Student Perspectives: Density Ratio Estimation with Missing Data

A post by Josh Givens, PhD student on the Compass programme.

Density ratio estimation is a highly useful field of mathematics with many applications.  This post describes my research undertaken alongside my supervisors Song Liu and Henry Reeve which aims to make density ratio estimation robust to missing data. This work was recently published in proceedings for AISTATS 2023.

Density Ratio Estimation


As the name suggests, density ratio estimation is simply the task of estimating the ratio between two probability densities. More precisely for two RVs (Random Variables) Z^0, Z^1 on some space \mathcal{Z} with probability density functions (PDFs) p_0, p_1 respectively, the density ratio is the function r^*:\mathcal{Z}\rightarrow\mathbb{R} defined by


Plot of the scaled density ratio alongside the PDFs for the two classes.

Density ratio estimation (DRE) is then the practice of using IID (independent and identically distributed) samples from Z^0 and Z^1 to estimate r^*. What makes DRE so useful is that it gives us a way to characterise the difference between these 2 classes of data using just 1 quantity, r^*.


The Density Ratio in Classification

We now give demonstrate this characterisability in the case of classification. To frame this as a classification problem define Y\sim\text{Bernoulli}(0.5) and Z by Z|Y=y\sim Z^{y}. The task of predicting Y given Z using some function \phi:\mathcal{Z}\rightarrow\{0,1\} is then our standard classification problem. In classification a common target is the Bayes Optimal Classifier, the classifier \phi^* which maximises \mathbb{P}(Y=\phi(Z)). We can write this classifier in terms of r^*  as we know that \phi^*(z)=\mathbb{I}\{\mathbb{P}(Y=1|Z=z)>0.5\} where \mathbb{I} is the indicator function. Then, by the total law of probability, we have


=\frac{p_1(z)\mathbb{P}(Y=1)}{p_1(z)\mathbb{P}(Y=1)+p_0(z)\mathbb{P}(Y=0)} =\frac{1}{1+\frac{1}{r}\frac{\mathbb{P}(Y=0)}{\mathbb{P}(Y=1)}}.

Hence to learn the Bayes optimal classifier it is sufficient to learn the density ratio and a constant. This pattern extends well beyond Bayes optimal classification to many other areas such as error controlled classification, GANs, importance sampling, covariate shift, and others.  Generally speaking, if you are in any situation where you need to characterise the difference between two classes of data, it’s likely that the density ratio will make an appearance.

Estimation Implementation – KLIEP

Now we have properly introduced and motivated DRE, we need to look at how we can go about performing it. We will focus on one popular method called KLIEP here but there are a many different methods out there (see Sugiyama et al 2012 for some additional examples.)

The intuition behind KLIEP is simple: as r^* \cdot p_0=p_1, if \hat r\cdot p_0 is “close” to p_1 then \hat r is a good estimate of r^*. To measure this notion of closeness KLIEP uses the KL (Kullback-Liebler) divergence which measures the distance between 2 probability distributions. We can now formulate our ideal KLIEP objective as follows:

\underset{r}{\text{min}}~ KL(p_1|p_0\cdot r)

\text{subject to:}~ \int_{\mathcal{Z}}r(z)p_0(z)\mathrm{d}z=1

where KL(p|p') represent the KL divergence from p to p'. The constraint  ensures that the right hand side of our KL divergence is indeed a PDF. From the definition of the KL-divergence we can rewrite the solution to this as \hat r:=\frac{\tilde r}{\mathbb{E}[r(X^0)]} where \tilde r is the solution to the unconstrained optimisation

\underset{r}{\text{min}}~\mathbb{E}[\log (r(Z^1))]-\log(\mathbb{E}[r(Z^0)]).

As this is now just an unconstrained optimisation over expectations of known transformations of Z^0, Z^1, we can approximate this using samples. Given samples z^0_1,\dotsc,z^0_n from Z_0 and samples z^1_1,\dotsc,z^1_n from Z_1 our estimate of the density ratio will be \hat r:=\left(\frac{1}{n}\sum_{i=1}^nr(z_i^0)\right)^{-1}\tilde r  where \tilde r solves

\underset{r}{\min}~ \frac{1}{n}\sum_{i=1}^n \log(r(z^1_i))-\log\left(\frac{1}{n}\sum_{i=1}^n r(z^0_i)\right).

Despite KLIEP being commonly used, up until now it has not been made robust to missing not at random data. This is what our research aims to do.

Missing Data

Suppose that instead of observing samples from Z, we observe samples from some corrupted version of Z, X. We assume that \mathbb{P}(\{X=\varnothing\}\cup \{X=Z\})=1 so that either X is missing or X takes the value of Z. We also assume that whether X is missing depends upon the value of Z. Specifically we assume \mathbb{P}(X=\varnothing|Z=z)=\varphi(z) with \varphi(z) not constant and refer to \varphi as the missingness function. This type of missingness is known as missing not at random (MNAR) and when dealt with improperly can lead to biased result. Some examples of MNAR data could be readings take from a medical instrument which is more likely to err when attempting to read extreme values or recording responses to a questionnaire where respondents may be more likely to not answer if the deem their response to be unfavourable. Note that while we do not see what the true response would be, we do at least get a response meaning that we know when an observation is missing.

Missing Data with DRE

We now go back to density ratio estimation in the case where instead of observing samples from  Z^0,Z^1  we observe samples from their corrupted versions X^0, X^1. We take their respective missingness functions to be \varphi_0, \varphi_1 and assume them to be known. Now let us look at what would happen if we implemented KLIEP with the data naively by simply filtering out the missing-values. In this case, the actual density ratio we would be estimating would be


and so we would get inaccurate estimates of the density ratio no matter how many samples are used to estimate it. The image below demonstrates this in the case were samples in class 1 are more likely to be missing when larger and class 0 has no missingness.

A plot of the density ratio using both the full data and only the observed part of the corrupted data

Our Solution

Our solution to this problem is to use importance weighting. Using relationships between the densities of X and Z we have that


As such we can re-write the KLIEP objective to keep our expectation estimation unbiased even when using these corrupted samples. This gives our modified objective which we call M-KLIEP as follows. Given samples x^0_1,\dotsc,x^0_n from X_0 and samples x^1_1,\dotsc,x^1_n from X_1 our estimate is \hat r=\left(\frac{1}{n}\sum_{i=1}^n\frac{\mathbb{I}\{x_i^0\neq\varnothing\}r(x_i^0)}{1-\varphi_o(x_i^o)}\right)^{-1}\tilde r where \tilde r solves


This objective will now target r^* even when used on MNAR data.

Application to Classification

We now apply our density ratio estimation on MNAR data to estimate the Bayes optimal classifier. Below shows a plot of samples alongside the true Bayes optimal classifier and estimated classifiers from the samples via our method M-KLIEP and a naive method CC-KLIEP which simply ignores missing points. Missing data points are faded out.

Faded points represent missing values. M-KLIEP represents our method, CC-KLIEP represents a Naive approach, BOC gives the Bayes optimal classifier

As we can see, due to not accounting for the MNAR nature of the data, CC-KLIEP underestimates the true number of class 1 samples in the top left region and therefore produces a worse classifier than our approach.

Additional Contributions

As well as this modified objective our paper provides the following additional contributions:

  • Theoretical finite sample bounds on the accuracy of our modified procedure.
  • Methods for learning the missingness functions \varphi_1,\varphi_0.
  • Expansions to partial missingness via a Naive-Bayes framework.
  • Downstream implementation of our method within Neyman-Pearson classification.
  • Adaptations to Neyman-Pearson classification itself making it robust to MNAR data.

For more details see our paper and corresponding github repository. If you have any questions on this work feel free to contact me at


Givens, J., Liu, S., & Reeve, H. W. J. (2023). Density ratio estimation and neyman pearson classification with missing data. In F. Ruiz, J. Dy, & J.-W. van de Meent (Eds.), Proceedings of the 26th international conference on artificial intelligence and statistics (Vol. 206, pp. 8645–8681). PMLR.
Sugiyama, M., Suzuki, T., & Kanamori, T. (2012). Density Ratio Estimation in Machine Learning. Cambridge University Press.

Compass at NeurIPS 2022

A post by Anthony Stephenson, Jack Simons, and Dan Ward, PhD students on the Compass programme.


Ant Stephenson, Jack Simons, and I (Dan Ward) had the pleasure of attending the 2022 Conference on Neural Information Processing Systems (NeurIPS), one of the largest machine learning conferences in the world. The conference was held in New Orleans, which gave us an opportunity to explore a lively city full of culture with delicious local cuisine. We thought we’d collaborate on a blog post together covering some of the highlights.

Memorable Talks

The conference had broad range of talks including technical presentations of research, applied projects, and discussions of the philosophical and ethical questions that arise in AI. To give a taste of some of the talks, we picked out some of our favourites below.

Noam Brown: Human Modelling and Strategic Reasoning in the Game of Diplomacy.

The Game of Diplomacy is a strategic board game invented in 1954. It’s unique feature, and of crucial importance of the game, is that players interact via natural language to form allegiances. Whilst AI has been successful in beating humans in many purely adversarial games (e.g. Chess, Go), this collaborative element poses unique challenges. Firstly, it isn’t obvious how to evaluate/devise strategies for collaboration/betrayal, especially in the self-play-based reinforcement learning paradigm. Secondly, as communication happens via natural language, the AI must be able to translate their strategic plan into text. This strange combination of problems lead to interesting and innovative solutions. Paper link here.

Geoffrey Hinton: The Forward-Forward Algorithm for Training Deep Neural Networks.

Among the great line-up of speakers was Professor Geoffrey Hinton, known for popularising backpropogation for deep neural networks. Inspired by producing a more biologically plausible algorithm for learning, he has proposed the ‘Forward-Forward’ algorithm which he claims can also explain the phenomena of sleep! Professor Geoffrey Hinton then went on to express his belief that using biologically-inspired hardware, so-called neuromorphic computing, may play a key role in advancing AI. The talk was certainly unconventional, but nevertheless entertaining. Paper link here.

David Chalmers: Could a Large Language Model be Conscious?

Amongst all the machine-learning experts was David Chalmers, a philosopher! There are important questions regarding the possibility that language models might be conscious. David Chalmers aimed to educate the machine-learning audience in attendance of how we can better think about these problems and re-phrase the questions that we’re asking. We concluded that these questions are, unsurprisingly, best left to philosophers!

Poster Sessions

Jack and Dan:

I (Dan), presented a poster of my work at the conference, on Robust Neural Posterior Estimation (paper link here). I was definitely surprised by the scale of the poster sessions, and the broad scope of all the work taking place. Below is some of the posters that me and Jack found interesting:

Contrastive Neural Ratio Estimation
Benjamin K. Miller · Christoph Weniger · Patrick Forré
Authors propose NRE-C which aims to generalise NRE-A (Hermans et al. (2019)) and NRE-B (Durkan et al. (2020)) into one method. NRE-C can recover both methods by taking their two introduced hyperparameters at certain limits. Paper link here.

Towards Reliable Simulation-Based Inference with Balanced Neural Ratio Estimation
Arnaud Delaunoy · Joeri Hermans · François Rozet · Antoine Wehenkel · Gilles Louppe
These authors also make a contribution to the field of neural ratio estimation in the simulation-based inference context. Authors propose the notion of a “balanced” classifier, which is a classifier in which the average output from the classifier over the positive data class plus the average output over the negative data class equals to 1. The authors argue that if one has a classifier is balanced then it will lead to more conservative posterior estimates, which is something which practitioners seek. To integrate this into an algorithm they suggest adding a penalisation term onto the standard logistic-loss which punishes classifiers as they become less balanced. Paper link here.

Training and Inference on Any-Order Autoregressive Models the Right Way
Andy Shih · Dorsa Sadigh · Stefano Ermon
A joint distribution can be decomposed into its univariate conditionals by the chain rule, although by doing so we implicitly choose an ordering in a model, which prevents arbitrary conditional inference. Any-order autoregressive models circumvent this generally by being trained such that all possible univariate conditionals are considered, but this leads to learning redundant information. The paper proposes a new method to train autoregressive models, using a subset of univariate conditionals that still supports arbitrary conditional inference. This research was also presented as a talk, but sadly we missed it!  Paper link here.


The poster sessions formed the bulk of the conference timetable, with 2 2-hour sessions per day, on Tuesday, Wednesday and Thursday. These were very busy, with many posters on a wide-range of topics and a large congregation of attendees. As a result, it was sometimes difficult to track down the subset of posters on material of particular interest and when this feat was achieved, on occasion it was still hard work to actually have a detailed conversation with the author(s). Nonetheless, it was interesting to see the how varied the subjects of the poster were and in addition get a feeling for “themes” of the conference: recurring, clearly in-vogue topics. Amongst the sea of posters, I did manage to find a number relating to GPs; of these, those I found most interesting were:

Posterior and Computational Uncertainty in Gaussian Processes:
Jonathan Wenger · Geoff Pleiss · Marvin Pförtner · Philipp Hennig · John Cunningham
Here the authors propose a way to naturally incorporate uncertainty introduced from the use of (iterative) GP approximation methods. Paper link here.

Sparse Gaussian Process Hyperparameters: Optimize or Integrate?
Vidhi Lalchand · Wessel Bruinsma · David Burt · Carl Edward Rasmussen
The authors attempt to integrate a fully-Bayesian inference procedure for sparse GPs, as an alternative to the commonly adopted approach of optimising the kernel hyperparameters by maximum likelihood estimation. Paper link here.

Log-Linear-Time Gaussian Processes Using Binary Tree Kernels:
Michael K. Cohen · Samuel Daulton · Michael A Osborne
The idea here feels a bit unorthodox; they use a “binary-tree” kernel which discretises the space, with quantization error determined by the number of leaves. This would seem to lose interpretability on the properties of the function prior (e.g. smoothness), but does appear to give empirical benefits in their experiments. Paper link here.


In addition to the main conference, on the Friday and Saturday at the end of the week there were a selection of workshops on a variety of sub-fields within machine learning. If you are fortunate enough for there to be a workshop dedicated to your research area, then they provide a space to gather people with research directly relevant to your own and facilitate helpful discussions and networking opportunities.


For me, the “Gaussian processes, spatiotemporal modeling and decision-making systems” workshop was the most useful part of the conference. It gave me the chance to speak to people working on interesting problems related to my own; discover the kind of directions they are heading in and lines of work they are contemplating. Additionally, I presented a poster during this workshop which allowed me to discuss my work with an audience well-versed on the topic and its possible significance.

The Big Easy

In addition to the actual conference, attending NeurIPS also gave us the opportunity to explore the city of New Orleans; aka The Big Easy. Upon arrival, we were immediately greeted in the airport by the sound of Louis Armstrong, a strong theme in the city, which features a park named after him. New ‘Awlins’ is well known for its jazz, but awareness of this fact does not necessarily prepare you for the sheer quantity, especially in the streets of the French Quarter, that awaits you. The real epicentre of jazz in the city is situated on Frenchmen street, on which a swathe of bars hosting nearly-nightly live music reside. We spent several evenings there, including one of particular note, where French president Emmanuel Macron suddenly appeared, trailed by an extensive retinue of blue-suited aides and bodyguards. Another street in New Orleans infamous for its nightlife is Bourbon street. Where Frenchmen street is focused on jazz, Bourbon street contains all manner of rowdy madness, assaulting your senses with noise, smells and sights as soon as you arrive. Both are necessary experiences when visiting The Big Easy.


All in all, the conference was a great opportunity to get a taste of the massive array of research that occurs in machine learning. We were all surprised by the scope of the research topics and talks, and enjoyed the opportunity to explore a new culture and city.

Student Perspectives: Spectral Clustering for Rapid Identification of Farm Strategies

A post by Dan Milner, PhD student on the Compass programme.

Image 1: Smallholder Farm – Yebelo, southern Ethiopia


This blog describes an approach being developed to deliver rapid classification of farmer strategies. The data comes from a survey conducted with two groups of smallholder farmers (see image 2), one group living in the Taita Hills area of southern Kenya and the other in Yebelo, southern Ethiopia. This work would not have been possible without the support of my supervisors James Hammond, from the International Livestock Research Institute (ILRI) (and developer of the Rural Household Multi Indicator Survey, RHoMIS, used in this research), as well as Andrew Dowsey, Levi Wolf and Kate Robson Brown from the University of Bristol.

Image 2: Measuring a Cows Heart Girth as Part of the Farm Surveys

Aims of the project

The goal of my PhD is to contribute a landscape approach to analysing agricultural systems. On-farm practices are an important part of an agricultural system and are one of the trilogy of components that make-up what Rizzo et al (2022) call ‘agricultural landscape dynamics’ – the other two components being Natural Resources and Landscape Patterns. To understand how a farm interacts with and responds to Natural Resources and Landscape Patterns it seems sensible to try and understand not just each farms inputs and outputs but its overall strategy and component practices. (more…)

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