Non-technical challenges of medical NLP research

Machine learning has recently made a lot of headlines in healthcare applications, like identifying tumors from images, or technology for personalized treatment. In this post, I describe my experiences as a healthcare ML researcher: the difficulties in doing research in this field, as well as reasons for optimism.

My research group focuses on applications of NLP to healthcare. For a year or two, I was involved in a number of projects in this area (specifically, detecting dementia through speech). From my own projects and from talking to others in my research group, I noticed that a few recurring difficulties frequently came up in healthcare NLP research — things that rarely occurred in other branches of ML. These are non-technical challenges that take up time and impede progress, and generally considered not very interesting to solve. I’ll give some examples of what I mean.

Collecting datasets is hard. Any time you want to do anything involving patient data, you have to undergo a lengthy ethics approval process. Even with something as innocent as an anonymous online questionnaire, there is a mandatory review by an ethics board before the experiment is allowed to proceed. As a result, most datasets in healthcare ML are small: a few dozen patient samples is common, and you’re lucky to have more than a hundred samples to work with. This is tiny compared to other areas of ML where you can easily find thousands of samples.

In my master’s research project, where I studied dementia detection from speech, the largest available corpus had about 300 patients, and other corpora had less than 100. This constrained the types of experiments that were possible. Prior work in this area used a lot of feature engineering approaches, because it was commonly believed that you needed at least a few thousand examples to do deep learning. With less data than that, deep learning would just learn to overfit.

Even after the data has been collected, it is difficult to share with others. This is again due to the conservative ethics processes required to share data. Data transfer agreements need to be reviewed and signed, and in some cases, data must remain physically on servers in a particular hospital. Researchers rarely open-source their code along with the paper, since there’s no point of doing so without giving access to the data; this makes it hard to reproduce any experimental results.

Medical data is messy. Data access issues aside, healthcare NLP has some of the messiest datasets in machine learning. Many datasets in ML are carefully constructed and annotated for the purpose of research, but this is not the case for medical data. Instead, data comes from real patients and hospitals, which are full of shorthand abbreviations of medical terms written by doctors, which mean different things depending on context. Unsurprisingly, many NLP techniques fail to work. Missing values and otherwise unreliable data are common, so a lot of not-so-glamorous data preprocessing is often needed.

I’ve so far painted a bleak picture of medical NLP, but I don’t want to give off such a negative image of my field. In the second part of this post, I give some counter-arguments to the above points as well as some of the positive aspects of research.

On difficulties in data access. There are good reasons for caution — patient data is sensitive and real people can be harmed if the data falls into the wrong hands. Even after removing personally identifiable information, there’s still a risk of a malicious actor deanonymizing the data and extracting information that’s not intended to be made public.

The situation is improving though. The community recognizes the need to share clinical data, to strike a balance between protecting patient privacy and allowing research. There have been efforts like the relatively open MIMIC critical care database to promote more collaborative research.

On small / messy datasets. With every challenge, there comes an opportunity. In fact, my own master’s research was driven by lack of data. I was trying to extend dementia detection to Chinese, but there wasn’t much data available. So I proposed a way to transfer knowledge from the much larger English dataset to Chinese, and got a conference paper and a master’s thesis from it. If it wasn’t for lack of data, then you could’ve just taken the existing algorithm and applied it to Chinese, which wouldn’t be as interesting.

Also, deep learning in NLP has recently gotten a lot better at learning from small datasets. Other research groups have had some success on the same dementia detection task using deep learning. With new papers every week on few-shot learning, one-shot learning, transfer learning, etc, small datasets may not be too much of a limitation.

Same applies to messy data, missing values, label leakage, etc. I’ll refer to this survey paper for the details, but the take-away is that these shouldn’t be thought of as barriers, but as opportunities to make a research contribution.

In summary, as a healthcare NLP researcher, you have to deal with difficulties that other machine learning researchers don’t have. However, you also have the unique opportunity to use your abilities to help sick and vulnerable people. For many people, this is an important consideration — if this is something you care deeply about, then maybe medical NLP research is right for you.

Thanks to Elaine Y. and Chloe P. for their comments on drafts of this post.

Learning the Teochew (Chaozhou) Dialect

Lately I’ve been learning my girlfriend’s dialect of Chinese, called the Teochew dialect.  Teochew is spoken in the eastern part of the Guangdong province by about 15 million people, including the cities of Chaozhou, Shantou, and Jieyang. It is part of the Min Nan (闽南) branch of Chinese languages.

Above: Map of major dialect groups of Chinese, with Teochew circled. Teochew is part of the Min branch of Chinese. Source: Wikipedia.

Although the different varieties of Chinese are usually refer to as “dialects”, linguists consider them different languages as they are not mutually intelligible. Teochew is not intelligible to either Mandarin or Cantonese speakers. Teochew and Mandarin diverged about 2000 years ago, so today they are about as similar as French is to Portuguese. Interestingly, linguists claim that Teochew is one of the most conservative Chinese dialects, preserving many archaic words and features from Old Chinese.

Above: Sample of Teochew speech from entrepreneur Li Ka-shing.

Since I like learning languages, naturally I started learning my girlfriend’s native tongue soon after we started dating. It helped that I spoke Mandarin, but Teochew is not close enough to simply pick up by osmosis, it still requires deliberate study. Compared to other languages I’ve learned, Teochew is challenging because very few people try to learn it as a foreign language, thus there are few language-learning resources for it.

Writing System

The first hurdle is that Teochew is primarily spoken, not written, and does not have a standard writing system. This is the case with most Chinese dialects. Almost all Teochews are bilingual in Standard Chinese, which they are taught in school to read and write.

Sometimes people try to write Teochew using Chinese characters by finding the equivalent Standard Chinese cognates, but there are many dialectal words which don’t have any Mandarin equivalent. In these cases, you can invent new characters or substitute similar sounding characters, but there’s no standard way of doing this.

Still, I needed a way to write Teochew, to take notes on new vocabulary and grammar. At first, I used IPA, but as I became more familiar with the language, I devised my own romanization system that captured the sound differences.

Cognates with Mandarin

Knowing Mandarin was very helpful for learning Teochew, since there are lots of cognates. Some cognates are obviously recognizable:

• Teochew: kai shim, happy. Cognate to Mandarin: kai xin, 开心.
• Teochew: ing ui, because. Cognate to Mandarin: ying wei, 因为

Some words have cognates in Mandarin, but mean something slightly different, or aren’t commonly used:

• Teochew: ou, black. Cognate to Mandarin: wu, 乌 (dark). The usual Mandarin word is hei, 黑 (black).
• Teochew: dze: book. Cognate to Mandarin: ce, 册 (booklet). The usual Mandarin word is shu, 书 (book).

Sometimes, a word has a cognate in Mandarin, but sound quite different due to centuries of sound change:

• Teochew: hak hau, school. Cognate to Mandarin: xue xiao, 学校.
• Teochew: de, pig. Cognate to Mandarin: zhu, 猪.
• Teochew: dung: center. Cognate to Mandarin: zhong, 中.

In the last two examples, we see a fairly common sound change, where a dental stop initial (d- and t-) in Teochew corresponds to an affricate (zh- or ch-) in Mandarin. It’s not usually enough to guess the word, but serves as a useful memory aid.

Finally, a lot of dialectal Teochew words (I’d estimate about 30%) don’t have any recognizable cognate in Mandarin. Examples:

• da bo: man
• no gya: child
• ge lai: home

Grammatical Differences

Generally, I found Teochew grammar to be fairly similar to Mandarin, with only minor differences. Most grammatical constructions can transfer cognate by cognate and still make sense in the other language.

One significant difference in Teochew is the many fused negation markers. Here, a syllable starts with the initial b- or m- joined with a final to negate something. Some examples:

• bo: not have
• boi: will not
• bue: not yet
• mm: not
• mai: not want
• ming: not have to

Phonology and Tone Sandhi

The sound structure of Teochew is not too different from Mandarin, and I didn’t find it difficult to pronounce. The biggest difference is that syllables may end with a stop: -t, -k, -p, and -m, whereas Mandarin syllables can only end with a vowel or nasal. The characteristic of a Teochew accent in Mandarin is replacing /f/ with /h/, and indeed there is no /f/ sound in Teochew.

The hardest part of learning Teochew for me were the tones. Teochew has either six or eight tones depending on how you count them, which isn’t difficult to produce in isolation. However, Teochew has a complex system of tone sandhi rules, where the tone of each syllable changes depending on the tone of the following syllable. Mandarin has tone sandhi to some extent (for example, the third tone sandhi rule where nǐ + hǎo is pronounced níhǎo rather than nǐhǎo). But Teochew takes this to a whole new level, where nearly every syllable undergoes contextual tone change.

Some examples (the numbers are Chao tone numerals, with 1 meaning lowest and 5 meaning highest tone):

• gu5: cow
• gu1 nek5: beef

Another example, where a falling tone changes to a rising tone:

• seng52: to play
• seng35 iu3 hi1: to play a game

There are tables of tone sandhi rules describing in detail how each tone gets converted to what other tone, but this process is not entirely regular and there are exceptions. As a result, I frequently get the tone wrong by mistake.

Resources for Learning Teochew

Teochew is seldom studied as a foreign language, so there aren’t many language learning resources for it. Even dictionaries are hard to find. One helpful dictionary is Wiktionary, which has the Teochew pronunciation for most Chinese characters.

Also helpful were formal linguistic grammars:

1. Xu, Huiling. “Aspects of Chaoshan grammar: A synchronic description of the Jieyang dialect.” Monograph Series Journal of Chinese Linguistics 22 (2007).
2. Yeo, Pamela Yu Hui. “A sketch grammar of Singapore Teochew.” (2011).

The first is a massively detailed, 300-page description of Teochew grammar, while the second is a shorter grammar sketch on a similar variety spoken in Singapore. They require some linguistics background to read. Of course, the best resource is my girlfriend, a native speaker of Teochew.

Visiting the Chaoshan Region

After practicing my Teochew for a few months with my girlfriend, we paid a visit to her hometown and relatives in the Chaoshan region. More specifically, Raoping County located on the border between Guangdong and Fujian provinces.

Left: Chaoshan railway station, China. Right: Me learning the Gongfu tea ceremony, an essential aspect of Teochew culture.

Teochew people are traditional and family oriented, very much unlike the individualistic Western values that I’m used to. In Raoping and Guangzhou, we attended large family gatherings in the afternoon, chatting and gossiping while drinking tea. Although they are still Han Chinese, the Teochew consider themselves a distinct subgroup within Chinese, with their unique culture and language. The Teochew are especially proud of their language, which they consider to be extremely hard for outsiders to learn. Essentially, speaking Teochew is what separates “ga gi nang” (roughly translated as “our people”) from the countless other Chinese.

My Teochew is not great. Sometimes I struggle to get the tones right and make myself understood. But at a large family gathering, a relative asked me why I was learning Teochew, and I was able to reply, albeit with a Mandarin accent: “I want to learn Teochew so that I can be part of your family”.

Above: Me, Elaine, and her grandfather, on a quiet early morning excursion to visit the sea. Raoping County, Guangdong Province, China.

Thanks to my girlfriend Elaine Ye for helping me write this post. Elaine is fluent in Teochew, Mandarin, Cantonese, and English.

Clustering Autoencoders: Comparing DEC and DCN

Deep autoencoders are a good way to learn representations and structure from unlabelled data. There are many variations, but the main idea is simple: the network consists of an encoder, which converts the input into a low-dimensional latent vector, and a decoder, which reconstructs the original input. Then, the latent vector captures the most essential information in the input.

Above: Diagram of a simple autoencoder (Source)

One of the uses of autoencoders is to discover clusters of similar instances in an unlabelled dataset. In this post, we examine some ways of clustering with autoencoders. That is, we are given a dataset and K, the number of clusters, and need to find a low-dimensional representation that contains K clusters.

Problem with Naive Method

An naive and obvious solution is to take the autoencoder, and run K-means on the latent points generated by the encoder. The problem is that the autoencoder is only trained to reconstruct the input, with no constraints on the latent representation, and this may not produce a representation suitable for K-means clustering.

Above: Failure example with naive autoencoder clustering — K-means fails to find the appropriate clusters

Above is an example from one of my projects. The left diagram shows the hidden representation, and the four classes are generally well-separated. This representation is reasonable and the reconstruction error is low. However, when we run K-means (right), it fails spectacularly because the two latent dimensions are highly correlated.

Thus, our autoencoder can’t trivially be used for clustering. Fortunately, there’s been some research in clustering autoencoders; in this post, we study two main approaches: Deep Embedded Clustering (DEC), and Deep Clustering Network (DCN).

DEC: Deep Embedded Clustering

DEC was proposed by Xie et al. (2016), perhaps the first model to use deep autoencoders for clustering. The training consists of two stages. In the first stage, we initialize the autoencoder by training it the usual way, without clustering. In the second stage, we throw away the decoder, and refine the encoder to produce better clusters with a “cluster hardening” procedure.

Above: Diagram of DEC model (Xie et al., 2016)

Let’s examine the second stage in more detail. After training the autoencoder, we run K-means on the hidden layer to get the initial centroids $\{\mu_i\}_{i=1}^K$. The assumption is the initial cluster assignments are mostly correct, but we can still refine them to be more distinct and separated.

First, we soft-assign each latent point $z_i$ to the cluster centroids $\{\mu_i\}_{i=1}^K$ using the Student’s t-distribution as a kernel:

$q_{ij} = \frac{(1 + ||z_i - \mu_j||^2 / \alpha)^{-\frac{\alpha+1}{2}}}{\sum_{j'} (1 + ||z_i - \mu_{j'}||^2 / \alpha)^{-\frac{\alpha+1}{2}}}$

In the paper, they fix $\alpha=1$ (the degrees of freedom), so the above can be simplified to:

$q_{ij} = \frac{(1 + ||z_i - \mu_j||^2)^{-1}}{\sum_{j'} (1 + ||z_i - \mu_{j'}||^2)^{-1}}$

Next, we define an auxiliary distribution P by:

$p_{ij} = \frac{q_{ij}^2/f_j}{\sum_{j'} q_{ij'}^2 / f_{j'}}$

where $f_j = \sum_i q_{ij}$ is the soft cluster frequency of cluster j. Intuitively, squaring $q_{ij}$ draws the probability distribution closer to the centroids.

Above: The auxiliary distribution P is derived from Q, but more concentrated around the centroids

Finally, we define the objective to minimize as the KL divergence between the soft assignment distribution Q and the auxiliary distribution P:

$L = KL(P||Q) = \sum_i \sum_j p_{ij} \log \frac{p_{ij}}{q_{ij}}$

Using standard backpropagation and stochastic gradient descent, we can train the encoder to produce latent points $z_i$ to minimize the KL divergence L. We repeat this until the cluster assignments are stable.

DCN: Deep Clustering Network

DCN was proposed by Yang et al. (2017) at around the same time as DEC. Similar to DEC, it initializes the network by training the autoencoder to only reconstruct the input, and initialize K-means on the hidden representations. But unlike DEC, it then alternates between training the network and improving the clusters, using a joint loss function.

Above: Diagram of DCN model (Yang et al., 2017)

We define the optimization objective as a combination of reconstruction error (first term below) and clustering error (second term below). There’s a hyperparameter $\lambda$ to balance the two terms:

This function is complicated and difficult to optimize directly. Instead, we alternate between fixing the clusters while updating the network parameters, and fixing the network while updating the clusters. When we fix the clusters (centroid locations and point assignments), then the gradient of L with respect to the network parameters can be computed with backpropagation.

Next, when we fix the network parameters, we can update the cluster assignments and centroid locations. The paper uses a rolling average trick to update the centroids in an online manner, but I won’t go into the details here. The algorithm as presented in the paper looks like this:

Comparisons and Further Reading

To recap, DEC and DCN are both models to perform unsupervised clustering using deep autoencoders. When evaluated on MNIST clustering, their accuracy scores are comparable. For both models, the scores depend a lot on initialization and hyperparameters, so it’s hard to say which is better.

One theoretical disadvantage of DEC is that in the cluster refinement phase, there is no longer any reconstruction loss to force the representation to remain reasonable. So the theoretical global optimum can be achieved trivially by mapping every input to the zero vector, but this does not happen in practice when using SGD for optimization.

Recently, there have been lots of innovations in deep learning for clustering, which I won’t be covering in this post; the review papers by Min et al. (2018) and Aljalbout et al. (2018) provide a good overview of the topic. Still, DEC and DCN are strong baselines for the clustering task, which newer models are compared against.

References

1. Xie, Junyuan, Ross Girshick, and Ali Farhadi. “Unsupervised deep embedding for clustering analysis.” International conference on machine learning. 2016.
2. Yang, Bo, et al. “Towards k-means-friendly spaces: Simultaneous deep learning and clustering.” Proceedings of the 34th International Conference on Machine Learning-Volume 70. JMLR. org, 2017.
3. Min, Erxue, et al. “A survey of clustering with deep learning: From the perspective of network architecture.” IEEE Access 6 (2018): 39501-39514.
4. Aljalbout, Elie, et al. “Clustering with deep learning: Taxonomy and new methods.” arXiv preprint arXiv:1801.07648 (2018).

NAACL 2019, my first conference talk, and general impressions

Last week, I attended my first NLP conference, NAACL, which was held in Minneapolis. My paper was selected for a short talk of 12 minutes in length, plus 3 minutes for questions. I presented my research on dementia detection in Mandarin Chinese, which I did during my master’s.

My talk was recorded, but the organizers have not uploaded them yet, so I can’t share it right now. I’ll update this page with a link to the video when it’s ready.

Visiting Minneapolis

Going to conferences is a good way as a grad student to travel for free. Some of my friends balked at the idea of going to Minneapolis rather than somewhere more “interesting”. However, I had never been there before, and in the summer, Minneapolis was quite nice.

Minneapolis is very flat and good for biking — you can rent a bike for \$2 per 30 minutes. I took the light rail to Minnehaha falls (above) and biked along the Mississippi river to the city center. The downside is that compared to Toronto, the food choices are quite limited. The majority of restaurants serve American food (burgers, sandwiches, pasta, etc).

Meeting people

It’s often said that most of the value of a conference happens in the hallways, not in the scheduled talks (which you can often find on YouTube for free). For me, this was a good opportunity to finally meet some of my previous collaborators in person. Previously, we had only communicated via Skype and email. I also ran into people whose names I recognize from reading their papers, but had never seen in person.

Despite all the advances in video conferencing technology, nothing beats face-to-face interaction over lunch. There’s a reason why businesses spend so much money to send employees abroad to conduct their meetings.

Talks and posters

The accepted papers were split roughly 50-50 into talks and poster presentations. I preferred the poster format, because you get to have a 1-on-1 discussion with the author about their work, and ask clarifying questions.

Talks were a mixed bag — some were great, but for many it was difficult to make sense of anything. The most common problem was that speakers tended to dive into complex technical details, and lost sense of the “big picture”. The better talks spent a good chunk of time covering the background and motivation, with lots of examples, before describing their own contribution.

It’s difficult to make a coherent talk in only 12 minutes. A research paper is inherently a very narrow and focused contribution, while the audience come from all areas of NLP, and have probably never seen your problem before. The organizers tried to group talks into related topics like “Speech” or “Multilingual NLP”, but even then, the subfields of NLP are so diverse that two random papers had very little in common.

Research trends in NLP

Academia has a notorious reputation for inventing impractically complex models to squeeze out a 0.2% improvement on a benchmark. This may be true in some areas of ML, but it certainly wasn’t the case here. There was a lot of variety in the problems people were solving. Many papers worked with new datasets, and even those using existing datasets often proposed new tasks that weren’t considered before.

A lot of papers used similar model architectures, like some sort of Bi-LSTM with attention, perhaps with a CRF on top. None of it is directly comparable to one another because everybody is solving a different problem. I guess it shows the flexibility of Bi-LSTMs to be so widely applicable. For me, the papers that did something different (like applying quantum physics to NLP) really stood out.

Interestingly, many papers did experiments with BERT, which was presented at this conference! Last October, the BERT paper bypassed the usual conventions and announced their results without peer review, so the NLP community knew about it for a long time, but only now it’s officially presented at a conference.

Hypothesis testing for difference in Pearson / Spearman correlations

The Pearson and Spearman correlation coefficients measure how closely two variables are correlated. They’re useful as an evaluation metric in certain machine learning tasks, when you want the model to predict some kind of score, but the actual value of the score is arbitrary, and you only care that the model puts high-scoring items above low-scoring items.

An example of this is the STS-B task in the GLUE benchmark: the task is to rate pairs of sentences on how similar they are. The task is evaluated using Pearson and Spearman correlations against the human ground-truth. Now, if model A has Spearman correlation of 0.55 and model B has 0.51, how confident are you that model A is actually better?

Recently, the NLP research community has advocated for more significance testing (Dror et al., 2018): report a p-value when comparing two models, to distinguish between true improvements and fluctuations due to random chance. However, hypothesis testing is rarely done for Pearson and Spearman metrics — it’s not mentioned in the hitchhiker’s guide linked above, and not supported by the standard ML libraries in Python and R. In this post, I describe how to do significance testing for a difference in Pearson / Spearman correlations, and give some references to the statistics literature.

Definitions and properties

The Pearson correlation coefficient is defined by:

$r_{xy} = \frac{\sum_i^n (x_i - \bar{x}) (y_i - \bar{y})}{\sqrt{\sum_i^n (x_i - \bar{x})^2} \sqrt{\sum_i^n (y_i - \bar{y})^2}}$

The Spearman rank-order correlation is defined as the Pearson correlation between the ranks of the two variables, and measures the relative order between them. Both correlation coefficients range between -1 and 1.

Pearson’s correlation is simpler, has nicer statistical properties, and is default option in most software packages. However, de Winter et al. (2016) argues that Spearman’s correlation works better with non-normal data and is more robust to outliers, so is generally preferred over Pearson’s correlation.

Significance testing

Suppose we have the predictions of model A and model B, and we wish to compute a p-value for whether their Pearson / Spearman correlation coefficients are different. Start by computing the correlation coefficients for both models against the ground truth.

Then, apply the Fisher transformation to each correlation coefficient:

$z = \frac{1}{2} \log(\frac{1+r}{1-r})$

This transforms r which is between -1 and 1 into z, which ranges the whole real number line. It turns out that z is approximately normal, with nearly constant variance that only depends on N (the number of data points) and not on r.

For Pearson correlation, the standard deviation of the estimator $\hat r_p$ is given by:

$\mathrm{SD}(\hat r_p) = \sqrt{\frac{1}{N-3}}$

For Spearman rank-order correlation, the standard deviation of the estimator $\hat r_s$ is given by:

$\mathrm{SD}(\hat r_s) = \sqrt{\frac{1.060}{N-3}}$

Now, we can compute the p-value because the difference of the two z values follows a normal distribution with known variance.

R implementation

The following R function computes a p-value for the two-tailed hypothesis test, given a ground truth vector and two model output vectors:

cor_significance_test <- function(truth, x1, x2, method="pearson") {
n <- length(truth)
cor1 <- cor(truth, x1, method=method)
cor2 <- cor(truth, x2, method=method)
fisher1 <- 0.5*log((1+cor1)/(1-cor1))
fisher2 <- 0.5*log((1+cor2)/(1-cor2))
if(method == "pearson") {
expected_sd <- sqrt(1/(n-3))
}
else if(method == "spearman") {
expected_sd <- sqrt(1.060/(n-3))
}
2*(1-pnorm(abs(fisher1-fisher2), sd=expected_sd))
}


Naturally, the one-tailed p-value is half of the two-sided one.

For details of other similar computations involving Pearson and Spearman correlations (eg: confidence intervals, unpaired hypothesis tests), I recommend the Handbook of Parametric and Nonparametric Statistical Procedures (Sheskin, 2000).

Caveats and limitations

The formula for the Pearson correlation is solid and very accurate. For Spearman, the constant 1.060 has no theoretical backing and was rather derived experimentally by Fieller et al. (1957), by running simulations using variables from a bivariate normal distribution. Fieller claimed that the approximation was accurate for correlations between -0.8 and 0.8. Borkowf (2002) warns that this approximation may be off if the distribution is far from a bivariate normal.

The procedure here for Spearman correlation may not be appropriate if the correlation coefficient is very high (above 0.8) or if the data is not approximately normal. In that case, you might want to try permutation tests or bootstrapping methods — refer to Bishara and Hittner (2012) for a detailed discussion.

References

1. Dror, Rotem, et al. “The hitchhiker’s guide to testing statistical significance in natural language processing.” Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). Vol. 1. 2018.
2. de Winter, Joost CF, Samuel D. Gosling, and Jeff Potter. “Comparing the Pearson and Spearman correlation coefficients across distributions and sample sizes: A tutorial using simulations and empirical data.” Psychological methods 21.3 (2016): 273.
3. Sheskin, David J. “Parametric and nonparametric statistical procedures.” Chapman & Hall/CRC: Boca Raton, FL (2000).
4. Fieller, Edgar C., Herman O. Hartley, and Egon S. Pearson. “Tests for rank correlation coefficients. I.” Biometrika 44.3/4 (1957): 470-481.
5. Borkowf, Craig B. “Computing the nonnull asymptotic variance and the asymptotic relative efficiency of Spearman’s rank correlation.” Computational statistics & data analysis 39.3 (2002): 271-286.
6. Bishara, Anthony J., and James B. Hittner. “Testing the significance of a correlation with nonnormal data: comparison of Pearson, Spearman, transformation, and resampling approaches.” Psychological methods 17.3 (2012): 399.

Why Time Management in Grad School is Difficult

Graduate students are often stressed and overworked; a recent Nature report states that grad students are six times more likely to suffer from depression than the general population. Although there are many factors contributing to this, I suspect that a lot of it has to do with poor time management.

In this post, I will describe why time management in grad school is particularly difficult, and some strategies that I’ve found helpful as a grad student.

As a grad student, I’ve found time management to be far more difficult than either during my undergraduate years as well as working in the industry. Here are a few reasons why:

1. Loose supervision: as a grad student, you have a lot of freedom over how you spend your time. There are no set hours, and you can go a week or more without talking to your adviser. This can be both a blessing and a curse: some find the freedom liberating while others struggle to be productive. In contrast, in an industry job, you’re expected to report to daily standup, you get assigned tickets each sprint, so others essentially manage your time for you.
2. Few deadlines: grad school is different from undergrad in that you have a handful of “big” deadlines a year (eg: conference submission dates, major project due dates), whereas in undergrad, the deadlines (eg: assignments, midterms) are smaller and more frequent.
3. Sparse rewards: most of your experiments will fail. That’s the nature of research — if you know it’s going to work, then it’s no longer research. It’s hard to not get discouraged when you struggle for weeks without getting a positive result, and start procrastinating on a multitude of distractions.

Basically, poor time management leads to procrastination, stress, burnout, and generally having a bad time in grad school 😦

Some time management strategies that I’ve found to be useful:

1. Track your time. When I first started doing this, I was surprised at how much time I spent doing random, half-productive stuff not really related to my goals. It’s up to you how to do this — I keep a bunch of Excel spreadsheets, but some people use software like Asana.
2. Know your plan. My adviser suggested a hierarchical format with a long-term research agenda, medium-term goals (eg: submit a paper to ICML), and short-term tasks (eg: run X baseline on dataset Y). Then you know if you’re progressing towards your goals or merely doing stuff tangential to it.
3. Focus on the process, not the reward. It’s tempting to celebrate when your paper gets accepted — but the flip side is you’re going to be depressed if it gets rejected. Your research will have have many failures: paper rejections and experiments that somehow don’t work. Instead, celebrate when you finish the first draft of your paper; reward yourself when you finish implementing an algorithm, even if it fails to beat the baseline.

Here, I plotted my productive time allocation in the last 6 months:

Most interestingly, only a quarter of my time is spent coding or running experiments, which seems to be much less than most grad students. I read a lot of papers to try to avoid reinventing things that others have already done.

On average, I spend about 6 hours a day doing productive work (including weekends) — a quite reasonable workload of about 40-45 hours a week. Contrary to some perceptions, grad students don’t have to be stressed and overworked to be successful; allowing time for leisure and social activities is crucial in the long run.

MSc Thesis: Automatic Detection of Dementia in Mandarin Chinese

My master’s thesis is done! Read it here:

MSc Thesis (PDF)

Slides

Talk Slides (PDF)

Part of this thesis is replicated in my paper “Detecting dementia in Mandarin Chinese using transfer learning from a parallel corpus” which I will be presenting at NAACL 2019. However, the thesis contains more details and background information that were omitted in the paper.

Onwards to PhD!