So much to do, so little time

Trying to squeeze sense out of chemical data

A Model Building IDE?

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Recently I came across a NIPS2015 paper from Vartak et al that describes a system (APIs + visual frontend) to support the iterative model building process. The problem they are addressing is common one in most machine learning settings – building multiple models (different type) using various features and identifying one or more optimal models to take into production. As they correctly point out, most tools such as scikit-learn, SparkML, etc. focus on providing methods and interfaces to build a single model – it’s up to the user to manage the multiple models, keep track of their performance metrics.

sherlock

My first reaction was, “why?”. Part of this stems from my use of the R environment which allows me to build up a infrastructure for building multiple models (e.g., caret, e1701), storing them (list of model objects, RData binary files or even pmml) and subsequent comparison and summarization. Naturally, this is specific to me (so not really a general solution) and essentially a series of R commands – I don’t have the ability to monitor model building progress and simultaneously inspect models that have been built.

In that sense, the authors statement,

For the most part, exploration of models takes place sequentially. Data scientists must write (repeated) imperative code to explore models one after another.

is correct (though maybe, said data scientists should improve their programming skills?). So a system that allows one to organize an exploration of model space could be useful. However, other statements such as

  • Without a history of previously trained models, each model must be trained from scratch, wasting computation and increasing response times.
  • In the absence of history, comparison between models becomes challenging and requires the data scientist to write special-purpose code.

seem to be relevant only when you are not already working in an environment that supports model objects and their associated infrastructure. In my workflow, the list of model object represents my history!

Their proposed system called SHERLOCK is built on top of SparkML and provides an API to model building, a database for model storage and a graphical interface (see above) to all of this. While I’m not convinced of some of the design goals (e.g., training variations of models based on previously trained models (e.g., with different feature sets) – wouldn’t you need to retrain the model from scratch if you choose a new feature set?), it’ll be interesting to see how this develops. Certainly, the UI will be key – since it’s pretty easy to generate a multitude of models with a multitude of features, but in the end a human needs to make sense of it.

On a separate note, this sounds like something RStudio could take a stab at.

Written by Rajarshi Guha

December 7th, 2015 at 3:09 am

Exploring ChEMBL Targets with Neo4j

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As part of an internal project I’ve recently started working with Neo4j for representing and querying relationships between entities (targets, compounds, etc.). What has really caught my attention is the Cypher graph query language – by allowing you to construct queries using graph notation, many tasks that would be complex or tedious in a traditonal RDBMS become much easier.

As an example, I loaded the ChEMBL target hierarchy and the targets as a graph. On it’s own it’s not particularly useful – the real utility arises when other datasets (and datatypes) are linked to the targets. But even at this stage, one can easily ask questions such as

Find all kinase proteins

which is simply a matter of identifying proteins that have a direct path to the Kinase target class.

Assuming you have ChEMBL loaded in to a MySQL database, you can generate a Neo4j graph database containing the targets and classification hierarchy using code from the neo4jexpt repository. Simply compile and run as (appropriately changing host name, user and password)

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$ mvn package
$ java -Djdbc.url="jdbc:mysql://host.name/chembl_20?user=USER&password=PASS" \
       -jar target/neo4j-ctl-1.0-SNAPSHOT.jar graph.db

Once complete, you should see a folder named graph.db. Using the Neo4j application you can then explore the graph in your browser by executing Cypher queries. For example, lets get the graph of the entire ChEMBL target classification hierarchy (and ensuring that we don’t include actual proteins)

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MATCH (n {TargetType:'TargetFamily'})-[r]-(m {TargetType:'TargetFamily'})
  RETURN r

(The various annotations such as TargetType and TargetFamily are based on my code). When visualized we get

prolif-bp

Lets get more specific, and extract the kinase portion of the classification hierarchy

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MATCH (n {TargetType:'TargetFamily'}),
      (m {TargetID:'Kinase'}),
      p = shortestPath( (n)-[:ChildOf*]->(m) )
  RETURN p

prolif-bp

Given that we’ve linked the protein themselves to the target classes, we can now ask for all proteins that are kinases

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MATCH (m {TargetType:'MolecularTarget'}),
      (n {TargetID:'Kinase'}),
      p = shortestPath( (m)-[*]->(n) )
  RETURN m

Or identify the target classes that are linked to more than 25 proteins

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MATCH ()-[r1:IsA]-(m:TargetBiology {TargetType:"TargetFamily"})
  WITH m, COUNT(r1) AS relCount
  WHERE relCount > 25
  RETURN m

which gives us a table of target classes and counts, part of which is shown below

prolif-bp

Overall this seems to be a very powerful platform to integrate data sources and types and effectively query for relationships. The browser based view is useful to practice Cypher and answer questions of the dataset. But a REST API is available as well as other tools such as Gremlin that allow for much more flexible applications and sophisticated queries.

Written by Rajarshi Guha

November 14th, 2015 at 6:10 pm

Surveying the Opinion of Chemists

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As part of a project I was wondering about reports of surveys that collected chemists assessments of differnt things. More specifically, I wasn’t looking for crowd-sourcing efforts for data curation (such as the in the Spectral Game) or data collection. Rather, I was interested in reports where somebody asked a group of chemists what they thought of some particular molecular “feature”. Here, “feature” is pretty broadly defined and could range from the quality of a probe molecule to whether a molecule is complex or not.

Surveying the literature (and with pointers from @dgelemi, @baoilleach, Jun Li, @georgeisyourman and @DrBostrom) here’s the following papers:

The number of people surveyed across these studies ranges from less than 10 to more than 300. Recently there appears to be a trend towards developing predictive models based on the results of such surveys. Also, molecular complexity seems pretty popular. Modeling opinion is always a tricky thing, though in my mind some aspects (e.g., complexity, diversity) lend themselves to more robust models than others (e.g., quality of a probe).

If there are other examples of such surveys in chemistry, I’d appreciate any pointers

Written by Rajarshi Guha

November 7th, 2015 at 1:21 pm

Post-doc (Molecular Informatics) Opening at NCATS

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I have a post-doc opening in the Informatics group at NCATS, to work on computational aspects of high throughput combination screening – topics will include predicting drug combination response, visualizing large combination screens (> 5000 combinations) and so on. The NCATS combination screening platform thas tested more than 65,000 compound combinations (in checkerboard style which means more than 4.5M individual dose combinations) along with single agent dose responses. You can view publicly released data at https://tripod.nih.gov/matrix-client.

The NCATS Informatics group is a collection of very smart people, with wide ranging interests in molecular informatics. We work closely with colleagues in biology and chemistry. As a result, we eat a lot of our own dog food. In addition, we’re committed to implementing our ideas in publicly available software tools as well as publishing in journals.

Lots of data, great people and tough problems. If this piques your interest visit the job posting for more details

Written by Rajarshi Guha

February 6th, 2015 at 8:52 pm

Applications Invited for CSA Trust Grant for 2015

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The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research. In support of its charter, the Trust has created a unique Grant Program and is now inviting the submission of grant applications for 2015.

Purpose of the Grants
The Grant Program has been created to provide funding for the career development of young researchers who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, process and retrieve information about chemical structures, reactions and compounds. One or more Grants will be awarded annually up to a total combined maximum of ten thousand U.S. dollars ($10,000). Grants are awarded for specific purposes, and within one year each grantee is required to submit a brief written report detailing how the grant funds were allocated. Grantees are also requested to recognize the support of the Trust in any paper or presentation that is given as a result of that support.

Who is Eligible?
Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information related research and who are developing careers that have the potential to have a positive impact on the utility of chemical information relevant to chemical structures, reactions and compounds, are invited to submit applications. While the primary focus of the Grant Program is the career development of young researchers, additional bursaries may be made available at the discretion of the Trust. All requests must follow the application procedures noted below and will be weighed against the same criteria.

Which Activities are Eligible?
Grants may be awarded to acquire the experience and education necessary to support research activities; e.g. for travel to collaborate with research groups, to attend a conference relevant to one’s area of research, to gain access to special computational facilities, or to acquire unique research techniques in support of one’s research.

Application Requirements:
Applications must include the following documentation:

  1. A letter that details the work upon which the Grant application is to be evaluated as well as details on research recently completed by the applicant;
  2. The amount of Grant funds being requested and the details regarding the purpose for which the Grant will be used (e.g. cost of equipment, travel expenses if the request is for financial support of meeting attendance, etc.). The relevance of the above-stated purpose to the Trust’s objectives and the clarity of this statement are essential in the evaluation of the application);
  3. A brief biographical sketch, including a statement of academic qualifications;
  4. Two reference letters in support of the application. Additional materials may be supplied at the discretion of the applicant only if relevant to the application and if such materials provide information not already included in items 1-4. Three copies of the complete application document must be supplied for distribution to the Grants Committee.

Deadline for Applications
Applications for the 2015 Grant is March 13, 2015. Successful applicants will be notified no later than May 2nd of the relevant year.

Address for Submission of Applications
The application documentation should be forwarded to: Bonnie Lawlor, CSA Trust Grant Committee Chair, 276 Upper Gulph Road, Radnor, PA 19087, USA. If you wish to enter your application by e-mail, please contact Bonnie Lawlor at chescot@aol.com prior to submission so that she can contact you if the e-mail does not arrive.

Written by Rajarshi Guha

February 2nd, 2015 at 5:20 pm

Posted in cheminformatics

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