Multi-state survival modeling of a Jira issues snapshot

Work items in a formal development process progress through a series of stages, e.g., starting at Open, perhaps moving to Withdrawn or Merged with another item, eventually reaching Development, and finishing at Done (with a few being Reopened, i.e., moving back to the start of the process).

This process can be modelled as a Markov chain, provided data on each stage of the process is available, for each work item; allowing values such as average time spent in each state and transition probabilities to be calculated.

The Jira issue/task/bug/etc tracking system has an option to generate a snapshot of the current status of work items in the system. The snapshot information on each item includes: start-date, current-state, time-in-state, date-of-snapshot.

If we assume that all work items pass through the same sequence of states, from Open to Done, then the snapshot contains enough information to build a multi-state survival model.

The key information is time-in-state, which can be used to calculate the date/time when an item transitioned from its previous state to its current state, providing a required link between all states.

How is a multi-state survival model better than creating a distinct survival model for each state?

The calculation of each state in a multi-state model takes into account information from the succeeding state, i.e., the time-in-state value in the succeeding state provides timing (from the Start state) on when a work item transitioned from its previous state. While this information could be added to each of the distinct models, it’s simpler to bundle everything together in one model.

A data analysis article by Robert Krasinski linked to the data used 🙂 The data does not include a description of the columns, but most of the names appear self-explanatory (I have no idea what key might be). Each of the 3,761 rows includes a story-point estimate, team-id, and a tag name for the work item.

Building a multi-state model provides a means for estimating the impact of team-id and story-points on time-in-state. I would expect items with higher story-point estimates to spend longer in Development, but I’m not sure how much difference there will be on other states.

I pruned the 22 states present in the data down to the following sequence of 13. Items might be Withdrawn or Merged with others items at any time, but I’m keeping things simple. These two states should also be absorbing in that there is no exit from them, I faked this by adding a transition to Done.

           Open
           Withdrawn
           Merged
           Backlog
           In Analysis
           In Refinement
           Ready for Development
           In Development
           Code Review
           Ready for Test
           In Testing
           Ready for Signoff
           Done

I’m familiar with building survival models, but have only ever built a couple of multi-state survival models. R supports several packages, which is the best one to use for this minimalist multi-state dataset?

The msm package is very much into state transition probabilities, or at least that is the impression I got from reading its manual. flexsurv and mstate are other packages I looked at. I decided to stay with the survival package, the default for simpler problems; the manuals contained lots of examples and some of them appeared similar to my problem.

Each row of work item information in the Jira snapshot looks something like the following:

 X daysInStatus      start         status    obsdate
 1         0.53 2020-05-12 In Development 2020-05-18

This work item transitioned from state Ready for Development at time obsdate-start-daysInStatus to state In Development at time obsdate-start-daysInStatus+10^{-3}, and was still in state In Development at time obsdate-start (when the snapshot was taken); the 10^{-3} is a small interval used to separate the states.

As is often the case with R packages, most of the work went into figuring out how to call the library functions with the data formatted just so, plus of course my own misunderstandings. Once the data was cleaned and process, the analysis was one line of code plus one to print the results; for instance, to estimate the mean time in each state by story-point value (code+data):

  sp_fit=survfit(Surv(tstop-tstart, state) ~ sp, data=merged_status)
  print(sp_fit)

Given the uncertainties in this model building process, I’m not going to discuss the results. This post is a proof of concept, which others can apply when the sequence of states is known with some degree of confidence, and good reasons for noise in the data are available.

Including natural language text topics in a regression model

The implementation records for a project sometimes include a brief description of each task implemented. There will be some degree of similarity between the implementation of some tasks. Is it possible to calculate the degree of similarity between tasks from the text in the task descriptions?

Over the years, various approaches to measuring document similarity have been proposed (more than you probably want to know about natural language processing).

One of the oldest, simplest and widely used technique is term frequency–inverse document frequency (tf-idf), which is based on counting word frequencies, i.e., is word context is ignored. This technique can work well when there are a sufficient number of words to ensure a good enough overlap between similar documents.

When the description consists of a sentence or two (i.e., a summary), the problem becomes one of sentence similarity, not document similarity (so tf-idf is unlikely to be of any use).

Word context, in a sentence, underpins the word embedding approach, which represents a word by an n-dimensional vector calculated from the local sentence context in which the word occurs (derived from a large amount of text). Words that are closer, in this vector space, are expected to have similar meanings. One technique for calculating the similarity between sentences is to compare the averages of the word embedding of the words they contain. However, care is needed; words appearing in the same context can create sentences having different meanings, as in the following (calculated sentence similarity in the comments):

import spacy
nlp=spacy.load("en_core_web_md") # _md model needed for word vectors
nlp("the screen is black").similarity(nlp("the screen is white"))
# 0.9768339369182919  # closer to 1 the more similar the sentences
nlp("implementing widgets would be little effort").similarity(nlp("implementing widgets would be a huge effort"))
# 0.9636533803238744
nlp("the screen is black").similarity(nlp("implementing widgets would be a huge effort"))
# 0.6596892830922606

The first pair of sentences are similar in that they are about the characteristics of an object (i.e., its colour), while the second pair are similar in that are about the quantity of something (i.e., implementation effort), and the third pair are not that similar.

The words in a document, or summary, are about some collection of topics. A set of related documents are likely to contain a discussion of a set of related topics in varying degrees. Latent Dirichlet allocation (LDA) is a widely used technique for calculating a set of (unseen) topics from a set of documents and their contained words.

A recent paper attempted to estimate task effort based on the similarity of the task descriptions (using tf-idf). My last semi-serious attempt to extract useful information from text, some years ago, was a miserable failure (it’s a very hard problem). Perhaps better techniques and tools are now available for me to leverage (my interest is in understanding what is going on, not making predictions).

My initial idea was to extract topics from task data, and then try to add these to regression models of task effort estimation, to see what impact they had. Searching to find out what researchers have recently been doing in this area, I was pleased to see that others were ahead of me, and had implemented R packages to do the heavy lifting, in particular:

  • The stm package supports the creation of Structural Topic Models; these add support for covariates to influence the process of fitting LDA models, i.e., a correlation between the topics and other variables in the data. Uses of STM appear to be oriented towards teasing out differences in topics associated with different values of some variable (e.g., political party), and the package authors have written papers analysing political data.
  • The psychtm package supports what the authors call supervised latent Dirichlet allocation with covariates (SLDAX). This handles all the details needed to include the extracted LDA topics in a regression model; exactly what I was after. The user interface and documentation for this package is not as polished as the stm package, but the code held together as I fumbled my way through.

To experiment using these two packages I used the SiP dataset, which includes summary text for each task, and I have previously analysed the estimation task data.

The stm package:

The textProcessor function handles all the details of converting a vector of strings (e.g., summary text) to internal form (i.e., handling conversion to lower case, removing stop words, stemming, etc).

One of the input variables to the LDA process is the number of topics to use. Picking this value is something of a black art, and various functions are available for calculating and displaying concepts such as topic semantic coherence and exclusivity, the most commonly used words associated with a topic, and the documents in which these topics occur. Deciding the extent to which 10 or 15 topics produced the best results (values that sounded like a good idea to me) required domain knowledge that I did not have. The plot below shows the extent to which the words in topic 5 were associated with the Category column having the value “Development” or “Management” (code+data):

Distribution of words contained in topics associated with Development and Management.

The psychtm package:

The prep_docs function is not as polished as the equivalent stm function, but the package’s first release was just last year.

After the data has been prepared, the call to fit a regression model that includes the LDA extracted topics is straightforward:

sip_topic_mod=gibbs_sldax(log(HoursActual) ~ log(HoursEstimate), data = cl_info,
                         docs = docs_vocab$documents, model = "sldax",
                         K = 10 # number of topics)

where: log(HoursActual) ~ log(HoursEstimate) is the simplest model fitted in the original analysis.

The fitted model had the form: HoursActual approx HoursEstimate^{0.81} e^{0.13 topic_1} e^{0.18 topic_2}..., with the calculated coefficient for some topics not being significant. The value 0.81 is close to that fitted in the original model. The value of topic_i is the fraction of the topic_i calculated to be present in the Summary text of the corresponding task.

I’m please to see that a regression model can be improved by adding topics derived from the Summary text.

The SiP data includes other information such as work Category (e.g., development, management), ProjectCode and DeveloperId. It is to be expected that these factors will have some impact on the words appearing in a task Summary, and hence the topics (the stm analysis showed this effect for Category).

When the model formula is changed to: log(HoursActual) ~ log(HoursEstimate)+ProjectCode, the quality of fit for most topics became very poor. Is this because ProjectCode and topics conveyed very similar information, or did I need to be more sophisticated when extracting topic models? This needs further investigation.

Can topic models be used to build prediction models?

Summary text can only be used to make predictions if it is available before the event being predicted, e.g., available before a task is completed and the actual effort is known. My interest in model building is to understand the processes involved, so I am not worried about when the text was created.

My own habit is to update, or even create Summary text once a task is complete. I asked Stephen Cullen, my co-author on the original analysis and author of many of the Summary texts, about the process of creating the SiP Summary sentences. His reply was that the Summary field was an active document that was updated over time. I suspect the same is true for many task descriptions.

Not all estimation data includes as much information as the SiP dataset. If Summary text is one of the few pieces of information available, it may be possible to use it as a proxy for missing columns.

Perhaps it is possible to extract information from the SiP Summary text that is not also contained in the other recorded information. Having been successful this far, I will continue to investigate.

Another nail for the coffin of past effort estimation research

Programs are built from lines of code written by programmers. Lines of code played a starring role in many early effort estimation techniques (section 5.3.1 of my book). Why would anybody think that it was even possible to accurately estimate the number of lines of code needed to implement a library/program, let alone use it for estimating effort?

Until recently, say up to the early 1990s, there were lots of different computer systems, some with multiple (incompatible’ish) operating systems, almost non-existent selection of non-vendor supplied libraries/packages, and programs providing more-or-less the same functionality were written more-or-less from scratch by different people/teams. People knew people who had done it before, or even done it before themselves, so information on lines of code was available.

The numeric values for the parameters appearing in models were obtained by fitting data on recorded effort and lines needed to implement various programs (63 sets of values, one for each of the 63 programs in the case of COCOMO).

How accurate is estimated lines of code likely to be (this estimate will be plugged into a model fitted using actual lines of code)?

I’m not asking about the accuracy of effort estimates calculated using techniques based on lines of code; studies repeatedly show very poor accuracy.

There is data showing that different people implement the same functionality with programs containing a wide range of number of lines of code, e.g., the 3n+1 problem.

I recently discovered, tucked away in a dataset I had previously analyzed, developer estimates of the number of lines of code they expected to add/modify/delete to implement some functionality, along with the actuals.

The following plot shows estimated added+modified lines of code against actual, for 2,692 tasks. The fitted regression line, in red, is: Actual = 5.9Estimated^{0.72} (the standard error on the exponent is pm 0.02), the green line shows Actual==Estimated (code+data):

Estimated and actual lines of code added+modified to implement a task.

The fitted red line, for lines of code, shows the pattern commonly seen with effort estimation, i.e., underestimating small values and over estimating large values; but there is a much wider spread of actuals, and the cross-over point is much further up (if estimates below 50-lines are excluded, the exponent increases to 0.92, and the intercept decreases to 2, and the line shifts a bit.). The vertical river of actuals either side of the 10-LOC estimate looks very odd (estimating such small values happen when people estimate everything).

My article pointing out that software effort estimation is mostly fake research has been widely read (it appears in the first three results returned by a Google search on software fake research). The early researchers did some real research to build these models, but later researchers have been blindly following the early ‘prophets’ (i.e., later research is fake).

Lines of code probably does have an impact on effort, but estimating lines of code is a fool’s errand, and plugging estimates into models built from actuals is just crazy.