The Sequence Memoizer

Probabilistic models of sequences play a central role in most machine translation, automated speech recognition, lossless compression, spell-checking, and gene identification applications to name but a few. Unfortunately, real-world sequence data often exhibit long range dependencies which can only be captured by computationally challenging, complex models. Sequence data arising from natural processes also often exhibits power-law properties, yet common sequence models do not capture such properties. The sequence memoizer is a new hierarchical Bayesian model for discrete sequence data that captures long range dependencies and power-law characteristics, while remaining computationally attractive. Its utility as a language model and general purpose lossless compressor is demonstrated.

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1. Introduction

It is an age-old quest to predict what comes next in sequences. Fortunes have been made and lost on the success and failure of such predictions. Heads or tails? Will the stock market go up by 5% tomorrow? Is the next card drawn from the deck going to be an ace? Does a particular sequence of nucleotides appear more often then usual in a DNA sequence? In a sentence, is the word that follows the United going to be States, Arab, Parcel, Kingdom, or something else? Using a probabilistic model of sequences fit to a particular set of data is usually an effective way of answering these kinds of questions.

Consider the general task of sequence prediction. For some sequences, the true probability distribution of the next symbol does not depend on the previous symbols in the sequence. For instance, consider flipping a coin that comes up heads with probability p or tails with probability 1 – p every time it is flipped. Subsequent flips of such a coin are completely independent and have the same distribution (in statistics, such coin flips are called independent and identically distributed [iid]). In particular, heads will occur with probability p irrespective of whether previous flips have come up heads or tails. Assuming we observe a sequence of such coin flips, all we need to do is to estimate p in order to fully characterize the process that generated the data.

For more interesting processes, the distribution of the next symbol often depends in some complex way on previous outcomes. One example of such a process is natural language (sequences of words). In English, the distribution of words that follow the single-word context United is quite different from the distribution of words that follow Cricket and rugby are amongst the most popular sports in the United. In the first case, the distribution is relatively broad (though not nearly as broad as the distribution given no context at all), giving significant probability to words such as States, Kingdom, Airlines, and so forth, whereas in the second case, the distribution is almost certainly highly peaked around Kingdom. Information from distant context (Cricket and rugby) impacts the distribution of the next word profoundly. Production of natural language is but one example of such a process; the real world is replete with other examples.

Employing models that capture long range contextual dependencies will often improve one’s ability to predict what comes next, as illustrated in the example above. Of course, modeling the distribution of the next symbol emitted by a process will only be improved by consideration of longer contexts if the generating mechanism actually does exhibit long range dependencies. Unfortunately, building models that capture the information contained in longer contexts can be difficult, both statistically and computationally. The sequence memoizer (SM) captures such long range dependencies in a way that is both statistically effective and scales well computationally.

While the SM and related models are useful for predicting the continuation of sequences, prediction is not the only application for these models. Automated speech recognition and machine translation require assessing the typicality of sequences of words (i.e., Is this sentence a probable English sentence?). Speaker or writer identification tasks require being able to distinguish typicality of phrases under word sequence models of different writers’ styles. Classifying a sequence of machine instructions as malicious or not requires establishing the typicality of the sequence under each class. Models of sequences can be used for predicting the continuation of sequences, clustering or classifying sequences, detecting change points in sequences, filling in gaps, compressing data, and more.

In this article we describe the SM in terms of general sequences over a discrete alphabet of symbols, though often we will refer to sequences of words when giving intuitive explanations.

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2. Predicting Sequences

To start, let Σ be the set of symbols that can occur in some sequence. This set can consist of dictionary entries, ASCII values, or {A, C, G, T} in case of DNA sequences. Suppose that we are given a sequence^a x = x₁, x₂, …, x_T of symbols from Σ and would like to estimate the probability that the next symbol takes on a particular value.

One way to estimate the probability that the next symbol takes some value s Σ is to use the relative frequency of its occurrence in x, i.e., if s occurs frequently in x we expect its probability of appearing next to be high as well. Assuming that x is long enough, doing this will be better than giving equal probability to all symbols in Σ. Let us denote by N(s) the number of occurrences of s in x. Our estimate of the probability of s being the next symbol is then . The function G is a discrete distribution over the elements of Σ it assigns a non-negative number G(s) to each symbol s signifying the probability of observing s, with the numbers summing to one over Σ.

Of course, this approach is only reasonable if the process generating x has no history dependence (e.g., if x is produced by a sequence of tosses of a biased coin). It is highly unsatisfying if there are contextual dependencies which we can exploit. If we start accounting for context, we can quickly improve the quality of the predictions we make. For instance, why not take into account the preceding symbol? Let u be another symbol. If the last symbol in x is u, then we can estimate the probability of the next symbol being s by counting the number of times s occurs after u in x. As before, we can be more precise and define

to be the estimated probability of s occurring after u, where N(us) is the number of occurrences of the subsequence us in x. The function G_u is again a discrete distribution over the symbols in Σ, but it is now a conditional distribution as the probability assigned to each symbol s depends on the context u.

In the hope of improving our predictions, it is natural to extend this counting procedure to contexts of length greater than one. The extension of this procedure to longer contexts is notationally straightforward, requiring us only to reinterpret u as a sequence of length n ≥ 1 (in fact, for the remainder of this article boldface type variables will indicate sequences, and we will use Σ* to denote the set of all finite sequences). Unfortunately, using this exact procedure for estimation with long contexts leads to difficulties, which we will consider next.

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3. Maximum Likelihood

Some readers may realize that the counting procedure described above corresponds to a ubiquitous statistical estimation technique called maximum likelihood (ML) estimation. The general ML estimation setup is as follows: we observe some data x which is assumed to have been generated by some underlying stochastic process and wish to estimate parameters Θ for a probabilistic model of this process. A probabilistic model defines a distribution P(x\Θ) over x parameterized by Θ, and the ML estimator is the value of Θ maximizing P(x\Θ). In our case, the data consists of the observed sequence, and the parameters are the conditional distributions G_u for some set of u‘s.

In a sense, ML is an optimistic procedure, in that it assumes that x is an accurate reflection of the true underlying process that generated it, so that the ML parameters will be an accurate estimate of the true parameters. It is this very optimism that is its Achilles heel, since it becomes overly confident about its estimates. This situation is often referred to as overfitting. To elaborate on this point, consider the situation in which we have long contexts. The denominator of (1) counts the number of times that the context u occurs in x. Since x is of finite length, when u is reasonably long, the chance that u never occurs at all in x can be quite high, so (1) becomes undefined with a zero denominator. More pernicious still is if we are “lucky” and u did occur once or a few times in x. In this case (1) will assign high probability to the few symbols that just by chance did follow u in x, and zero probability to other symbols. Does it mean that these are the only symbols we expect to see in the future following u, or does it mean that the amount of data we have in x is insufficient to characterize the conditional distribution G_u? Given a complex process with many parameters the latter is often the case, leading to ML estimates that sharpen far too much around the exact observations and don’t reflect our true uncertainty.

Obviously, if one uses models that consider only short context lengths, this problem can largely be avoided if one has enough data to estimate some (relatively) smaller number of conditional distributions. This is precisely what is typically done: one makes a fixed-order Markov assumption and restricts oneself to estimating collections of distributions conditioned on short contexts (for instance, an nth-order Markov model, or an m-gram language model). The consequence of doing this is that ML estimation becomes feasible, but longer-range dependencies are discarded. By assumption and design, they cannot be accounted for by such restrictive models.

Even having imposed such a restriction, overfitting often remains an issue. This has led to the development of creative approaches to its avoidance. The language modeling and text compression communities have generally called these smoothing or back-off methodologies (see Chen and Goodman³ and references therein). In the following, we will propose a Bayesian approach that retains uncertainty in parameter estimation and thus avoids overconfident estimates.

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4. Bayesian Modeling

As opposed to ML, the Bayesian approach is inherently conservative. Rather than trusting the data fully, Bayesian parameter estimation incorporates both evidence from the data as well as from prior knowledge of the underlying process. Furthermore, uncertainty in estimation is taken into account by treating the parameters Θ as random, endowed with a prior distribution P(Θ) reflecting the prior knowledge we have about the true data generating process. The prior distribution is then combined with the likelihood P(x|Θ) to yield, via Bayes’ Theorem (the namesake of the approach), the posterior distribution P(Θ/x) = P(Θ)P(x|Θ)/P(x), which specifies the belief about the parameter Θ after combining both sources of information. Computations such as prediction are then done taking into account the a posteriori uncertainty about the underlying parameters.

What kinds of prior knowledge about natural sequence data might we wish to employ? We make use of two: that natural sequence data often exhibits power-law properties, and that conditional distributions of similar contexts tend to be similar themselves, particularly in the sense that recency matters. We will consider each of these in turn in the rest of this section.

 4.1. Power-law scaling

As with many other natural phenomena like social networks and earthquakes, occurrences of words in a language follow a power-law scaling.²³ This means that there are a small number of words that occur disproportionately frequently (e.g., the, to, of), and a very large number of rare words that, although each occurs rarely, when taken together make up a large proportion of the language. The power-law scaling in written English is illustrated in Figure 1. In this subsection we will describe how to incorporate prior knowledge about power-law scaling in the true generative process into our Bayesian approach. To keep the exposition simple, we will start by ignoring contextual dependencies and instead focus only on one way of estimating probability distributions that exhibit power-law scaling.

To see why it is important to incorporate knowledge about power-law scaling, consider again the ML estimate given by the relative frequency of symbol occurrences . For the frequently occurring symbols, their corresponding probabilities will be well estimated since they are based on many observations of the symbols. On the other hand, our estimates of the rare symbol probabilities will not be good at all. In particular, if a rare symbol did not occur in our sequence (which is likely), our estimate of its probability will be zero, while the probability of a rare symbol that did occur just by chance in our sequence will be overestimated. Since most symbols in Σ will occur quite rarely under a power-law, our estimates of G(s) will often be inaccurate.

To encode our prior knowledge about power-law scaling, we use a prior distribution called the Pitman–Yor process (PYP),¹⁵ which is a distribution over the discrete probability distribution G={G(s)}_{s Σ}. It has three parameters: a base distribution G₀={G₀(s)}_{s Σ}, which is the mean of the PYP and reflects our prior belief about the frequencies of each symbol, a discount parameter α between 0 and 1 which governs the exponent of the power-law, and a concentration parameter c which governs the variability around the mean G₀. When α = 0, the PYP loses its power-law properties and reduces to the more well-known Dirichlet process. In this paper, we assume c = 0 instead for simplicity; see Gasthaus and Teh⁶ for the more general case when c is allowed to be positive. When we write it means that G has a prior given by a PYP with the given parameters. Figure 1 illustrates the power-law scaling produced by PY processes.

To convey more intuition about the PYP we can consider how using it affects our estimate of symbol frequencies. Note that in our Bayesian framework G is random, and one of the standard steps in a procedure called inference is to estimate a posterior distribution P(G/x) from data. The probability that symbol s Σ occurs next is then:

where in this case stands for expectation with respect to the posterior distribution P(G/x). This integral is a standard Bayesian computation that sometimes has an analytic solution but often does not. When it does not, like in this situation, it is often necessary to turn to numerical integration approaches, including sampling and Monte Carlo integration.¹⁶

In the case of the PYP, [G(s)] can be computed as described at a high level in the following way. In addition to the counts {N(s‘)}_{s‘ Σ}, assume there is another set of random “counts” {M(s‘)}_{s‘ Σ} satisfying 1 ≤ M(s‘) ≤ N(s‘) if N(s‘) > 0 and M(s‘) = 0 otherwise. The probability of symbol s Σ occurring next is then given by:

Given this, it is natural to ask what purpose these M(s)’s serve. By studying Equation 3, it can be seen that each M(s) reduces the count N(s) by αM(s) and that the total amount subtracted is then redistributed across all symbols in Σ proportionally according to the symbols’ probability under the base distribution G₀. Thus non-zero counts are usually reduced, with larger counts typically reduced by a larger amount. Doing this mitigates the overestimation of probabilities of rare symbols that happen to appear by chance. On the other hand, for symbols that did not appear at all, the estimates of their probabilities are pulled upward from zero, mitigating underestimation of their probability. We describe this effect as “stealing from the rich and giving to the poor.” This is precisely how the PYP manifests a power-law characteristic. If one thinks of the M(s)’s and α as parameters then one could imagine ways to set them to best describe the data. Intuitively this is not at all far from what is done, except that the M(s)’s and α are themselves treated in a Bayesian way, i.e., we average over them under the posterior distribution in Equation 3.

 4.2. Context trees

We now return to making use of the contextual dependencies in x and to estimating all of the conditional distributions G_u relevant to predicting symbols following a general context u. The assumption we make is that if two contexts are similar, then the corresponding conditional distributions over the symbols that follow those contexts will tend to be similar as well. A simple and natural way of defining similarity between contexts is that of overlapping contextual suffixes. This is easy to see in a concrete example from language modeling. Consider the distribution over words that would follow u = in the United States of. The assumption we make is that this distribution will be similar to the distribution following the shorter context, the United States of, which we in turn expect to be similar to the distribution following United States of. These contexts all share the same length three suffix.

In this section and the following one, we will discuss how this assumption can be codified using a hierarchical Bayesian model.^{8, 11} To start, we will only consider fixed, finite length contexts. When we do this we say that we are making an nth order Markov assumption. This means that each symbol only depends on the last n observed symbols. Note that this assumption dictates that distributions are not only similar but equal among contexts whose suffixes overlap in their last n symbols. This equality constraint is a strong assumption that we will relax in Section 5.

We can visualize the similarity assumption we make by constructing a context tree: Arrange the contexts u (and the associated distributions G_u) in a tree where the parent of a node u, denoted σ(u), is given by its longest proper suffix (i.e., u with its first symbol from the left removed). Figure 2 gives an example of a context tree with n = 3 and Σ = {0,1}. Since for now we are making an nth order Markov assumption, it is sufficient to consider only the contexts u Σ*_u = {u’ Σ*: |u‘| ≤ n} of length at most n. The resulting context tree has height n and the total number of nodes in the tree grows exponentially in n. The memory complexity of models built on such context trees usually grows too large and too quickly for reasonable values of n and |Σ|. This makes it nearly impossible to estimate all of the distributions G_u in the naïve way described in Section 2. This estimation problem led us to hierarchical Bayesian modeling using Pitman–Yor processes.

 4.3. Hierarchical Pitman–Yor processes

Having defined a context tree and shown that the Pitman-Yor prior over distributions exhibits power-law characteristics, it remains to integrate the two.

Recall that means that G is a random distribution with a PYP prior parameterized by a discount parameter α and a base distribution G₀. The expected value of G under repeated draws from the PYP is the base distribution G₀. Because of this fact we can use this process to encode any assumption that states that on average G should be similar to G₀. To be clear, this is just a prior assumption. As always, observing data may lead to a change in our belief. We can use this mechanism to formalize the context tree notion of similarity. In particular, to encode the belief that G_u should be similar to G_σ(u), we can use a PYP prior for G_u with base distribution G_σ(u). We can apply the same mechanism at each node of the context tree, leading to the following model specification:

The second line says that a priori the conditional distribution G_u should be similar to G_σ(u), its parent in the context tree. The variation of G_u around its mean G_σ(u) is described by a PYP with a context length-dependent discount parameter α_|u|. At the top of the tree the distribution Gε for the empty context ε is similar to an overall base distribution G₀, which specifies our prior belief that each symbol s will appear with probability G₀(s). The third line describes the nth order Markov model for x: It says that the distribution over each symbol x_i in x, given that its context consisting of the previous n symbols x_i-n:i−1 is u, is simply G_u.

The hierarchical Bayesian model in Equation 4 is called the hierarchical Pitman-Yor process.¹⁸ It formally encodes our context tree similarity assumption about the conditional distributions using dependence among them induced by the hierarchy, with more similar distributions being more dependent. It is this dependence which allows the model to share information across the different contexts, and subsequently improve the estimation of all conditional distributions. It is worth noting that there is a well-known connection between the hierarchical PYP and a type of smoothing for m-gram language models called interpolated Kneser–Ney.^{10, 18}

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5. Sequence Memoizer

The name sequence memoizer (SM) refers to both an extension of the hierarchical PYP model presented in the previous section, as well as to the set of techniques required to make practical use of the extended model. We first describe how the SM model extends the hierarchical PYP model and then discuss how to reduce the complexity of the model to make it computationally tractable. Finally, we sketch how inference is done in the SM.

 5.1. The model

The SM model is a notationally subtle but important extension to the hierarchical PYP model (4) is described in the previous section. Instead of limiting the context lengths to n, the model is extended to include the set of distributions in all contexts of any (finite) length. This means that the distribution over each symbol is now conditioned on all previous symbols, not just the previous n.

Formally, the SM model is defined exactly as the hierarchical PYP model in Equation 4, but with two differences. First, the contexts range over all finite nonempty strings, u Σ*\ε. Second, in the third line of Equation 4, instead of conditioning only on the previous n symbols, we condition on all previous symbols, so that x_i|x_1:i−1 = u, G_u ~ G_u. The assumptions embodied in the resulting model remain the same as that for the hierarchical PYP model: power-law scaling and similarity between related contexts.

The SM model can be interpreted as the limit of a hierarchical PYP model as the Markov order n tends to infinity. One’s first impression of such a model might be that it would be impossible to handle, both statistically because of overfitting and other problems, and computationally because the model as described so far cannot even be represented in a computer with finite memory! Fortunately the Bayesian approach, where we compute the posterior distribution and marginalize over the parameters as in Equation 2 to obtain estimators of interest, prevents overfitting. Additionally, the techniques we develop in the next subsection make computation in this model practical.

 5.2. Compacting the context tree

While lifting the finite restriction on context lengths seems very desirable from a modeling perspective, the resulting SM model is a prior over an infinite number of parameters (conditional distributions) {G_u}_{u Σ}*. In order to compute in this model, the number of conditional distributions that is accessed must be reduced to a finite number. The key to realizing that this is possible is that given a finite length sequence of symbols x, we only need access to a finite number of conditional distributions. In particular, we only need G_x1:i where i = 0, …, T and all the ancestors of each G_x1:i in the context tree. The ancestors are needed because each G_u has a prior that depends on its parent G_σ(u). The resulting set of conditional distributions that the sequence x actually depends on consists of G_u where u ranges over all contiguous substrings of x, a finite set of O(T²) contexts. All other contexts in the tree can effectively be ignored. We denote this subtree of the context tree that x actually depends on by T (x); Figure 2b shows an example with x = 0110.

Computation with such a quadratically sized context tree is possible but inefficient, especially if the sequence length is large. A second step reduces the tree down to a linear number of nodes. The key observation underlying this reduction is that many of the contexts that appear in T (x) only appear in non-branching chains, i.e., each node on the chain only has one child in T (x). For example, in Figure 2b, the context 11 only occurs as a suffix of the longer context 011, and is part of the non-branching chain . In such a situation, G₁₁ serves no purpose except to relate G₀₁₁ with G₁. If we can directly express the prior of G₀₁₁ in terms of G₁, then we can effectively ignore G₁₁ and marginalize it out from the model.

Fortunately, a remarkable property related to an operation on Pitman–Yor processes called coagulation allows us to perform this marginalization exactly.¹⁴ Specifically in the case of and , the property states simply that where G₁₁ has been marginalized out. In other words, the prior for G₀₁₁ is another PYP whose discount parameter is simply the product of the discount parameters along the chain leading into it on the tree (x), while the base distribution is simply the head of the chain G₁.

In general, applying the same marginalization procedure to all the non-branching chains of T (x), we obtain a compact context tree (x) where all internal nodes have at least two children (all others have been integrated out). This is illustrated in Figure 2c, where each chain is replaced by an edge labeled by the sequence of symbols on the original edges of the chain (in the example only is replaced by . One can easily show that the number nodes in the compact context tree (x) is at most twice the length of the sequence x (independent of |Σ|).

At this point some readers may notice that the compact context tree has a structure reminiscent of a data structure for efficient string operations called a suffix tree.⁹ In fact, the structure of the compact context tree is given by the suffix tree for the reverse sequence x_T, x_T−1, …, x₁. Similar extensions from fixed-length to unbounded-length contexts, followed by reductions in the context trees, have also been developed in the compression literature.^4,19

 5.3. Inference and prediction

As a consequence of the two marginalization steps described in the previous subsection, inference in the full SM model with an infinite number of parameters is equivalent to inference in the compact context tree (x) with a linear number of parameters. Further, the prior over the conditional distributions on (x) still retains the form of a hierarchical PYP: each node still has a PYP prior with its parent as the base distribution. This means that inference algorithms developed for the finite-order hierarchical PYP model can be easily adapted to the SM. We will briefly describe the inference algorithms we employ.

In the SM model we are mainly interested in the predictive distribution of the next symbol being some s Σ given some context u, conditioned on an observed sequence x. As in Equation 2, this predictive distribution is expressed as an expectation [G_u(s)] over the posterior distribution of Just as in Equation 3 as well, it is possible to express [G_u(s)] as an expectation over a set of random counts :

Again, the first term in the numerator can be interpreted as a count of the number of times s occurs in the context u, the second term is the reduction applied to the count, while the third term spreads the total reduction across Σ according to the base distribution G_σ(u)(S). Each context u now has its own discount parameter α_u, which is the product of discounts on the non-branching chain leading to u on (x), while the parent σ(u) is the head of the chain. Notice that Equation 5 is defined recursively, with the predictive distribution G_u in context u being a function of the same in the parent σ(u) and so on up the tree.

The astute reader might notice that the above does not quite work if the context u does not occur in the compact context tree (x). Fortunately the properties of the hierarchical PYP work out in our favor, and the predictive distribution is simply the one given by the longest suffix of u that is in (x). If this is still not in (x), then a converse of the coagulation property (called fragmentation) allows us to reintroduce the node back into the tree.

To evaluate the expectation (5), we use stochastic (Monte Carlo) approximations where the expectation is approximated using samples from the posterior distribution. The samples are obtained using Gibbs sampling¹⁶ as in Teh¹⁸ and Wood,²¹ which repeatedly makes local changes to the counts, and using sequential Monte Carlo⁵ as in Gasthaus et al.,⁷ which iterates through the sequence x₁, x₂, …, x_T, keeping track of a set of samples at each step, and updating the samples as each symbol x_i is incorporated into the model.

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6. Demonstration

We now consider two target applications: language modeling and data compression. It is demonstrated that the SM model is able to achieve better performance than most state-of-the-art techniques by capturing long-range dependencies.

 6.1. Language modeling

Language modeling is the task of fitting probabilistic models to sentences (sequences of words), which can then be used to judge the plausibility of new sequences being sentences in the language. For instance, “God save the Queen” should be given a higher score than “Queen the God save” and certainly more than “glad slave the spleen” under any model of English. Language models are mainly used as building blocks in natural language processing applications such as statistical machine translation and automatic speech recognition. In the former, for example, a translation algorithm might propose multiple sequences of English words, at least one of which is hoped to correspond to a good translation of a foreign language source. Usually only one or a few of these suggested sequences are plausible English language constructions. The role of the language model is to judge which English construction is best. Better language models generally lead to better translators.

Language model performance is reported in terms of a standard measure called perplexity. This is defined as 2^l(x) where is the average log-loss on a sequence x and the average number of bits per word required to encode the sequence using an optimal code. Another interpretation of perplexity is that it is the average number of guesses the model would have to make before it guessed each word correctly (if it makes these guesses by drawing samples from its estimate of the conditional distribution). For the SM model P(x_i|x_1:i−1) is computed as in Equation 5. Both lower log-loss and lower perplexity are better.

Figure 3 compares the SM model against nth order Markov models with hierarchical PYP priors, for various values of n, on a four million word New York Times corpus^b. Table 1 compares the hierarchical PYP Markov model and the SM model against other state-of-the-art models, on a 14 million word Associated Press news article corpus. The AP corpus is a benchmark corpus for which the performance of many models is available. It is important to note that it was processed by Bengio et al.² to remove low frequency words. Note that this is to the detriment of the SM, which is explicitly designed to improve modeling of low word frequencies due to power-law scaling. It is also a relatively small corpus, limiting the benefits of the SM model at capturing longer range dependencies.

Our results show that the SM model is a competitive language model. However, perplexity results alone do not tell the whole story. As more data is used to estimate a language model, typically its performance improves. This means that computational considerations such as memory and runtime must enter into the discussion about what constitutes a good language model. In many applications, fast prediction is imperative, in others, particularly in online settings, incorporation of new data into the model must be fast. In comparison to more complex language models, prediction in the SM has real-world time complexity that is essentially the same as that of a smoothed finite-order Markov model, while its memory complexity is linear in the amount of data. The computational complexity of Markov models theoretically does not depend on the amount of data but is exponential in the Markov order, rendering straightforward extensions to higher orders impractical. The SM model directly fixes this problem while remaining computationally tractable. Constant space, constant time extensions to the SM model¹ have been developed, which show great promise for language modeling and other applications.

 6.2. Compression

Shannon’s celebrated results in information theory¹⁷ have led to lossless compression technology that, given a coding distribution, nearly optimally achieves the theoretical lower limit (given by the log-loss) on the number of bits needed to encode a sequence. Lossless compression is closely related to sequence modeling: an incrementally constructed probabilistic sequence model such as the SM can be used to adaptively construct coding distributions which can then be directly used for compression based on entropy coding.

We demonstrate the theoretical performance of a lossless compressor based on the SM model on a number of standard compression corpora. Table 2 summarizes a comparsion of our lossless compressor against other state-of-the-art compressors on the Calgary corpus, a well-known compression benchmark consisting of 14 files of different types and varying lengths.

In addition to the experiments on the Calgary corpus, SM compression performance was also evaluated on a 100MB excerpt of the English version of Wikipedia (XML text dump).¹² On this excerpt, the SM model achieved a log-loss of 1.66 bits/symbol amounting to a compressed file size of 20.80MB. While this is worse than 16.23MB achieved by the best demonstrated Wikipedia compressor, it demonstrates that the SM model can scale to sequences of this length. We have also explored the performance of the SM model when using a larger symbol set (Σ,). In particular, we used the SM model to compress UTF-16 encoded Chinese text using a 16-bit alphabet. On a representative text file, the Chinese Union version of the bible, we achieved a log-loss of 4.91 bits per Chinese character, which is significantly better than the best results in the literature (5.44 bits).²²

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7. Conclusion

The SM achieves improved compression and language modeling performance. These application-specific performance improvements are arguably worthwhile scientific achievements by themselves. Both have the potential to be tremendously useful, and may yield practical consequences of societal and commercial value.

We encourage the reader, however, not to mentally categorize the SM as a compressor or language model. Nature is replete with discrete sequence data that exhibits long-range dependencies and power-law characteristics. The need to model the processes that generate such data is likely to grow in prevalence. The SM is a general purpose model for discrete sequence data that remains computationally tractable despite its power and despite the fact that it makes only very general assumptions about the data generating process.

Our aim in communicating the SM is also to encourage readers to explore the fields of probabilistic and Bayesian modeling in greater detail. Expanding computational capacity along with significant increases in the amount and variety of data to be analyzed across many scientific and engineering disciplines is rapidly enlarging the class of probabilistic models that one can imagine and employ. Over the coming decades hierarchical Bayesian models are likely to become increasingly prevalent in data analysis oriented fields like applied statistics, machine learning, and computer science. It is our belief that the SM and its ilk will come to be seen as relatively simple building blocks for the enormous and powerful hierarchical models of tomorrow.

Source code and example usages of the SM are available at http://www.sequencememoizer.com/. A lossless compressor built using the SM can be explored at http://www.deplump.com/.

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Acknowledgments

We wish to thank the Gatsby Charitable Foundation and Columbia University for funding.

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