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Which Datasets Lead to Predictive Models?

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I came across a recent paper from the Tropsha group that discusses the issue of modelability – that is, can a dataset (represented as a set of computed descriptors and an experimental endpoint) be reliably modeled. Obviously the definition of reliable is key here and the authors focus on a cross-validated classification accuracy as the measure of reliability. Furthermore they focus on binary classification. This leads to a simple definition of modelability – for each data point, identify whether it’s nearest neighbor is in the same class as the data point. Then, the ratio of number of observations whose nearest neighbor is in the same activity class to the number observations in that activity class, summed over all classes gives the MODI score. Essentially this is a statement on linear separability within a given representation.

The authors then go show a pretty good correlation between the MODI scores over a number of datasets and their classification accuracy. But this leads to the question – if one has a dataset and associated modeling tools, why compute the MODI? The authors state

we suggest that MODI is a simple characteristic that can be easily computed for any dataset at the onset of any QSAR investigation

I’m not being rigorous here, but I suspect for smaller datasets the time requirements for MODI calculations is pretty similar to building the models themselves and for very large datasets MODI calculations may take longer (due to the requirement of a distance matrix calculation – though this could be alleviated using ANN or LSH). In other words – just build the model!

Another issue is the relation between MODI and SVM classification accuracy. The key feature of SVMs is that they apply the kernel trick to transform the input dataset into a higher dimensional space that (hopefully) allows for better separability. As a result MODI calculated on the input dataset should not necessarily be related to the transformed dataset that is actually operated on by the SVM. In other words a dataset with poor MODI could be well modeled by an SVM using an appropriate kernel.

The paper, by definition, doesn’t say anything about what model would be best for a given dataset. Furthermore, it’s important to realize that every dataset can be perfectly predicted using a sufficiently complex model. This is also known as an overfit model. The MODI approach to modelability avoids this by considering a cross-validated accuracy measure.

One application of MODI that does come to mind is for feature selection - identify a descriptor subset that leads to a predictive model. This is justified by the observed correlation between the MODI scores and the observed classification rates and would avoid having to test feature subsets with the modeling algorithm itself. An alternative application (as pointed out by the authors) is to identify subsets of the data that exhibit a good MODI score, thus leading to a local QSAR model.

More generally, it would be interesting to extend the concept to regression models. Intuitively, a dataset that is continuous in a given representation should have a better modelability than one that is discontinuous. This is exactly the scenario that can be captured using the activity landscape approach. Sometime back I looked at characterizing the roughness of an activity landscape using SALI and applied it to the feature selection problem – being able to correlate such a measure to predictive accuracy of models built on those datasets could allow one to address modelability (and more specifically, what level of continuity should a landscape present to be modelable) in general.

Written by Rajarshi Guha

December 4th, 2013 at 4:21 pm

Posted in cheminformatics

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Exploring co-morbidities in medical case studies

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A previous post described a first look at the data available in, primarily looking at summaries of high level meta-data. In this post I start looking at the cases themselves. As I noted previously, BMC has performed some form of biomedical entity recognition on the abstracts (?) of the case studies, resulting in a set of keywords for each case study. The keywords belong to specific types such as Condition, Medication and so on. The focus of this post will be to explore the occurrence of co-morbidities – which conditions occur together, to what extent and whether such occurrences are different from random. The code to extract the co-morbidity data and generate the analyses below is available in

Before doing any analyses we need to do some clean up of the Condition keywords. This includes normalizing terms (replacing ‘comatose’ with ‘coma’, converting all diabetes variants such as Type 1 and Type 2 to just diabetes), fixing spelling variants (replacing ‘foetal’ with ‘fetal’), removing stopwords and so on. The Python code to perform this clean up requires that we manually identify these transformations. I haven’t done this rigorously, so it’s not a totally cleansed dataset. The cleanup code looks like

def cleanTerms(terms):
    repMap = {'comatose':'coma',
              'lymphomas': 'lymphoma',
    stopwords = ['state','syndrome'', low grade', 'fever', 'type ii', 'mellitus', 'type 2', 'type 1', 'systemic', 'homogeneous', 'disease']
    l = []
    term = [x.lower().strip() for x in terms]
    for term in terms:
        for sw in stopwords: term = term.replace(sw, '')
        for key in repMap.keys():
            if term.find(key) >= 0: term = repMap[key]
        term = term.encode("ascii", "ignore").replace('\n','').strip()
    l = filter(lambda x: x != '-', l)

Since each case study can be associated with multiple conditions, we generate a set of unique condition pairs for each case, and collect these for all 28K cases I downloaded previously.

cases = pickle.load(open('cases.pickle'))
allpairs = []
for case in cases:
    ## get all conditions for this case
    conds = filter(lambda x: x['type'] == 'Condition', [x for x in case['keywords']])
    conds = cleanTerms([x['text'] for x in conds])
    if len(conds) == 0: continue
    pairs = [ (x,y) for x,y in list(combinations(conds, 2))]

It turns out that across the whole dataset, there are a total of 991,466 pairs of conditions corresponding to 576,838 unique condition pairs and 25,590 unique conditions. Now, it’s clear that some condition pairs may be causally related (some of which are trivial cases such as cough and infection), whereas others are not. In addition, it is clear that some condition pairs are related in a semantic, rather than causal, fashion – carcinoma and cancer. In the current dataset we can’t differentiate between these classes. One possibility would be to code the conditions using ICD10 and collapse terms using the hierarchy.

Number of co-morbidities vs frequency of occurrence

Number of co-morbidities vs frequency of occurrence

Having said that, we work with what we currently have – and it’s quite sparse. In fact the 28K case studies represent just 0.16% of all possible co-morbidities. Within the set of just under 600K unique observed co-morbidities, the bulk occur just once. For the rest of the analysis we ignore these singleton co-morbidities (leaving us with 513,997  co-morbidities). It’s interesting to see the distribution of frequencies of co-morbidities. The first figure plots the number of co-morbidities that occur at least N times – 99,369 co-morbidities occur 2 or more times in the dataset and so on.

Another way to visualize the data is to plot a pairwise heatmap of conditions. For pairs of conditions that occur in the cases dataset we can calculate the probability of occurrence (i.e., number of times the pair occurs divided by the number of pairs). Furthermore, using a sampling procedure we can evaluate the number of times a given pair would be selected randomly from the pool of conditions. For the current analysis, I used 1e7 samples and evaluated the probability of a co-morbidity occurring by chance. If this probability is greater than the observed probability I label that co-morbidity as not different from random (i.e., insignificant). Ideally, I would evaluate a confidence interval or else evaluate the probability analytically (?).

For the figure below, I considered the 48 co-morbidities (corresponding to 25 unique conditions) that occurred 250 or more times in the dataset. I display the lower triangle for the heatmap – grey indicates no occurrences for a given co-morbidity and white X’s identify co-morbidities that have a non-zero probability of occurrence but are not different from random. As noted above, some of these pairs are not particularly informative – for example, tumor and metastasis occur with a relatively high probability, but this is not too surprising

Probability of occurrence for co-morbidities occurring more than 250 times

Probability of occurrence for co-morbidities occurring more than 250 times

It’s pretty easy to modify to look at other sets of co-morbidities. Ideally, however, we would precompute probabilities for all co-morbidities and then support interactive visualization (maybe using D3).

It’s also interesting to look at co-morbidities that include a specific condition. For example, lets consider tuberculosis (and all variants). There are 948 unique co-morbidities that include tuberculosis as one of the conditions. While the bulk of them occur just twice, there are a number with relatively large frequencies of occurrence – lymphadenopathy co-occurs with tuberculosis 203 times. Rather than tabulate the co-occurring conditions, we can use the frequencies to generate a word cloud, as shown below. As with the co-morbidity heatmaps, this could be easily automated to support interactive exploration. On a related note, it’d be quite interesting to compare the frequencies discussed here with data extracted from a live EHR system

A visualization of conditions most frequently co-occurring with tuberculosis

A visualization of conditions most frequently co-occurring with tuberculosis

So far this has been descriptive – given the size of the data, we should be able to try out some predictive models. Future posts will look at the possibilities of modeling the case studies dataset.

Written by Rajarshi Guha

October 12th, 2013 at 10:43 pm

Exploring medical case studies

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I recently came across from BMC, a collection of more than 29,000 peer-reviewed case studies collected from a variety of journals. I’ve been increasingly interested in the possibilities of mining clinical data (inspired by impressive work from Atul Butte, Nigam Shah and others), so this seemed like a great resource to explore

The folks at BMC have provided a REST API, which is still in development – as a result, there’s no public documentation and it still has a few rough edges. However, thanks to help from Demitrakis Kavallierou, I was able to interact with the API and extract summary search information as well as 28,998 case studies as of Sept 23, 2013. I’ve made the code to extract case studies available as Running this, gives you two sets of data.

  1. A JSON file for each year between 2000 and 2014, containing the summary results for all cases in that year which includes a summary view of the case, plus facets for a variety of fields (age, condition, pathogen, medication, intervention etc.)
  2. A pickle file containing the case reports, as a list of maps. The case report contains the full abstract, case report identifier and publication meta-data.

A key feature of the case report entries is that BMC has performed some form of entity recognition so that it provides a list of keywords identified by different types: ‘Condition’, ‘Symptom’, ‘Medication’ etc. Each case may have multiple occurences for each type of keyword and importantly, each keyword is associated with the text fragment it is extracted from. As an example consider case 10.1136/bcr.02.2009.1548. The entry extracts two conditions

{u'sentence': u'She was treated by her family physician for presumptive interscapular myositis with anti-inflammatory drugs, cold packs and rest.',
u'text': u'Myositis',
u'type': u'Condition'}


{u'sentence': u'The patient denied any constitutional symptoms and had no cough.',
u'text': u'Cough',
u'type': u'Condition'}

I’m no expert in biomedical entity recognition, but the fact that BMC has performed it, saves me from having to become one, allowing me to dig into the data. But there are the usual caveats associated with text mining – spelling variants, term variants (insulin and insulin therapy are probably equivalent) and so on.

Count of cases deposited per year

Count of cases deposited per year

However, before digging into the cases themselves, we can use the summary data, and especially the facet information (which is, by definition, standardized) to get some quick summaries from the database. For example we see the a steady increase of case studies deposited in the literature over the last decade or so.

Interestingly, the number of unique conditions, medications or pathogens reported for these case studies is more or less constant, though there seems to be a downward trend for conditions. The second graph highlights this trend, by plotting the number of unique facet terms (for three types of facets) per year, normalized by the number of cases deposited that year.

Normalized count of unique facet terms by year

Normalized count of unique facet terms by year

This is a rough count, since I didn’t do any clean up of the text – so that misspellings of the same term (say, acetaminophen and acetaminaphen will be counted as two separate medication facets) may occur.

Another interesting task would be to enrich the dataset with additional annotations - ICD9/ICD10 for conditions, ATC for drugs – which would allow a higher level categorization and linking of case studies. In addition, one could use the CSLS service to convert medication names to chemical structures and employ structural similarity to group case studies.

The database also records some geographical information for each case. Specifically, it lists the countries that the authors are from. While interesting to an extent, it would have been nice if the country of occurrence or country of treatment were specifically extracted from the text. Currently, one might infer that the treatment occurred in the same country as the author is from, but this is likely only true when all authors are from the same country. Certainly, multinational collaborations will hide the true number of cases occurring in a given country (especially so for tropical diseases).

But we can take a look at how the number of cases reported for specific conditions, varies with geography and time. The figure below shows the cases whose conditions included the term tuberculosis

Tuberculosis cases by country and year

Tuberculosis cases by country and year

The code to extract the data from the pickle file is in Assuming you have cases.pickle in your current path, usage is

$ python condition_name

and will output the data into a CSV file, which you can the process using your favorite tools.

In following blog posts, I’ll start looking at the actual case studies themselves. Interesting things to look at include exploring the propensity of co-morbidities, analysing the co-occurrence of conditions and medications or conditions and pathogens, to see whether the set of treatments associated with a given condition (or pathogen) has changed over time. Both these naturally lead to looking at the data with eye towards repurposing events.

Written by Rajarshi Guha

October 10th, 2013 at 7:20 pm

Life and death in a screening campaign

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So, how do I enjoy my first day of furlough? Go out for a nice ride. And then read up on some statistics. More specifically, I was browsing the The R Book  and came across survival models. Such models are used to characterize time to events, where an event could be death of a patient or failure of a part and so on. In these types of models the dependent variable is the number of time units that pass till the event in question occurs. Usually the goal is to model the time to death (or failure) as a function of some properties of the individuals.

It occurred to me that molecules in a drug development pipeline also face a metaphorical life and death. More specifically, a drug development pipeline consists of a series of assays – primary, primary confirmation, secondary (orthogonal), ADME panel, animal model and so on. Each assay can be thought of as representing a time point in the screening campaign at which a compound could be discarded (“death”) or selected (“survived”) for further screening. While there are obvious reasons for why some compounds get selected from an assay and others do not (beyond just showing activity), it would be useful if we could quantify how molecular properties affect the number and types of compounds making it to the end of the screening campaign. Do certain scaffolds have a higher propensity of “surviving” till the in vivo assay? How does molecular weight, lipophilicity etc. affect a compounds “survival”? One could go up one level of abstraction and do a meta-analysis of screening campaigns where related assays would be grouped (so assays of type X all represent time point Y), allowing us to ask whether specific assays can be more or less indicative of a compounds survival in a campaign. Survival models allow us to address these questions.

How can we translate the screening pipeline to the domain of survival analysis? Since each assay represents a time point, we can assign a “survival time” to each compound equal to the number of assays it is tested in. Having defined the Y-variable, we must then select the independent variables. Feature selection is a never-ending topic so there’s lots of room to play. It is clear however, that descriptors derived from the assays (say ADMET related descriptors) will not be truly independent if those assays are part of the sequence.

Having defined the X and Y variables, how do we go about modeling this type of data? First, we must decide what type of survivorship curve characterizes our data. Such a curve characterizes the proportion of individuals alive at a certain time point. There are three types of survivorship curves: I, II and III corresponding to scenarios where individuals have a higher risk of death at later times, a constant risk of death and individuals have a higher risk of death at earlier times, respectively.

For the case of the a screening campaign, a Type III survivorship curve seems most appropriate. There are other details, but in general, they follow from the type of survivorship curve selected for modeling. I will note that the hazard function is an important choice to be made when using parametric models. There a variety of functions to choose from, but either require that you know the error distribution or else are willing to use trial and error. The alternative is to use a non-parametric approach. The most common approach for this class of models is the Cox proportional hazards model. I won’t go into the details of either approach, save to note that using a Cox model does not allow us to make predictions beyond the last time point whereas a parametric model would. For the case at hand, we are not really concerned with going beyond the last timepoint (i.e., the last assay) but are more interested in knowing what factors might affect survival of compounds through the assay sequence. So, a Cox model should be sufficient. The survival package provides the necessary methods in R.

OK – it sounds cute, but has some obvious limitations

  1. The use of a survival model assumes a linear time line. In many screening campaigns, the individual assays may not follow each other in a linear fashion. So either they must be collapsed into a linear sequence or else some assays should be discarded.
  2. A number of the steps represent ‘subjective selection’. In other words, each time a subset of molecules are selected, there is a degree of subjectivity involved – maybe certain scaffolds are more tractable for med chem than others or some notion of interesting combined with a hunch that it will work out. Essentially chemists will employ heuristics to guide the selection process – and these heuristics may not be fully quantifiable. Thus the choice of independent variables may not capture the nuances of these heuristics. But one could argue that it is possible the model captures the underlying heuristics via proxy variables (i.e., the descriptors) and that examination of those variables might provide some insight into the heuristics being employed.
  3. Data size will be an issue. As noted, this type of scenario requires the use of a Type III survivorship curve (i.e., most death occurs at earlier times and the death rate decreases with increasing time). However, decrease in death rate is extremely steep – out of 400,000 compounds screened in a primary assay, maybe 2000 will be cherry picked for confirmation and about 50 molecules may be tested in secondary, orthogonal assays. If we go out further to ADMET and in vivo assays, we may have fewer than 10 compounds to work with. At this stage I don’t know what effect such a steeply decreasing survivorship curve would have on the model.

The next step is to put together a dataset to see what we can pull out of a survival analysis of a screening campaign.

Written by Rajarshi Guha

October 2nd, 2013 at 10:22 pm

Learning Representations – Digits, Cats and Now Molecules

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Deep learning has been getting some press in the last few months, especially with the Google paper on recognizing cats (amongst other things) from Youtube videos. The concepts underlying this machine learning approach have been around for many years, though recent work by Hinton and others have led to fast implementations of the algorithms as well as better theoretical understanding.

It took me a while to realize that deep learning is really about learning an optimal, abstract representation in an unsupervised fashion (in the general case), given a set of input features. The learned representation can be then used as input to any classifier. A key aspect to such learned representations is that they are, in general, agnostic with respect to the final task for which they are trained. In the Google “cat” project this meant that the final representation developed the concept of cats as well as faces. As pointed out by a colleague, Bengio et al have published an extensive and excellent review of this topic and Baldi also has a nice review on deep learning.

In any case, it didn’t take too long for this technique to be applied to chemical data. The recent Merck-Kaggle challenge was won by a group using deep learning, but neither their code nor approach was publicly described. A more useful discussion of deep learning in cheminformatics was recently published by Lusci et al where they develop a DAG representation of structures that is then fed to a recursive neural network (RNN). They then use the resultant representation and network model to predict aqueous solubility.

A key motivation for the new graph representation and deep learning approach was the observation

one cannot be certain that the current molecular descriptors capture all the relevant properties required for solubility prediction

A related motivation was that they desired to apply deep learning methods directly to the molecular graph, which in general, is of variable size compared to fixed length representations (fingerprints or descriptor sets). It’s an interesting approach and you can read the paper for more details, but a few things caught my eye:

  • The motivation for the DAG based structure description didn’t seem very robust. Shouldn’t a learned representation be discoverable from a set of real-valued molecular descriptors (or even fingerprints)? While it is possible that all the physical aspects of aquous solubility may not be captured in the current repetoire of molecular descriptors, I’d think that most aspects are. Certainly some characterizations may be too time consuming (QM descriptors) for a cheminformatics setting.
  • The results are not impressive, compared to pre-existing model for the datasets they used. This is all the more surprising given that the method is actually an ensemble of RNN’s. For example, in Table 2 the best RNN model has an R2 of 0.92 versus 0.91 for the pre-existing model (a 2D kernel). But R2 is usually a good metric for non-linear regression. But even the RMSE is only 0.03 units better than the pre-existing model.However, it is certainly true that the unsupervised nature of the representation learning step is quite attractive – this is evident in the case of the intrinsic solubility dataset, where they achieve similar results to the prior model. But the prior model employed a manually selected set of topological descriptors.
  • It would’ve been very interesting to look at the transferabilty of the learned representation by using it to predict another physical property unrelated (at least directly) to solubility.

One characteristic of deep learning methods is that they work better when provided a lot of training data. With the exception of the Huuskonen dataset (4000 molecules), none of the datasets used were very large. If training set size is really an issue, the Burnham solubility dataset with 57K observations would have been a good benchmark.

Overall, I don’t think the actual predictions are too impressive using this approach. But the more important aspect of the paper is the ability to learn an internal representation in an unsupervised manner and the promise of transferability of such a representation. In a way, it’d be interesting to see what an abstract representation of a molecule could be like, analogous to what a deep network thinks a cat looks like.

Written by Rajarshi Guha

July 2nd, 2013 at 2:41 am