanding comes from Data Science courses and – for me – I should point to the overall picture of Data Science again and again. In courses and seminars, which want to teach Data Science as a discipline, the focus will of course be on the core area: programming, tools and methods from mathematics & statistics.

Is Data Science the new Statistics?

Table of Contents

1 Introduction

2 Emerging of Data Science

3 Big data technologies

4 Two data worlds: Predictive vs inferential statistics

5 How to study data science

6 Conclusions

7 References

Introduction

As a student of Statistics and the winner of Data Science Scholarship I am often surrounded by computer scientists, mathematicians, physicists and of course statisticians. During conversation, I was asked questions such as “So what actually do I do? What is Data Science?”. These are some very difficult questions and as like you will see during reading this document many before me tried to answer those questions. There is a dispute between statisticians and computer scientists what is the origin of data science and who should teach it. According to the Institute of Mathematical Statistics in the: “The IMS presidential address: let us own data science” we can find a simple recipe for data scientist. [1]

“Putting the traits of Turner and Carver together gives a good portrait of a data scientist:

  • Statistics (S)
  • Domain/Science knowledge (D)
  • Computing (C)
  • Collaboration/teamwork (C)
  • Communication to outsiders (C)

That is, data science = SDCCC = S DC3

However, despite all the challenges that I will need to overcome in answering those questions I will try to do it. I will refer to ideas from several reputable sources, in which I will also tell you: what is in the data science that I am really fascinated about? What is magical in this creation of statistics and computer science that I am drawn to?

Emerging of Data Science

On Tuesday, the 8th of September 2015, University of Michigan announced the 100 million dollars “Data Science Initiative” (DSI), hired 35 new faculty members. On the DSI website we can read about this initiative:

“This coupling of scientific discovery and practice involves the collection, management, processing, analysis, visualisation, and interpretation of vast amounts of heterogeneous data associated with a diverse array of scientific, translational and interdisciplinary applications”2

But that sounds like a bread and butter for statisticians. So, is it really a new creation or is it something that exists for many years but it didn’t sound so sexy as data science? In the article written by Karl Broman, (the University of Wisconsin) we can read:

“When physicists do mathematics, they’re don’t say they’re doing “number science”. They’re doing math. If you’re analyzing data, you’re doing statistics. You can call it data science or informatics or analytics or whatever, but it ‘s still statistics. If you say that one kind of data analysis is statistics and another kind is not, you’re not allowing innovation. We need to define the field broadly. You may not like what some statisticians do. You may feel they don’t share your values. They may embarrass you. But that shouldn’t lead us to abandon the term “statistics”.

Reading the definition of data science on the Data Science Association’s “Professional Code of Conduct”:

“Data scientist means a professional who uses scientific methods to liberate and create meaning from raw data”

These sound like K. Browman maybe right. Maybe I should go on MSc Statistics like many before me did. Maybe Data Science is simply a new sexy name for statistician only data is big, technology more advanced rather than it used to be so you need to have programming skills to handle the data. Maybe let say loudly data science is a modern version of statistics? But maybe not? Because we can also find statements like the following:

“Statistics is the least important part of data science”. [3]

Further, we can read:

“There ‘s so, much that goes on with data that is about computing, not statistics. I do think it would be fair to consider statistics (which includes sampling, experimental design, and data collection as well as data analysis (which itself includes model building, visualization, and model checking as well as inference)) as a subset of data science. . . .”.[3]

So maybe people from computer science are right. Maybe I should go and study programming and forget about expanding my knowledge in statistics? After all, we all know that computer science always had much bigger funding and having MSc computer science was always like a magic star for employers. What should I do? Let me research further.

Big data technologies

Is the data size important to distinguish between data science and statistics? Going back to the “Let us own data science” article we can read that a statistician, Hollerith, invented the punched card reader to allow e cient compilation of a US census, the first elements of machine learning. So, no, machine learning is not an invention of computer scientists. It was well known for statistician for decades already. What about different techniques used in DOE (Design of Experiments) or sampling methods to decrease the sample size. If the data used by statisticians would be only small they wouldn’t have to discover methods such PCA (Principle component analysis) or dimensionality reduction techniques. So, no, data can be big and/or small for statisticians, so what is the difference between data science and statistics and what department should I choose?

When I spoke to computer scientists they try to convince me to choose computer science department. Their reasons being that there are many different programmes that I need to know to deal with large datasets. For instance: Java, Hadoop, SQL, Python, and much more. Moreover, programming can only be taught to the best standard through computer science courses Is it true? Can’t we do the same calculations using statistical software such as R, SAS or even Matlab? But on the other hand, doesn’t the newest technology always work faster? And if so, wouldn’t be better to use the newest technology when we program and write loops?

But, I don’t want to underestimate the effort made by statisticians and data analyst over last 50 years in developing statistical programmes. Their efforts have resulted in the emergence of today’s technology. Early statistical packages such as SPSS or Minitab (from 1960’s) allowed to develop more advanced programmes having roots in mini computer era such as STATA or my favourite R which in turn allowed progress to advanced technology even further and create Python, Hadoop, SQL and so on. Becker and Chambers (with S) and later Ihaka, Gentleman, and members of the R Core team (with R) worked on developing the statistical software. These names should be convincing about how powerful statistical programming languages can be. Many operations that we can do in Hadoop or SQL we can also do easily in R.

Two data worlds: Predictive vs inferential statistics

So maybe Data Science is a creature merged by statisticians working on computer science department? Maybe there are two different approaches to statistics: mathematical statistics and computer science statistics and the computer science statisticians are data scientists because according to Yanir Seroussi in his blog:

“A successful data scientist needs to be able to “become one with the data” by exploring it and applying rigorous statistical analysis (right-hand side of the continuum). But good data scientists also understand what it takes to deploy production systems, and are ready to get their hands dirty by writing code that cleans up the data or performs core system functionality (lefthand side of the continuum). Gaining all these skills takes time.”[4]

Okay, so my reasoning that some statisticians work on computer science department is right, as well as there exists subject like computational statistics, so maybe I should go for computer science department but study statistics.

In fact, I am not the first one to arrive at the conclusion. Everything started from a confession made by John Tukey in “The Future of Data Analysis” article published in “The Annals of Mathematical Statistics” :

For a long time, I have thought I was a statistician, interested in inferences from the particular to the general. But as I have watched mathematical statistics evolve, I have had cause to wonder and to doubt. … All in all I have come to feel that my central interest is in data analysis, which I take to include, among other things: procedures for analyzing data, techniques for interpreting the results of such procedures, ways of planning the gathering of data to make its analysis easier, more precise or more accurate, and all the machinery and results of (mathematical) statistics which apply to analyzing data

If I am right then above confession was a critical moment. The time when mathematical statistics become more inferential and computational statistics concentrated more on predictive statistics. Applied statisticians working on predictive analytics that are more interested in applying the knowledge rather than developing long proofs decided to move on computer science department.

Additionally, the following is crucial discussion made by Leo Biermann in his paper published in Statistical Science titled “Statistical modelling: the two cultures”. It enables us to understand and differentiate views from both types of statistician, namely mathematical and statistical.

Statistics starts with data. Think of the data as being generated by a black box in which a vector of input variables x (independent variables) go in one side, and on the other side the response variables y come out. Inside the black box, nature functions to associate the predictor variables with the response variables … There are two goals in analyzing the data:

  • Prediction. To be able to predict what the responses are going to be to future input variables
  • InferenceTo [infer] how nature is associating the response variables to the input variables.”

Furthermore, in the same dispute we can read:

“The statistical community has been committed to the almost exclusive use of [generative] models. This commitment has led to irrelevant theory, questionable conclusions, and has kept statisticians from working on a large range of interesting current problems. [Predictive] modeling, both in theory and practice, has developed rapidly in fields outside statistics. It can be used both on large complex data sets and as a more accurate and informative alternative to data modeling on smaller data sets. If our goal as a field is to use data to solve problems, then we need to move away from exclusive dependence on [generative] models …”

So, we can say that Data Science evolved from Predictive Analytics which in turn evolved from Statistics but it becomes separate science. Tukey and Wilk 1969 compared this new science to established sciences and further circumscribed the role of Statistics within it:

“ … data analysis is a very di cult field. It must adapt itself to what people can and need to do with data. In the sense that biology is more complex than physics, and the behavioural sciences are more complex than either, it is likely that the general problems of data analysis are more complex than those of all three. It is too much to ask for close and effective guidance for data analysis from any highly formalized structure, either now or in the near future. Data analysis can gain much from formal statistics, but only if the connection is kept adequately loose”

How to study data science

So, what is exactly predictive analytics culture? I think that everyone who used Kaggle competition before can agree with me that description of common task framework (CTF) formulated by Marc Liberman in 2009 is a perfect description of Kaggle competitions, and hackathons events; where latter has worked as training sessions for newbies in the data world. An instance of the CTF has these ingredients:

  1. A publicly available training data set involving, for each observation, a list of (possibly many) feature measurements, and a class label for that observation.
  2. A set of enrolled competitors whose common task is to infer a class prediction rule from the training data.
  3. A scoring referee, to which competitors can submit their prediction rule. The referee runs the prediction rule against a testing dataset which is sequestered behind a Chinese wall. The referee objectively and automatically reports the score (prediction accuracy) achieved by the submitted rule

Kaggle competitions are not only training platforms for newbies like me but also very challenging statistical competitions where experienced statisticians can win “pocket money”. A famous example is the Netflix Challenge where the common task was to predict Netflix user movie selection. The winning team (which included ATT Statistician Bob Bell) won 1 mln dollars.

Comparing modules that are available on master in data science at University of Berkley[6]:

  1. Both
  • Applied machine learning
  • Experiments and causality
  1. Statistics
  • Research design and application for data and analysis
  • Statistics for Data Science
  • Behind the data: humans and values
  • Statistical methods for discrete response, Time Series and panel data
  • Data visualisation
  1. Computer Science
  • Python for Data Science
  • Storing and Retrieving Data
  • Scalling up! Really Big Data
  • Machine Learning at scale
  • Natural Language Processing with Deep Learning

We can really see that data science is a subject that demands skills from both computer science and statistics. So, it is another confirmation for me that it is the best time to change department for my postgraduate study, that is, to study statistics on computer science department.

In the 50 Years of Data Science article we can read: “The activities of Greater Data Science are classified into 6 divisions:

  1. Data exploration and preparation
  2. Data representation and transformation
  3. Computing with data
  4. Data visualization and presentation
  5. Data Modelling
  6. Science about data science [5]

I will quickly go through all of them using my Ebola research example, this required using machine learning on time series data.

  1. The most demanding part. Many people told me before starting this project that: collecting, cleaning, wrangling and preparing data take 60% of all the time that you need to spend on data science project. I didn’t realise how much this 60% means in real time. I didn ‘t realise that the 60 percent will take so much time and that after this I will be exhausted. Exhausted but ready for the next step.
  2. This point is actually part of the first one, or maybe just like many other things in statistics: everything is one huge connected bunch.Data that you can find can be very nice, well behaving, written in CSV or JSON or any other format file that you can quickly download and use, but what if not? What if your data is ‘dirty’and not stored as a file (e.g. only appear on a website)? What if data is coded? Do you need to decode it?
  3. The even bigger challenge, but what a fun? You need to know a few different programming languages or least as I do know a little bit of R, a little bit of Python, quite well Tableau and Excel. So you can use different program in different scenarios or for different tasks. For example, using Panda to do EDA and ggplot 2 to do data vis.
  4. Graphs are pretty, right? If you are still reading my article, I bet you know what is heat map, spatial vis in big cities or different infographics. Surely, I would like to highlight, that we respect only the ones that are not only pretty but also valid. Nevertheless, time that is required to create these visualisations is another matter.
  5. The data modelling, finally? I don’t need to say a lot about this. All forms of inferential and predictive analytic are allowed and accepted.
  6. My favourite part, not the end yet. All the conferences and meetups that I can attend on. All the seminars where we all present our current projects.

Conclusions

After graduation, I will be graduated Statistician. Even more, I will be a mathematical statistician whom mostly during degree dealt with inferential statistics. On the other hand, winning data science scholarship gave me exposure to predictive analytic which I highly enjoyed. Therefore, for my next stage, I will just change my department and concentrate more on predictive analytic. There are many statisticians working on computer science department. They possess both statistical knowledge and advanced software engineering skills, they are called data scientists. It would be a pleasure for me to join them. I don’t mind if it will be MSc. Computer Science, MSc. Data Science, MSc. Big Data or whatever the name will be. I do mind to have sufficient exposure to deal with “dirty” data using statistical modelling and machine learning using modern technology. This is what data science is for me. Maybe for you, it will be something else. Maybe you will be more satisfied with expanding massively programming skills. But for me, programming is a tool, modern technology is my friend and my bread and butter will be predictive analytic.

References

  1. IMS Presidential Address: Let us own data science
  2. Data science is statistics
  3. A Gelman, Columbia University
  4. Yanir Seroussi: What is data Science?
  5. 50 Years Data Science
  6. Curriculum: data science@Berkley

Data Science and Predictive Analytics in Healthcare

Doing data science in a healthcare company can save lives. Whether it’s by predicting which patients have a tumor on an MRI, are at risk of re-admission, or have misclassified diagnoses in electronic medical records are all examples of how predictive models can lead to better health outcomes and improve the quality of life of patients.  Nevertheless, the healthcare industry presents many unique challenges and opportunities for data scientists.

The impact of data science in healthcare

Healthcare providers have a plethora of important but sensitive data. Medical records include a diverse set of data such as basic demographics, diagnosed illnesses, and a wealth of clinical information such as lab test results. For patients with chronic diseases, there could be a long and detailed history of data available on a number of health indicators due to the frequency of visits to a healthcare provider. Information from medical records can often be combined with outside data as well. For example, a patient’s address can be combined with other publicly available information to determine the number of surgeons that practice near a patient or other relevant information about the type of area that patients reside in.

With this rich data about a patient as well as their surroundings, models can be built and trained to predict many outcomes of interest. One important area of interest is models predicting disease progression, which can be used for disease management and planning. For example, at Fresenius Medical Care (where we primarily care for patients with chronic conditions such as kidney disease), we use a Chronic Kidney Disease progression model that can predict the trajectory of a patient’s condition to help clinicians decide whether and when to proceed to the next stage in their medical care. Predictive models can also notify clinicians about patients who may require interventions to reduce risk of negative outcomes. For instance, we use models to predict which patients are at risk for hospitalization or missing a dialysis treatment. These predictions, along with the key factors driving the prediction, are presented to clinicians who can decide if certain interventions might help reduce the patient’s risk.

Challenges of data science in healthcare

One challenge is that the healthcare industry is far behind other sectors in terms of adopting the latest technology and analytics tools. This does present some challenges, and data scientists should be aware that the data infrastructure and development environment at many healthcare companies will not be at the bleeding edge of the field. However it also means there are a lot of opportunities for improvement, and even small simple models can yield vast improvements over current methods.

Another challenge in the healthcare sector arises from the sensitive nature of medical information. Due to concerns over data privacy, it can often be difficult to obtain access to data that the company has. For this reason, data scientists considering a position at a healthcare company should be aware of whether there is already an established protocol for data professionals to get access to the data. If there isn’t, be aware that simply getting access to the data may be a major effort in itself.

Finally, it is important to keep in mind the end-use of any predictive model. In many cases, there are very different costs to false-negatives and false-positives. A false-negative may be detrimental to a patient’s health, while too many false-positives may lead to many costly and unnecessary treatments (also to the detriment of patients’ health for certain treatments as well as economy overall). Education about the proper use of predictive models and their limitations is essential for end-users. Finally, making sure the output of a predictive model is actionable is important. Predicting that a patient is at high-risk is only useful if the model outputs is interpretable enough to explain what factors are putting that patient at risk. Furthermore, if the model is being used to plan interventions, the factors that can be changed need to be highlighted in some way – telling a clinician that a patient is at risk because of their age is not useful if the point of the prediction is to lower risk through intervention.

The future of data science in the healthcare sector

The future holds a lot of promise for data science in healthcare. Wearable devices that track all kinds of activity and biometric data are becoming more sophisticated and more common. Streaming data coming from either wearables or devices providing treatment (such as dialysis machines) could eventually be used to provide real-time alerts to patients or clinicians about health events outside of the hospital.

Currently, a major issue facing medical providers is that patients’ data tends to exist in silos. There is little integration across electronic medical record systems (both between and within medical providers), which can lead to fragmented care. This can lead to clinicians receiving out of date or incomplete information about a patient, or to duplication of treatments. Through a major data engineering effort, these systems could (and should) be integrated. This would vastly increase the potential of data scientists and data engineers, who could then provide analytics services that took into account the whole patients’ history to provide a level of consistency across care providers. Data workers could use such an integrated record to alert clinicians to duplications of procedures or dangerous prescription drug combinations.

Data scientists have a lot to offer in the healthcare industry. The advances of machine learning and data science can and should be adopted in a space where the health of individuals can be improved. The opportunities for data scientists in this sector are nearly endless, and the potential for good is enormous.