Sunday, 25 December 2016

Making a dent in machine learning, or how to play a fast ball game


Neil Lawrence had an interesting observation about the current state of machine learning, and linked it to fast ball games:
“[…] the dynamics of the game will evolve. In the long run, the right way of playing football is to position yourself intelligently and to wait for the ball to come to you. You’ll need to run up and down a bit, either to respond to how the play is evolving or to get out of the way of the scrum when it looks like it might flatten you.”
Neil Lawrence is known for his work in Gaussian Processes and is a proponent of data efficiency. He used to be professor at University of Sheffield, is now with Amazon. Apparently the strategy works. The ball has come to him.

I once heard about a professor who said he would come to top conferences just to learn what others were busy doing and tried to do something else.

I also read somewhere from a top physicist that students who applied to work with him often expressed the wish to study shiny-and-clean fields. Some other fields were too messy and seemed unsexy. The professor insisted that the messy fields were exactly the best to work on.

In "Letters to a young scientist", Edward Osborne Wilson told his life story. He spent his entire life cataloging ants since childhood, right at the time where ant ecology wasn't a shiny field. He is considered as father of biodiversity.

Wonder what to do in deep learning now?

It is an extremely fast ball game with thousands of top players. You will be either crushed with ideas being stolen weekly, or out of steam pretty quickly.

It looks like most of the low hanging fruits have been picked.

Then ask yourself, what is your unique position? What are your strengths and advantages that people do not have? Can you move faster than others? It may be by having access to data, access to expertise in the neighborhood, or borrowing angles outside the field. Sometimes digging up old ideas is highly beneficial, too.

Alternatively, just calm down, and do boring-but-important stuffs. Important problems are like the goal areas in ball games. The ball will surely come.

30 years of a Swiss army knife: Restricted Boltzmann machines


I read somewhere, but cannot recall exactly who said so, that in ancient worlds, 30 years are long enough for the new generation to settle down with a new system, regime or ideology. As there are only a few days away from 2017, I would like to look back the history of a 30-year old model which has captured my research attention for the past 10 years.

To some of you, restricted Boltzmann machine (RBM) may be a familiar name, especially for those who follow the current deep learning literature since the beginning. But RBM has also passed its prime time, so you may have heard about it in passing.

I was attracted to RBM for several reasons. When I was studying conditional random fields in 2004 and was looking for a fast way to train with arbitrary structures, Contrastive Divergence (CD) appears to be an interesting one. While CD is a generic technique, it was derived especially for RBMs. Second, RBM has "Boltzmann" in the name, which is kind of interesting, because physicists are kind of sexy :)

Needless too say, another big reason is that RBM, together with its cousin, Autoencoder are building blocks of unsupervised deep nets, which started the current revolution -- deep learning.

The greatest reason is that I think RBM is one of the most important classes of data models known to date, perhaps comparable to PCA in dimensionality-reduction  and k-means in clustering in terms of usefulness.

First introduced in 1986 by  Paul Smolensky under the name Harmonium in a classic two-volume book known as PDP (Parallel Distributed Processing), co-edited by Rumelhart and McLelland. RBMs were subsequently popularised by Geoff Hinton in the 2000s, especially in 2001 with the introduction of Contrastive Divergence (CD), and  in 2006 with the introduction of a deep version known as Deep Belief Nets (DBN).

Statistically, RBM is a probabilistic model of data, i.e., it assigns a probability (or density) to a multivariate data. Initially, RBMs are limited to binary data (known as Bernoulli-Bernoulli RBM), but subsequently extended to Gaussian data (known as Gaussian-Bernoulli RBM), and mixed-types (known as Mixed-variate RBM, or Thurstonian Boltzmann machine).

Source: http://deeplearning.net/tutorial/_images/rbm.png

RBM is a special case of Boltzmann machine, which is in turn a special case of Markov random field. It has two layers, one for observed data, the other for latent representation. Due to its special bipartite structure, MCMC inference can be implemented in a block-wise fashion. Learning is relatively fast with CD or its Persistent version. Estimating of latent representation is very fast with a single matrix operation. RBM is also a powerful model in the sense that it can represent any distribution given enough hidden units. As a Markov random field, it has log-linear paramerization which makes it easy to incorporate a variety of domain knowledge.

With all of these advantages, RBMs have been used successfully in many applications, ranging from density modelling, feature extraction, dimensional reduction, clustering, topic modeling, imputation, classification, retrieval and anomaly detection.

Some bias selection of developments
  • 1986: first introduced as Harmonium.
  • 2001: fast approximate biased learning introduced as Contrastive Divergence (CD)
  • 2004: generalized Harmonium introduced
  • 2006: used successfully in Deep Belief Networks
  • 2007: demonstrated with great success on a very large-scale task within the Netflix challenge
  • 2007: temporal RBM
  • 2008: recurrent temporal RBM
  • 2008: classification RBM
  • 2008: persistent CD introduced, essentially another variant of Young's.
  • 2008: convolutional RBMs
  • 2008: universality property proved
  • 2009: topic models with Replicated Softmax
  • 2009: matrix modelling with non i.i.d. RBMs, ordinal data, semi-restricted RBM
  • 2009: implicit mixtures of RBMs
  • 2010: factored high-order RBM
  • 2010: mean-covariance RBM
  • 2010: rectifier linear units RBM
  • 2010: deep BM
  • 2011: mixed-variate RBM
  • 2012: a proper modeling of ordinal matrix data
  • 2013: Thurstonian BM for joint modeling of most known data types
  • 2013: nonnegative RBMs for parts-based representation
  • 2015: trained with graph priors, demonstrating better generalization
  • 2015: extended to tensor-objects
  • 2016: infinite RBM
In short, most of the work has been on extending the representational power of RBM to suit problem structures. The rest is about analysing theoretical properties of RBMs, making deep nets out of RBMs, and improving training speed & accuracy. For the past few years, research about RBMs has slowed down significantly, mostly because the superb accuracy of supervised deep nets, and the ease of deployment of deterministic nets on large-scale problems. 

Some of our own work

Thursday, 22 December 2016

Machine learning in three lines



How can we characterize machine learning as a field? What make machine learning work?

Machine learning is a fast changing field. The list of ideas is practically endless: Decision trees, ensemble learning, random forests, boosting, neural networks, hidden Markov models, graphical models, kernel methods, conditional random fields, sparsity, compressed sensing, budgeted learning, multi-kernel learning, transfer learning, co-training, active learning, multitask learning, deep learning, lifelong learning and many more.

The problem is, ideas come and go, and bounce back, roughly every 10-15 years. Long enough for a grad student learns the tricks, makes a big noise, graduates when it is still hot and gets a good academic job,  IF he is lucky to start early in the cycle. Also long enough so that the new batch of students are not aware of the hot things of the previous wave. How familiar is "particle filtering" to you?
Popular in the late 1990s and early 2000s, particle filtering is a fast way to generate samples of state for a dynamic system when an observation is made.
When I started my grad training in 2004, I asked one of my supervisors on what hot topic I should focus on. He said, pick either graphical models or kernel methods (which meant SVM at the time). I picked graphical models, and then was given conditional random fields (CRFs) to work on. By the time I submitted my PhD thesis in early 2008, CRFs were largely gone. SVMs were gone a couple of years before that, just around the time neural nets bounced back under a new umbrella, deep learning, in 2006. It used to be all about convex loss functions (SVMs & CRFs), now everything is non-convex. Local minima? Doesn't matter, adaptive stochastic gradient descents such as Adagrad, Adam or RMSprop will find a really good one for you.

Applying machine learning is like flying commercial aircraft

Ever wanted to apply a technique to your problem? A sure way is to employ a PhD in machine learning! Packages available, but what are the correct ways to use, let alone the best way? Think about flying commercial aircrafts. There are hundreds of knobs to tune. There are even autopilot mode. We just need to have two human pilots: one to tune the right knob at the right time, and the other making sure that the correct things are being done.

Wanna use deep learning? You need to decide between: feedforward, recurrent, convolutional nets and any combination of these three. Will attention be used? How about memory? Which loss function? Embedding size? Optimizers and their parameters? and many many more.

I work with clinicians on clinical problems. At least two of them -- young, smart and highly motivated -- insisted to come over and observe how I do machine learning and learn to do it themselves. They claimed they could do Statra, R and sometimes Python. My boss was crossed. This is not how collaboration should work, right? You want to learn our art for free, then trash us?

But I told the boss, let them come.

They came and left, even more puzzled. I ended up doing the job I usually did and so did they.

Machine learning in three lines

I once delivered an internal talk on deep learning. My boss requested that I talked only about three things. Just three things. This bugged me a lot. But the trick actually worked.

Here I am trying to characterize the current state of machine learning in general and it should apply to deep learning. Machine learning works by:
  1. Having good priors of the problem at hand (80-90% gain)
  2. Accounting for data uncertainty and model uncertainty with ensemble and Bayesian methods. (1-5% gain)
  3. Reusing models when data/model redundancies are available (5-10% gain)
Priors are king

By "good priors", I meant several things:
  • Features that capture all meaningful signals from data. Getting good features are the job of feature engineering, which usually accounts for 80-90% of total effort in a machine learning project. Once you have good features, most modern classifiers will work just fine. Deep learning succeed partly because it solves this problem.
  • Problem structures are respected. For example, sequential data would suggest the use of Hidden Markov Models (HMM) or chain-like Conditional Random Fields (CRF). In deep learning, it reduces to architecture engineering!
  • Knowledge about the model class. E.g., will linearity be the dominant model? What are the expected complexity and nonlinearity? Will interpretability needed? What is about transparency? Is sparsity important? For neural nets, how many layers?  For SVMs, will one kernel type be enough?
  • Assumptions about data manifold. One well-studied phenomenon is the intrinsic low dimensionality of data embedded in a very high dimensional space. This is usually manifested through data redundancies. Another assumption is separation of classes, e.g., the region at the class boundary is usually sparse, but is very dense near the class examplars. This assumption essentially gives rise to semi-supervised learning.
  • Assumptions about the data spaceHow many data instances? Will characterizing the data variance enough? If yes then use PCA. What about factors of variation are the key? If yes then RBM perhaps helps.
Don't forget uncertainty

Even with a good prior, we would never be sure that our choices are correct. Model uncertainty is there and must be accounted for. A popular way is to use many (diverse) models, then employ model averaging, ensemble methods and Bayesian approach. Deep learning has dropout as one of the best tricks invented in the past 10 years. It works like wonder. Bayesian neural nets, which were studied in mid 1990s, is also back!

In fact, every single modern challenge was won by some ensemble, mostly gradient boosting by the time of this writing AND model blending. One of the best known example is the Netflix challenge, which was won by blending hundreds of models -- so complex that Netflix found it was useless to implement in practice.

Many are easier than one

I often told my 5-year old daughter: do one thing at a time. But by listening to me AND playing at the same time, she has already multi-tasked. Humans seem to learn better that way. We learn by making senses of many co-occurring feedback signals.

A key idea in recent machine learning is model reuse. It has many forms:

  • Domain adaption, which is about reusing previous model on similar domains with minimal changes.
  • Transfer learning, which is about reusing models on similar tasks with minimal changes. In neural nets, it is equivalent to not forgetting the old trained nets when learning a new concepts.
  • Multi-task learning, which is about learning more than ones correlated tasks at a time. The idea is that models can be partly shared among tasks, leading to less training data and less overfitting.
  • Lifelong learning, which is like continual version of transfer learning. Just like humans, we learn to do new things from birth to death, every single day! Popularized by Sebastian Thrun in mid 1990s, lifelong learning is now back in various forms: never-ending learning at CMU, reinforce learning in robotics and games at a various labs.
  • Multi-X, where X is substituted by view, modality, instance, label, output/outcome, target, type and so on.

Tuesday, 20 December 2016

Everything old is new again: Nested sequential models


Recently, multi-layer RNN architectures have been demonstrated to work better than single-layer versions. The Google's Neural Machine Translation machine, for example, has 8 layers of LSTMs as of Dec 2016.

The idea goes back to earlier days of multi-layer HMMs in the 1990s, which are special cases of Dynamic Bayesian Networks. These were then followed by multi-layer Conditional Random Fields (CRFs), which are also special case of Dynamic CRFs.

The idea is that higher layers represent more abstract semantics. In temporal sequences, one would expect that the "clock" of the upper layers is slower than that of the lower layers. But most existing work has to explicitly design the temporal resolution by hand.

Learning the temporal resolution automatically is an attractive idea. In 1998, Hierarchical HMM was introduced, here parent state is assumed to generate a child sequence, and each child in turn generates a grandchild subsequence and so forth. The network becomes nested. Learning and inference cost cubic time, which is prohibitive for long sequences.

A CRF counterpart is known as Hierarchical Semi-Markov CRF introduced by us in 2008.

Both HHMMs and HSCRFs are member of the Stochastic Context-Free Grammar family, which is known for its cubic time complexity.  Not just being slow, HHMMs and HSCRFs are hopeless in large-scale tasks that require many bits to represent the world.

Given the recent successes of RNNs (mostly LSTM and GRU) for sequential tasks, one would naturally ask whether we can achieve the same feat as in HHMMs, that is, the hierarchy is learnt automatically from data. It proves to be a difficult task, until very recently. Check this paper by Bengio's group for more detail. I'm very curious to see how the idea plays out in practice. Let's wait and see.

Work by us:
  • Hierarchical semi-Markov conditional random fields for deep recursive sequential data, Truyen Tran, Dinh Phung, Hung Bui, Svetha Venkatesh,  Artificial Intelligence, 2017. (Extension of the NIPS'08 paper).
  • MCMC for Hierarchical Semi-Markov Conditional Random Fields, Truyen Tran, Dinh Q. Phung, Svetha Venkatesh and Hung H. Bui. In NIPS'09 Workshop on Deep Learning for Speech Recognition and Related Applications. December, 2009, Whistler, BC, Canada.
  • Hierarchical Semi-Markov Conditional Random Fields for Recursive Sequential Data, Truyen Tran, Dinh Q. Phung, Hung H. Bui, and Svetha Venkatesh. In Proc. of 21st Annual Conference on Neural Information Processing Systems, Dec 2008, Vancouver, Canada. 
  • AdaBoost.MRF: Boosted Markov random forests and application to multilevel activity recognition, Truyen Tran, Dinh Quoc Phung, Hung Hai Bui, and Svetha Venkatesh. In Proc. of  IEEE Conference on Computer Vision and Pattern Recognition, volume Volume 2, pages 1686-1693, New York, USA, June 2006.

Monday, 19 December 2016

Everything old is new again: Deep statistical relational learning


In the age of combinatorial innovation, old things will be given a new shiny face, even nothing really new happens. The same holds for Statistical Relation Learning (SRL) -- a sub-field of machine learning for characterizing the relational structure of the world.

Started in late 1990s, SRL had gone through a fruitful period of about 10 years and reached its peak in 2007 with the publication of a book titled "Introduction to Statistical Relational Learning" co-edited by Lise Getoor and the late Ben Taskar (who died unexpectedly in 2013 at the age of 36 at his academic peak). Many significant models appeared in the first half of the 2000s, including Conditional Random Fields (CRF, 2001), Relational Markov networks (2002) and Markov Logic Networks (2006). Despite being more powerful than non-relational alternatives, SRL still relies on manual feature engineering, which will soon reach its limit of utility.

Developed rather in parallel is Deep Learning (DL), where the current wave officially started in 2006 with the publication of Deep Belief Networks in Science. Deep learning is concerned about learning data abstraction (aka features), favoring end-to-end learning through multiple steps of non-linear computation.

A combinatorial thinking would naturally lead to the question whether these two sub-fields can work together. The answer is a big YES, because SRL and DL are rather complementary. For example, in the past 3 years, there have been lots of papers marrying CRF and deep nets. While CRFs offer a semi-formal framework for joint learning and inference, deep nets offer learning of features (with feedforward nets), deterministic dynamics (with recurrent nets), and translation invariance (with convolutional nets). The marriage would be a happy one. But like any marriage of convenience, it won't go very far. Some genuine blending is needed.

Our recent work,  Column Networks, scheduled to appear in AAAI'17, blends the SRL and DL even further so that learning and inference can be carried out naturally. The term "column" refers to the famous columnar structure of neo-cortex in mammals. Interestingly, Column Networks share design features of all three main deep net architectures:

  • A column is a feedfoward net,
  • Parameters are tied across layers, which is essentially the idea behind recurrent nets.
  • The network between columns is designed so that the multi-relations between columns are invariant across columns, hence the translation invariance property of convolutional nets.
As Column Networks are very generic, expect more to come in the next few months. Stay tuned.

Updated references

  • Column Networks for Collective Classification, T Pham, T Tran, D Phung, S Venkatesh, AAAI'17.
  • Graph-induced restricted Boltzmann machines for document modeling, Tu D. Nguyen, Truyen Tran, D. Phung, and S. Venkatesh, Information Sciences. doi: 10.1016/j.ins.2015.08.023
  • Neural Choice by Elimination via Highway Networks, Truyen Tran, Dinh Phung and Svetha Venkatesh,  PAKDD workshop on Biologically Inspired Techniques for Data Mining (BDM'16), April 19-22 2016, Auckland, NZ.
  • Predicting delays in software projects using networked classification, Morakot Choetikertikul, Hoa Khanh Dam, Truyen Tran, Aditya Ghose, 30th IEEE/ACM International Conference on Automated Software Engineering, November 9–13, 2015 Lincoln, Nebraska, USA.
  • Learning vector representation of medical objects via EMR-driven nonnegative restricted Boltzmann machines (e-NRBM), Truyen Tran, Tu D. Nguyen, D. Phung, and S. Venkatesh, Journal of Biomedical Informatics, 2015, pii: S1532-0464(15)00014-3. doi: 10.1016/j.jbi.2015.01.012. 
  • Cumulative Restricted Boltzmann Machines for Ordinal Matrix Data Analysis, Truyen Tran, Dinh Phung and Svetha Venkatesh, in Proc. of. the 4th Asian Conference on Machine Learning (ACML2012), Singapore, Nov 2012.
  • Ordinal Boltzmann Machines for Collaborative Filtering. Truyen Tran, Dinh Q. Phung and Svetha Venkatesh. In Proc. of 25th Conference on Uncertainty in Artificial Intelligence, June, 2009, Montreal, Canada. 
  • Hierarchical Semi-Markov Conditional Random Fields for Recursive Sequential Data, Truyen Tran, Dinh Q. Phung, Hung H. Bui, and Svetha Venkatesh. In Proc. of 21st Annual Conference on Neural Information Processing Systems, Dec 2008, Vancouver, Canada.
  • AdaBoost.MRF: Boosted Markov random forests and application to multilevel activity recognition, Truyen Tran, Dinh Quoc Phung, Hung Hai Bui, and Svetha Venkatesh. In Proc. of  IEEE Conference on Computer Vision and Pattern Recognition, volume Volume 2, pages 1686-1693, New York, USA, June 2006.

Machine learning four years after the turning point


In May 2012 I wrote a note titled "Machine at its turning point" to argue for the new wave of machine learning in that we do not need to worry about having a convex loss but rather be happy with non-convex ones. At the time I did not know about AlexNet and its record-breaking result on the ImageNet benchmark. It was published 7 months later in NIPS'12.

AlexNet was truely a turning point for machine learning. It declared the winning of deep neural nets over others, which were combination of clever manual feature engineering and some variants of SVMs or random forests. AlexNet is remarkable in many ways: Dropout, rectifier linear units, end-to-end training on massive data with GPUs, data augmentation and carefully designed convolutional nets.

It was the year that Yann LeCun posted his complaints about the computer vision community, but quickly retracted his boycott given the aftershock of AlexNet.

Recently, there has been an interesting comment floating around: In machine learning, we ask what we can do for neural networks, and in applied domains, we ask what can neural networks do for X. And the list of Xs keeps growing from cognitive domain to non-cognitive domains. Andrew Ng made an interesting point that for domains where humans can do well to map A to B in less than a second, it is ripe for machine automation.

This year also marks the 10th year after Deep Belief Nets, the model that announces the beginning of the current wave of neural nets. Early this year, AlhaGo of DeepMind defeated one of the best Go champions 4 to 1, officially ending the superiority of human on this ancient game. AlphaGo is a mixture of convolutional nets to read the board positions and evaluate the moves, and random tree-search moves.

Many things have changed since 2012. It is clear that supervised learning works if we have sufficient labels without pre-training. Unsupervised learning, after an initial burst with Boltzmann machines and Autoencoders, failed to deliver.  There are new interesting developments, however, with Variational Autoencoder (VAE) and Generative Adversarial Nets (GAN), both invented in 2014. At this point, GAN is the best technique to generate faithful images. It is considered by Yann LeCun as one of the best ideas in recent years.

The machine learning community has witnessed 10-15 year mini-cycles. Neural networks, graphical models, kernel methods, statistical relational learning and currently, deep learning. So what is up for deep learning? If we consider 2006 as the year of beginning of current deep learning, then it is already 10 years, enough for a mini-cycle. But if we consider 2012 as the true landmark, then we have 6 more years to count.

Like other methodologies, deep learning will eventually morph into something else in 5 years time. We may call it by other names. With programming becomes reasonably effortless and with the availability of powerful CPUs/GPUs designed specifically for deep learning, the low hanging fruits will soon be picked up.

Practice-wise, as feature engineering is an unsung hero of machine learning prior to 2012, architecture engineering is at the core of deep learning these days.

It is also time for the hardcores. Data efficiency, statistics, geometry, information theory, Bayesian and other "serious" topics. Like any major progresses in science and engineering, nothing really occurs over night. At this point, deep learning is already mixed with graphical models, planning, inference, symbolic reasoning, memory, execution, Bayesian among other things. All together, something fancy will happen, just like what I noted about Conditional Random Fields years ago, that it is the combination of incremental innovations that pushes the boundary of certain field to a critical point. It also concurs with the idea of emergence intelligence, where human intelligence is really the emerging product of many small advances over apes.

For a more comprehensive review, see my recent tutorials at AI'16 on the topic. Some incremental innovations were produced at PRaDA (Deakin University), listed below.

Work by us:
  • Multilevel Anomaly Detection for Mixed Data, K Do, T Tran, S Venkatesh, arXiv preprint arXiv: 1610.06249.
  • A deep learning model for estimating story points, M Choetkiertikul, HK Dam, T Tran, T Pham, A Ghose, T Menzies, arXiv preprint arXiv: 1609.00489
  • Deepr: A Convolutional Net for Medical Records, Phuoc Nguyen, Truyen Tran, Nilmini Wickramasinghe, Svetha Venkatesh, To appear in IEEE Journal of Biomedical and Health Informatics.
  • Column Networks for Collective Classification, T Pham, T Tran, D Phung, S Venkatesh, AAAI'17
  • DeepSoft: A vision for a deep model of software, Hoa Khanh Dam, Truyen Tran, John Grundy and Aditya Ghose, FSE VaR 2016.
  • Faster Training of Very Deep Networks Via p-Norm Gates, Trang Pham, Truyen Tran, Dinh Phung, Svetha Venkatesh, ICPR'16.
  • Hierarchical semi-Markov conditional random fields for deep recursive sequential data, Truyen Tran, Dinh Phung, Hung Bui, Svetha Venkatesh, To appear in Artificial Intelligence.
  • DeepCare: A Deep Dynamic Memory Model for Predictive Medicine, Trang Pham, Truyen Tran, Dinh Phung, Svetha Venkatesh, PAKDD'16, Auckland, NZ, April 2016. 
  • Neural Choice by Elimination via Highway Networks, Truyen Tran, Dinh Phung and Svetha Venkatesh,  PAKDD workshop on Biologically Inspired Techniques for Data Mining (BDM'16), April 19-22 2016, Auckland, NZ.
  • Tensor-variate Restricted Boltzmann Machines, Tu D. Nguyen, Truyen Tran, D. Phung, and S. Venkatesh, AAAI 2015
  • Thurstonian Boltzmann machines: Learning from multiple inequalities, Truyen Tran, D. Phung, and S. Venkatesh, In Proc. of 30th International Conference in Machine Learning (ICML’13), Atlanta, USA, June, 2013.

Model stability: Learn it many more times, but on different datasets


How often do you actually publish your data-derived models? Chances are you almost never do, if you are machine learning type. Only quite recently, when training a big deep net is very expensive, people start publishing models. And it helps people who come afterward significantly.

This is quite contrary to fields like medicine, where the models (often regression coefficients for a GLM) are routinely published. This is because in those fields, model is the actual finding, not the learning algorithm that produces it.

In a way, empirical sciences progress as new models are found, published and verified. One key requirement is that the models are reproducible. Empirical models, those derived from data,  must be stable across different datasets by different research groups to be accepted as a rule.

But this has not been well-respected in data-driven fields.

Anyone who use decision trees to derive a prediction rule from a reasonably complex data would experience a phenomenon that trees will differ drastically if you change just few data points. Unfortunately there have been many trees published in the medicine literature, probably because trees are highly interpretable. But I doubt that anyone could ever reproduce a tree from their own data.

At a recent "Big Data" conference I asked a bioinformatics professor why people keep publishing new "findings" of genes, which are supposed to cause or worsen a medical condition. The trouble is that different groups claim different subsets, many of which do not overlap at all. Needless to say, all of those findings are statistically significant, on their own dataset. The professor did not answer my question directly. She said people had different hypotheses and thus focused on those genes whey suspected. Sometimes, the biases or resource limitations prevent people from looking elsewhere.

For the past few years I have worked on deriving simple prediction rules for healthcare from high-dimensional data. The standard method of the day is sparsity-induced techniques such as Lasso. Every time I changed the data a little bit, either by changing some patients due to different selection criteria, or changing some features (there are endless possibilites), I would have a different feature subset and their coefficients with comparable predictive power!

For those who care, stability and sparsity are not the best friends. Sparse models are known to be unstable. Same as feature selection techniques.

Model instability is a daunting issue for empirical sciences (e.g., the so-called evidence-based medicine). There are two jobs that must be done. One is quantifying the instability. The other is deriving strategies to stabilize the estimation.

The first job has been studied to a great detail in the context of confidence interval estimation. For standard GLMs, the estimation is well-known, but as soon as sparsity comes into play, the job is much harder. A solution is simulation-based, a.k.a., the one-size-fit-all bootstrap. That is, for a dataset, resample it to obtain the new set of the same size, and re-estimate the model. Parameter confidence intervals can then be calculated from multiple estimates, says B times, where B is usually in the order of thousands. While this method is straightforward with modern computer, its theoretical properties still need further investigation.

The second job is much less studied. At PRaDA (Deakin University), we have attempted to solve the problem from several directions, and for several GLM instances such as logistic regression, ordinal regression and Cox's model. The main idea is to exploit the domain knowledge or statistics, so that the degree of freedom is limited. Some of the recent works are listed in the References below.

In subsequent posts, we will cover some specific techniques. Stay tuned.

Updated references

  • Preterm Birth Prediction: Deriving Stable and Interpretable Rules from High Dimensional Data,  Truyen Tran, Wei Luo, Dinh Phung, Jonathan Morris, Kristen Rickard, Svetha Venkatesh, Conference on Machine Learning in Healthcare, LA, USA Aug 2016.
  • Stabilizing Linear Prediction Models using Autoencoder, Shivapratap Gopakumara, Truyen Tran, Dinh Phung, Svetha Venkatesh, International Conference on Advanced Data Mining and Applications (ADMA 2016).
  • Stabilizing Sparse Cox Model using Statistic and Semantic Structures in Electronic Medical Records. Shivapratap Gopakumar, Tu Dinh Nguyen, Truyen Tran, Dinh Phung, and Svetha Venkatesh, PAKDD'15, HCM City, Vietnam, May 2015.
  • Stabilizing high-dimensional prediction models using feature graphs, Shivapratap Gopakumar, Truyen Tran, Tu Dinh Nguyen, Dinh Phung, and Svetha Venkatesh, IEEE Journal of Biomedical and Health Informatics, 2014 DOI:10.1109/JBHI.2014.2353031S 
  • Stabilizing sparse Cox model using clinical structures in electronic medical records, S Gopakumar, Truyen Tran, D Phung, S Venkatesh, 2nd International Workshop on Pattern Recognition for Healthcare Analytics, August 2014
  • Stabilized sparse ordinal regression for medical risk stratification, Truyen Tran, Dinh Phung, Wei Luo, and Svetha Venkatesh, Knowledge and Information Systems, 2014, DOI: 10.1007/s10115-014-0740-4.