DeepChem — A framework for using ML and DL for Life Science and Chemoinformatics

Application of Machine Learning and Deep Learning for Drug Discovery, Genomics, Microsocopy and Quantum Chemistry can create radical impact and holds the potential to significantly accelerate the process of medical research and vaccine development, which is a necessity for any pandemic like Covid19.

Before we even begin, this article is a very high level one and specifically targeted for Data Scientists and ML Researchers interested in Drug Discovery, especially during the time of an existing pandemic like Covid19_. _If you are some one with a strong background in Bio-informatics or Chem-informatics and wants to venture into the world of data science for these use-cases, please reach out to me through any of the options mentioned here, and we can discuss few interesting opportunities for the greater good of mankind.

DeepChem, an open source framework, which internally uses TensorFlow, that has been specifically designed to simplify the creation of deep learning models for various life science applications.

In this tutorial, we will see how to setup DeepChem and we will see how to use DeepChem for :

1. training a model that can predict toxicity of molecules

2. training a model to predict solubility of molecules

3. using SMART strings to query molecular structures.

Setting Up DeepChem

Although, in multiple sources, I have seen users have expressed their concern in setting up DeepChem in Windows, Linux and Mac environments, but I found it quite easy to do that using pip installer.

The DeepChem development team, is very active and they do provide daily builds, so I would like everyone to take a look at their pypi page: https://pypi.org/project/deepchem/#history and install a suitable version in case if the latest version has any issue. A simple _pip install deepchem _would install the very latest version.

Next, along with DeepChem, you would require TensorFlow to be installed. I had installed the latest version of TensorFlow using _pip install tensorflow _and RDkit which is an open source Cheminformatics software package. For RDkit and for installing in Windows, I did not find any reliable pip installer, so that installed it from https://anaconda.org/rdkit/rdkit using the conda installer : conda install -c rdkit rdkit

Once these three modules are installed, we are ready to start with our experiments.

#drug-discovery #deepchem #bioinformatics #cheminformatics #aditya-bhattacharya #data science

What is GEEK

Buddha Community

DeepChem — A framework for using ML and DL for Life Science and Chemoinformatics

DeepChem — A framework for using ML and DL for Life Science and Chemoinformatics

Application of Machine Learning and Deep Learning for Drug Discovery, Genomics, Microsocopy and Quantum Chemistry can create radical impact and holds the potential to significantly accelerate the process of medical research and vaccine development, which is a necessity for any pandemic like Covid19.

Before we even begin, this article is a very high level one and specifically targeted for Data Scientists and ML Researchers interested in Drug Discovery, especially during the time of an existing pandemic like Covid19_. _If you are some one with a strong background in Bio-informatics or Chem-informatics and wants to venture into the world of data science for these use-cases, please reach out to me through any of the options mentioned here, and we can discuss few interesting opportunities for the greater good of mankind.

DeepChem, an open source framework, which internally uses TensorFlow, that has been specifically designed to simplify the creation of deep learning models for various life science applications.

In this tutorial, we will see how to setup DeepChem and we will see how to use DeepChem for :

1. training a model that can predict toxicity of molecules

2. training a model to predict solubility of molecules

3. using SMART strings to query molecular structures.

Setting Up DeepChem

Although, in multiple sources, I have seen users have expressed their concern in setting up DeepChem in Windows, Linux and Mac environments, but I found it quite easy to do that using pip installer.

The DeepChem development team, is very active and they do provide daily builds, so I would like everyone to take a look at their pypi page: https://pypi.org/project/deepchem/#history and install a suitable version in case if the latest version has any issue. A simple _pip install deepchem _would install the very latest version.

Next, along with DeepChem, you would require TensorFlow to be installed. I had installed the latest version of TensorFlow using _pip install tensorflow _and RDkit which is an open source Cheminformatics software package. For RDkit and for installing in Windows, I did not find any reliable pip installer, so that installed it from https://anaconda.org/rdkit/rdkit using the conda installer : conda install -c rdkit rdkit

Once these three modules are installed, we are ready to start with our experiments.

#drug-discovery #deepchem #bioinformatics #cheminformatics #aditya-bhattacharya #data science

Uriah  Dietrich

Uriah Dietrich

1618449987

How To Build A Data Science Career In 2021

For this week’s data science career interview, we got in touch with Dr Suman Sanyal, Associate Professor of Computer Science and Engineering at NIIT University. In this interview, Dr Sanyal shares his insights on how universities can contribute to this highly promising sector and what aspirants can do to build a successful data science career.

With industry-linkage, technology and research-driven seamless education, NIIT University has been recognised for addressing the growing demand for data science experts worldwide with its industry-ready courses. The university has recently introduced B.Tech in Data Science course, which aims to deploy data sets models to solve real-world problems. The programme provides industry-academic synergy for the students to establish careers in data science, artificial intelligence and machine learning.

“Students with skills that are aligned to new-age technology will be of huge value. The industry today wants young, ambitious students who have the know-how on how to get things done,” Sanyal said.

#careers # #data science aspirant #data science career #data science career intervie #data science education #data science education marke #data science jobs #niit university data science

PANDAS: Most Used Functions in Data Science

Most useful functions for data preprocessing

When you get introduced to machine learning, the first step is to learn Python and the basic step of learning Python is to learn pandas library. We can install pandas library by pip install pandas. After installing we have to import pandas each time of the running session. The data used for example is from the UCI repository “https://archive.ics.uci.edu/ml/datasets/Heart+failure+clinical+records

  1. Read Data

2. Head and Tail

3. Shape, Size and Info

4. isna

#pandas: most used functions in data science #pandas #data science #function #used python data #most used functions in data science

Why Use WordPress? What Can You Do With WordPress?

Can you use WordPress for anything other than blogging? To your surprise, yes. WordPress is more than just a blogging tool, and it has helped thousands of websites and web applications to thrive. The use of WordPress powers around 40% of online projects, and today in our blog, we would visit some amazing uses of WordPress other than blogging.
What Is The Use Of WordPress?

WordPress is the most popular website platform in the world. It is the first choice of businesses that want to set a feature-rich and dynamic Content Management System. So, if you ask what WordPress is used for, the answer is – everything. It is a super-flexible, feature-rich and secure platform that offers everything to build unique websites and applications. Let’s start knowing them:

1. Multiple Websites Under A Single Installation
WordPress Multisite allows you to develop multiple sites from a single WordPress installation. You can download WordPress and start building websites you want to launch under a single server. Literally speaking, you can handle hundreds of sites from one single dashboard, which now needs applause.
It is a highly efficient platform that allows you to easily run several websites under the same login credentials. One of the best things about WordPress is the themes it has to offer. You can simply download them and plugin for various sites and save space on sites without losing their speed.

2. WordPress Social Network
WordPress can be used for high-end projects such as Social Media Network. If you don’t have the money and patience to hire a coder and invest months in building a feature-rich social media site, go for WordPress. It is one of the most amazing uses of WordPress. Its stunning CMS is unbeatable. And you can build sites as good as Facebook or Reddit etc. It can just make the process a lot easier.
To set up a social media network, you would have to download a WordPress Plugin called BuddyPress. It would allow you to connect a community page with ease and would provide all the necessary features of a community or social media. It has direct messaging, activity stream, user groups, extended profiles, and so much more. You just have to download and configure it.
If BuddyPress doesn’t meet all your needs, don’t give up on your dreams. You can try out WP Symposium or PeepSo. There are also several themes you can use to build a social network.

3. Create A Forum For Your Brand’s Community
Communities are very important for your business. They help you stay in constant connection with your users and consumers. And allow you to turn them into a loyal customer base. Meanwhile, there are many good technologies that can be used for building a community page – the good old WordPress is still the best.
It is the best community development technology. If you want to build your online community, you need to consider all the amazing features you get with WordPress. Plugins such as BB Press is an open-source, template-driven PHP/ MySQL forum software. It is very simple and doesn’t hamper the experience of the website.
Other tools such as wpFoRo and Asgaros Forum are equally good for creating a community blog. They are lightweight tools that are easy to manage and integrate with your WordPress site easily. However, there is only one tiny problem; you need to have some technical knowledge to build a WordPress Community blog page.

4. Shortcodes
Since we gave you a problem in the previous section, we would also give you a perfect solution for it. You might not know to code, but you have shortcodes. Shortcodes help you execute functions without having to code. It is an easy way to build an amazing website, add new features, customize plugins easily. They are short lines of code, and rather than memorizing multiple lines; you can have zero technical knowledge and start building a feature-rich website or application.
There are also plugins like Shortcoder, Shortcodes Ultimate, and the Basics available on WordPress that can be used, and you would not even have to remember the shortcodes.

5. Build Online Stores
If you still think about why to use WordPress, use it to build an online store. You can start selling your goods online and start selling. It is an affordable technology that helps you build a feature-rich eCommerce store with WordPress.
WooCommerce is an extension of WordPress and is one of the most used eCommerce solutions. WooCommerce holds a 28% share of the global market and is one of the best ways to set up an online store. It allows you to build user-friendly and professional online stores and has thousands of free and paid extensions. Moreover as an open-source platform, and you don’t have to pay for the license.
Apart from WooCommerce, there are Easy Digital Downloads, iThemes Exchange, Shopify eCommerce plugin, and so much more available.

6. Security Features
WordPress takes security very seriously. It offers tons of external solutions that help you in safeguarding your WordPress site. While there is no way to ensure 100% security, it provides regular updates with security patches and provides several plugins to help with backups, two-factor authorization, and more.
By choosing hosting providers like WP Engine, you can improve the security of the website. It helps in threat detection, manage patching and updates, and internal security audits for the customers, and so much more.

Read More

#use of wordpress #use wordpress for business website #use wordpress for website #what is use of wordpress #why use wordpress #why use wordpress to build a website

Sasha  Lee

Sasha Lee

1624601340

From Science to Data Science

  1. Introduction and Hypothesis

I loved to work as a scientist. There is a deep feeling of completion and happiness when you manage to answer why. Finding out why such animal would go there, why would they do this at that time of the year, why is that place so diverse… This applies to any kind of field. This is the reason why I want to advocate that if you are a scientist, you might want to have a look at what is called Data Science in the technological field. Be aware, I will not dwell in the details of titles such as Data engineer, data analyst, data scientist, AI researcher. Here, when I refer to Data Science, I mean the science of finding insights from data collected about a subject.

So, back to our **_why. _**In science, in order to answer your why, you will introduce the whole context surrounding it and then formulate an hypothesis. “The timing of the diapause in copepods is regulated through their respiration, ammonia excretion and water column temperature”. Behaviour of subject is the result of internal and external processes.

In marketing, you would have to formulate similar hypothesis in order to start your investigation: “3-days old users un-suscribes due to the lack of direct path towards the check-out”. Behaviour of subject is the result of internal (frustration) and external (not optimized UE/UI) processes.

Although I would have wanted to put that part at the end, as for any scientific paper, it goes without saying that your introduction would present the current ideas, results, and hypotheses of your field of research. So, as a researcher, you need to accumulate knowledge about your subject, and you go looking for scientific articles. The same is true for techs as well. There are plenty of scientific and non-scientific resources out-there that will allow you to better understand, interpret and improve your product. Take this article, for instance, Medium is a wonderful base of knowledge on so many topics! But you could also find passionating articles on PloS One on Users Experience or Marketing Design and etc.

2. Material and Methods

As a Marine biologist and later an Oceanographer, I took great pleasure to go at the field and collect data (platyhelminths, fish counts, zooplankton , etc…). Then we needed to translate the living “data” into numeric data. In the technological industry, it is the same idea. Instead of nets, quadrats, and terrain coverage, you will setup tracking event, collect postbacks from your partners and pull third-parties data. The idea is the same, “how do I get the information that will help me answer my why”. So a field sampling mission and a data collection planning have a lot in common.

#ai #data-science #science #tech #data science #from science