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A novel, fast, HMMwithDuration implementation – for application with a new, pattern recognition informed, nanopore detector
BMC Bioinformatics volume 8, Article number: S19 (2007)
Abstract
Background
Hidden Markov Models (HMMs) provide an excellent means for structure identification and feature extraction on stochastic sequential data. An HMMwithDuration (HMMwD) is an HMM that can also exactly model the hiddenlabel length (recurrence) distributions – while the regular HMM will impose a bestfit geometric distribution in its modeling/representation.
Results
A Novel, Fast, HMMwithDuration (HMMwD) Implementation is presented, and experimental results are shown that demonstrate its performance on twostate synthetic data designed to model Nanopore Detector Data. The HMMwD experimental results are compared to (i) the ideal model and to (ii) the conventional HMM. Its accuracy is clearly an improvement over the standard HMM, and matches that of the ideal solution in many cases where the standard HMM does not. Computationally, the new HMMwD has all the speed advantages of the conventional (simpler) HMM implementation. In preliminary work shown here, HMM feature extraction is then used to establish the first pattern recognitioninformed (PRI) sampling control of a Nanopore Detector Device (on a "live" datastream).
Conclusion
The improved accuracy of the new HMMwD implementation, at the same order of computational cost as the standard HMM, is an important augmentation for applications in gene structure identification and channel current analysis, especially PRI sampling control, for example, where speed is essential. The PRI experiment was designed to inherit the high accuracy of the well characterized and distinctive blockades of the DNA hairpin molecules used as controls (or blockade "testprobes"). For this test set, the accuracy inherited is 99.9%.
Introduction
It appears possible to obtain kinetic features directly from the channel blockade signals obtained during the capture of certain molecules in a nanopore detector, shown in Fig. 1 (see further details on the Detector in the Background), where individual blockade levels appear to correlate with binding or conformational states of the molecule [1–3]. The extraction of kinetic features from nanopore detector measurements, e.g., obtaining the median dwell times of the most frequented channel blockade levels, requires that we faithfully preserve the dwell times of the various blockade states (or "levels") encountered during the channelcapture event, to the exclusion of short noise pulses that might normally be misinterpreted as short dwell times. During analysis using conventional Hidden Markov Models (HMMs), both the combination of firstorder modeling and pulsed noise conspire to produce premature state transitions and hence incorrect assessment of kinetic features. From the preliminary work in [4], in particular, we know that bilevel synthetic data with Poissondistributed dwell times provides an example of such a pulsed noise instability. Here we clarify how to solve the problem with (1) dwelltime dependence in the statetostate transitions; and (2) emission variance amplification (EVA projection); and show new experimental results.
The conventional HMM is first order and fixed (scalar) in the transition probabilities for remaining in a given state, which leads to a geometric length distribution for remaining in that state [5] – i.e., conventional HMMs automatically impose geometric length distributions on their samestate regions, such as exon or intron lengths or blockade level durations. An HMMwithDuration (HMMwD) is an HMM where true, or a much more complete, knowledge of the length distributions on samestate regions is incorporated into the model [6]. Here we describe a novel HMMwD where the nongeometric length distribution information is incorporated via dwelltime dependent transition probabilities (for transitions of state to self) [4]. New experimental results are shown, and compared to an exact HMMwD (described in [7]).
Part of the novelty of the new "cellular" HMMwD that is proposed is that it is defined at the celllevel in its dynamic programming table construction, much like the conventional HMM, with one column's computation only dependent on information held in the prior column (in an overall table computation involving a single pass through the table). Our HMMwD can be defined for either the Viterbi or the Forward/Backward algorithms (see Methods). This is convenient because we have a method for distributed HMM processing based on such table computations (paper in preparation), that takes advantage of the basic, underlying Markov assumption to do distributed processing with simplicity of the "chunk" distributed processing that we use for the SVM training [8]. That method is shown to work very effectively for the Viterbi algorithm (similar distribution methods for the Forward/Backward distribution algorithm are also discussed there). The endresult of all of this is that very sophisticated feature extraction tools can be brought to bear for realtime pattern recognition informed operation.
Realtime control of a nanopore detector, based on live, streaming measurements and sufficiently fast pattern recognition identification of any blockading ("captured") analyte, holds great promise for single molecule experiments. Realtime sampling control of a nanopore detector, alone, can boost nanopore detector sampling productivity by orders of magnitude, depending on the mix of desirable signal classes vs. undesirable in the data being analyzed. An example of such an experiment is the focus of the proofofprinciple experiment performed here. If there is a 1 to 100 ratio of desirable to undesirable, for example, then one obtains desirable signal sampling only about 1% of the time with a passive sampling system. With pattern recognition informed sampling this can potentially be changed to desirable signal sampling almost 99% of the time. In a realtime setting the challenge is to perform the HMM feature extraction sufficiently quickly (whereas the SVM is trained offline, so operates very quickly online). In this work we show that this can be accomplished with pattern recognition used to identify DNA molecules within the first few hundred milliseconds of their blockade of the detector channel.
We establish a realtime experimental setup for Patter Recognition Informed (PRI) sampling control via integration of LabWindows automation capabilities with our "inhouse" Channel Current Cheminformatics (CCC) methods (see Methods). Data acquired with LabWindows is passed to a network of CCC software clients, on a streaming real time basis, for analysis and classification. The classification results are then quickly returned to the LabWindows automation software for experimental feedback control. Further details of a realtime test of PRI sampling is described in the Results. The classification inherits the 99.9% accuracy of the non realtime implementation (established in prior work [1]) as nothing has changed in regards to the features extracted and the classifier used.
To make these Channel Current Cheminformatics and Machine Learning tools available to fellow researchers, we are developing webaccessible machinelearning tools. Using hidden Markov model (HMM) processing, and finite state automata (FSAs), we are able to extract robust features and obtain very accurate support vector machine (SVM) classification results. The Machine Learning webinterfaces described here are for both machine learning experts and nonexperts, particularly biologists and biophysicists/biochemists. For nonexperts, default values are specified on the key parameters.
Webaccessible tools for HMMbased feature extraction and SVM classification are accessible at http://logos.cs.uno.edu/~nano/. Examples of the Web interfaces are shown in the Results. The web tools can help in identification of blockade levels, the level transition and lifetime characteristics, and the fast blockade "spike" characteristics. The SVM classification is of general use for any kind of classification problem, and a number of novel kernels and novel implementations are employed. SVMbased clustering is also implemented in a novel way to yield a nonparametric clustering approach, which is used to cluster signals into multiple classes (particularly important for complex multiorientation datasampling situations such as with an antibody).
Background
Nanopore detector
Single biomolecules, and the ends of biopolymers such as DNA, have been examined in solution with nanometerscale precision using nanopore blockade detection [1–3, 9–11]. In early studies [2], it was found that complete basepair dissociations of dsDNA to ssDNA, "melting", could be observed for sufficiently short DNA hairpins. In later work [1–3, 9], the nanopore detector attained Angstrom resolution and was used to "read" the ends of dsDNA molecules, and was operated as a chemical biosensor. In [9–13], the nanopore detector was used to observe the conformational kinetics of the end regions of individual DNA hairpins (see Fig. 1, Lower Panel).
The αhemolysin (αHL) channel, a protein heptamer formed by seven identical 33 kD protein molecules secreted by Staphylococcus aureus, is used as the channel in the nanopore device due to its stable conformation (in the strongly favored heptamer formation, which has minimal gating) and its overall geometry (see Fig. 1, Lower Panel). DNA and RNA interaction with the αhemolysin channel during translocation is nonnegligible (but not too strong either, i.e., it is not such that the molecule "gets stuck"). Although dsDNA is too large to translocate, about ten basepairs at one end can still be drawn into the large cisside vestibule. This permits very sensitive experiments since the ends of "captured" dsDNA molecules can be observed for extensive periods of time to resolve features, allowing highly accurate classification of the captured end of dsDNA molecules [1–3, 9–13]. This is a very brief and limited synopsis of the Nanopore Detector background relevant to this paper. For other references on Nanopore Detectors see the review of Nanopore Detectors presented in [14]; early work involving alphaHemolysin Nanopore Detectors can be found in [1–3, 9–11, 15–25]; rapidly growing research endeavors on Nanopore Detectors based on solidstate and other synthetic platforms can be found in [26–36].
Cheminformatics
The pattern recognition informed (PRI) signal processing architecture builds and "closes the loop" on the prototype architecture presented in [1] (see Fig. 2). The signal processing architecture is used to perform a preliminary test of PRI sampling control (see Results). The processing is designed to rapidly extract useful information from noisy blockade signals using feature extraction protocols, wavelet analysis, Hidden Markov Models (HMMs) and Support Vector Machines (SVMs). For blockade signal acquisition and simple, timedomain featureextraction, a timedomain Finite State Automaton (τFSA) approach is used [37] that is based on tuning a variety of threshold parameters (see Fig. 3 and [1] for full description of the model). A generic HMM is then used to characterize current blockades by identifying a sequence of subblockades as a sequence of state emissions [1, 9–11]. The parameters of the genericHMM can then be estimated using a method called Expectation/Maximization, or 'EM" [5], to effect denoising. The HMM method with EM is part of the standard implementation used in what follows. Classification of feature vectors obtained by the HMM for each individual blockade event is then performed using SVMs.
EVA projection
The HMM method is based on a stationary set of emission and transition probabilities. Emission broadening, via amplification of the emission state variances, is a filtering heuristic that leads to levelprojection that strongly preserves transition times between major levels (see Fig. 4, and [4], and Methods for further details). This approach does not require the user to define the number of levels (classes), which is a major advantage compared to existing tools that require the user to determine the levels (classes) and perform a state projection. This allows kinetic features to be extracted with a "simple" FSA (Finite State Automaton) that requires minimal tuning. Figure 5 (reproduced from [4]) shows the benefits of EVA filtering.
Preliminary HMM with Duration and EVA for channel current signal analysis
One important application of the HMMwithduration method used in [4] includes kinetic feature extraction from EVA projected channel current data (the HMMwithDuration is shown to offer a critical stabilizing capability in an example in [4]). The EVAprojected/HMMwD processing offers a handsoff (minimal tuning) method for extracting the mean dwell times for various blockade states (the core kinetic information).
The HMMwithDuration implementation, described in [4], has been tested in terms of its performance at parsing synthetic blockade signals (see Fig. 5). The synthetic data ranges over an exhaustive set of possibilities for thorough testing of the HMMwithDuration. The synthetic data used in [4] was designed to have two levels with lifetime in each level determined by a governing distribution (Poisson and Gaussian distributions with a range of mean values were considered). The HMM here was performed with 0 EM iterations.
SVM classification used in PRI sampling selection
Support Vector Machines (SVMs) are variationalcalculus based methods that are constrained to have structural risk minimization (SRM) such that they provide noise tolerant solutions for pattern recognition [38, 39]. Simply put, an SVM determines a hyperplane that optimally separates one class from another (see Fig. 6). Once learned, the hyperplane allows data to be classified according to the region (separated by the hyperplane) in which it resides. Currently there are two approaches to implementing multiclass SVMs. One arranges several binary classifiers as a decision tree such that they perform a multiclass decisionmaking function (SVMexternal classification – an example of this is the architecture used here, see Fig. 2). The second approach involves solving a single optimization problem corresponding to the entire data set (with multiple hyperplanes), with multiclass discriminator optimization performed internally. The SVMinternal approach, when it is stable and properly generalizable (an active area of research), is preferred (see Results for interface), since a tuning over Decision tree topologies and weightings is avoided [40]. The online discriminatory speed of a trained SVM is simply that of evaluating an inner product, so it's operational constraint on the PRI feedback endeavor is negligible compared to that of the HMM feature extraction stage. For this reason, there is little discussion of SVMs in this paper, even though SVMs comprise much of the complexity of the HMM/SVM PRI feedback system.
Generalized HMMs
The work by Johnson in [41] is an excellent source of references on generalized HMMs (but entirely focused on speech applications). The approaches to HMM duration described in [41] are broken into three categories: 1) Hidden semiMarkov models (HSMMs), 2) variable transition HMMs (VTHMMs), and 3) standard HMMs with more states, etc. The current work thus would fall into the VTHMM category. In [41] they assert that VTHMM methods are essentially variations on Ferguson's [42] explicit duration HMM (EDHMM), placed in the HSMM category, yet acknowledge the differences in computational complexity. In [43], Levinson gives estimates of transitions and emissions for state durations modeled by gamma distributions, but no explicit method provided or used to decode actual signals. In [44], Ramesh et al estimate the duration dependent state transitions, A_{ij}(d), in general rather than assume, as in the current work, that A_{ij}(d) = C_{ij} for i ≠ j, but do not offer any performance analysis per se of the Viterbi decoding algorithm. Also, [44] provides insight into the work by Ferguson [41] in that, the expansion state HMM (ESHMM) in [41] uses multiple expansion states in order to finitely approximate the duration of a given state of the original system. The current work uses only one model state for each known physical state, and uses time dependent selftransition probabilities to capture state duration information.
In [45], Mitchell et al model duration explicitly using expansion substates, rather than an explicitly time dependent selftransition probability as in the current work. It also manages computational complexity via parallel platform architecture. The paper listed as [46], is the only prior work that is found to model the selftransitions using the cumulative duration in the form A_{ii}(d_{i}) = 1  P(d_{i}), and this was only in a much more restricted sense than that described here. The authors there considered only a twostate system for which the "splitting" in probabilities upon exiting one state is trivial. In [46], Vaseghi computes the duration dependent state transitions directly from the Viterbi output, thus avoiding the costly forwardbackward computation and this is similar the methods employed here for general multistate HMMs. This is useful in situations where the exit transitions are not already known and must be estimated from the data. Otherwise, like most of the references included here, though it can apply specifically to the current work, it involves algorithms that are more generic and computationally complex and not the clear, extremely fast, and simple implementation described here.
As in most other works cited here, Sin et al. [47] involves more generic computations and hence more computational complexity, though in the examples provided avoids the complexity of multiple exit transitions from any given state by restricting the actual computations performed to only lefttoright type models, where there is only one exit transition per state. (Future work might be to use the framework in [47] to confirm the choice of splitting factor for multiple exit transitions, see Discussion.) Park et al [48] also performs analysis using only lefttoright models, where the splitting factor for multiple exit transitions is not an issue. Though emissions for a given state in cheminformatic data are not expected to be timedependent – other than noise component, future work would be to use the framework in [48] to confirm stationary emissions. Finally, in Yoma et al. [49] the analysis is restricted again to the typical lefttoright models of speech recognition, where considerations of splitting factor for exit transitions are trivial.
Results
HMM with Duration experimental tests
Results for our new, implicit HMMwD, are presented in Figure 7 and in the figures in Additional Files 1–3, along with the comparative results from an explicit HMMwD (for a two state system) that is used for comparative analysis (a detailed analysis with the explicit HMMwD is given in [7]). The explicit twostate HMMwD has 2n states, where n is the number of dwell bins in the quantization of the dwelltime distribution. The computations that are needed scale quadratically in n. So, for n = 1000, the explicit HMMwD can take 1,000,000times longer to compute than the HMMwD described here (or the conventional HMM). Performance of the new HMMwD is given in comparison to the conventional HMM is also shown in Figure 7 and in the figures in Supplemental Files 1–3. Specifically, the figures in Additional File 1–3 show the Average and Standard Deviation of Viterbi Decoding Accuracy over 10 different trials (instances) of 10 klength synthetic 2level signal data, where both levels have identical Poisson duration but the separation between the 2 levels varies. From top to bottom, the Viterbi response improves as the number of steps increases in the decoding HMM's approximation of the 1 kstep generating HMM's Poisson durations. From left to right in each plot, the Viterbi response improves as the separation of the 2 levels (emission means) increases. In the figure in Additional File 1 are shown the results with only 1 step used in the Viterbi decoding HMM's approximation of the 1 kstep generating HMM's Poisson durations. In the figure in Additional File 2 are shown the results with 10 steps used in the Viterbi decoding HMM's approximation of the 1 kstep generating HMM's Poisson durations. In the figure in Additional File 3 are shown the results with 100 steps used in the Viterbi decoding HMM's approximation of the 1 kstep generating HMM's Poisson durations. The simplicity of the binary signal case actually provides a challenging case for differentiating the performance of the HMMwD methods from the conventional HMM, so the preliminary results shown here show promise for the overall validity and utility of the method.
The next example considered is that of a 3state system, again, the strong performance of our new HMMwithDuration method is demonstrated, see Figures 8 and 9 and the figure in Additional File 4. The figure in Additional File 4 shows the decoding performance with distributions with means 19 (for geometric), 19.5 and 20 (with Poisson distributed dwelltimes) (in the Top panel), and in the Bottom Panel the figure shows decoding performance with distributions with means 19 (for geometric), 19.75 and 20.5 (with Poisson distributed dwelltimes). As a challenging, preliminary, test case, the duration means for all the distributions are kept the same (at 200). (See Fig. 8 caption for further details.)
In another test, we compare the performance of our twostate HMMwD to explicit HMMwD and conventional HMM (see Tables 1 and 2), with different size data generation and length distribution representation. The comparative scores shown are not optimised for use of the internal HMMwD, but are meant to explore the validity of the model and the behaviour of the accuracy of the different methods – which is consistently ordered as conventional HMM good, implicit HMMwD better, explicit HMMwD best (but the latter at much great computational cost). The results clearly demonstrate the superior performance of the HMMwithduration over its simpler HMM without Duration formulation. With use of the EVAprojection method this affords a robust means to obtain kinetic feature extraction. The HMM with duration is, thus, critical for accurate kinetic feature extraction, via a pairing of the HMMwithDuration stabilization with EVAprojection.
Pattern recognition informed feedback via LabWindows automation
A blockade signal's stationary statistics, or phases thereof, reveals information about the kinetics of the biopolymer resulting from interactions with surroundings, or from undergoing conformational changes. LabVIEW Automation software is used to help manage the feedback linkage between patchclamp amplifier measurements and inhouse cheminformatics software. This has been used to demonstrate molecular identification in the first 100 ms of capture, with return of classification information to the control of the amplifier – for voltagecontrolled sample ejection if desired. Screencaptures of the interfaces are shown in the figures in Additional Files 5–7. Additional File 5 shows the Acquisition Server interface and LabWindows C development environment. Additional File 6 shows a real time 9at vs 9gc classification (with 9at identification indicated by the led being on). Additional File 7 shows a real time 9gc identification.
The LabWindows Server initiates the distributed CCC computations by sending data to a cluster of Linux Clients via a TCP/IP channel. The Linux clients run the expensive HMM analysis as distributed processes (similarly for offline SVM training). The sample classification is then used by the Server to provide feedback to the nanopore apparatus to increase the effective sampling time on the molecules of interest (meant to boost nanopore detector productivity by magnitudes, as described in the Background).
Channel current cheminformatics and MachineLearning web interfaces
The tFSA/HMMbased channel current cheminformatics webinterfaces are as follows: (1), As the tFSA runs, signal regions are identified for processing by the HMM. (2), A 50state genericHMM (typically) is used to obtain feature vectors, to be used by a SVM, consisting of three components: (i) Blockade Histogram: blockade level occupation probabilities (stat's on Viterbi path); (ii) The Emission Variances; and (iii) Compression of Transition probabilities to weighted sum of transition profiles from two dominant levels (the UL and LL states) (one of the interfaces for this process is shown in the figure in Additional File 8). And (3), Kinetic features are then extracted (often with EVAprojected data from step 2). An SVM interface and all other software described is available via the webpage: http://logos.cs.uno.edu/~nano/. As with the external and internal multiclass SVM discriminator implementations, the strong performance of the binary SVM enables SVMExternal as well as SVMInternal approaches to clustering [40].
Methods and discussion
Conventional HMM
An HMM consists of 2 main computations (Durbin et al [5]):

1.
BaumWelch Iteration of recursively defined forward/backward probabilities (symbols x, states π)
f_{ l }(i + 1) = P(x_{1}...x_{i+1}, π_{i+1}= l) = e_{ l }(x_{i+1})π_{ k }f_{ k }(i)a_{ kl }
b_{ k }(i) = P(x_{i+1}...x_{ L } π_{ i }= k) = π_{ l }a_{ kl }e_{ l }(x_{i+1})b_{ l }(i + 1)

2.
Viterbi Path Determination
v_{ l }(i) = e_{ l }(x_{ i })max_{ k }(v_{ k }(i  1)a_{ kl })
ptr_{ i }(l) = argmax_{ k }(v_{ k }(i  1)a_{ kl })
In the HMMwD described here, each of the stationary transition probabilities a_{ kl }are replaced by a dwelltime dependent update factor. The forward/backward probabilities used in the standard HMMEM algorithm occur when evaluating p(Z_{0...L1}) by breaking the sequence probability p(Z_{0...L1}) into two pieces via use of a single hidden variable treated as a Bayesian parameter: p(Z_{0...L1}) = Σ_{k}p(Z_{0...i}, s_{i} = k)p(Z_{i+1...L1}, s_{i} = k) = Σ_{k}f_{ki}b_{ki}, where f_{ki} = p(Z_{0...i}, s_{i} = k) and b_{ki} = p(Z_{i+1...L1}, s_{i} = k). Given stationarity, the state transition probabilities and the state probabilities at the ith observation satisfy the trivial relation p_{qi} = Σ_{k}a_{kq}p_{k(i1)}, where p_{qi} = p(S_{i} = q), and p_{q0} = p(S = q), and the latter probabilities are the state priors. The trivial recursion relation that is implied can be thought of as an operator equation, with operation the product by a_{kq} followed by summation (contraction) on the k index. The operator equation can be rewritten using an implied summation convention on repeated Greekfont indices (Einstein summation convention): p_{q} = a_{βq}p_{β}. Transitionprobabilities in a similar operator role, but now taking into consideration local sequence information via the emission probabilities, are found in recursively defined expressions for the forward variables, f_{ki} = e_{ki}(a_{βk}f_{β(i1)}), and backward variables, b_{ki} = a_{kβ}e_{β(i+1)}b_{β(i+1)}. The recursive definitions on forward and backward variables permit efficient computation of observed sequence probabilities using dynamic programming tables. It is at this critical juncture that side information must mesh well with the states (column components in the table), i.e., in a manner like the emission or transition probabilities. Length information, for example, can be incorporated via lengthdistributionbiased transition probabilities (introduced in [4]), and that is what is experimentally validated done here.
EVA projection
Using a standard implementation of a HMM with emissions probabilities parameterized by Gaussian distributions: emission_probabilities[i][k] = exp((k  i)*(k  i)/(2*variance)), where "i" and "k" are each a state where 0 <= i, k <= 49 in a 50 state system. To perform EVA, the variance is simply multiplied by a factor that essentially widens the gaussian distribution parameterized to best fit the emissions, and the equation simply becomes exp((ki)*(ki)/(2*variance*eva_factor)). The choice of this amplification factor is important. If too large of a factor is used, then the power signal will be altered to the point where the state transition information will be invalid. But for a sizable range of this parameter, HMM with EVA will remove the noise from the power signal while strictly maintaining the state transitions. In practice, any multiplicative factor between 2 and 10 works well.
After EVAprojection, a simple FSA can easily extract level duration information. Each level is identified by a simple threshold of blockade readings, typically one or two percent of baseline. Then, the HMM with EVA processed data is swept through with a small window to eliminate any remaining noise or spike artifacts that may distort actual level duration statistics. It is important to note that there must be a sufficient amount of data to support the level duration statistics. A small sample will simply not be representative of the true kinetic information. Further, it is important that the FSA is tuned properly in order to properly identify levels.
HMM with Duration via cumulant transition probability
The transition probabilities for state 'e' to remain in state 'e', a "ee" transition can be computed as: Prob(ee  e_{length} = L) = Prob(e_{length} ≥ L + 1)/Prob(e_{length} ≥ L). The transition probabilities out of state 'e' can have some subtleties, as shown in the following where the states are exon (e), intron (i), and junk (j). In this case, the transition probabilities governing the following transitions, (jj) > (je), (ee) > (ej), (ee) > (ei), (ii) > (ie) are computed as: Prob(ei  e_{length} = L) = Prob(e_{length} = L)/Prob(e_{length} ≥ L) × 40/(40 + 60) and Prob(ej  e_{length} = L) = Prob(e_{length} = L)/Prob(e_{length} ≥ L) × 60/(40 + 60), where the total number of (ej) transitions is 60 and the total number of (ei) transitions is 40. The pseudocode to track the critical length information, on a cellular basis in the dynamic programming table, goes as follows:

1.
Maintain separate counters for the junk, exon and intron regions.

2.
The counters are updated as follows:

a.
The exon counter is set to 2 for a (je)  (ee) transition

b.
The exon counter gets incremented by 1 for every (ee)  (ee) transition
Prob(e_{length} ≥ L + 1) is computed as: Prob(e_{length} ≥ L + 1) = 1  ∑_{i=1..L}Prob(e_{length} = i). Hence we generate a list such that for each index k > 0, the value 1  ∑_{i=1..k}Prob(e_{length} = i) is stored.
Simplifying from three state model, {e, i, j}, to a twostate model, {e, i}, for a moment: after n occurrences of state 'e', the 2 cases of update factor to handle are:
P(e_{n+1}ee..e_{n}) = P(length e ≥ n+1)/P(length e ≥ n)
P(iee..e_{n}) = P(length e = n)/P(length e ≥ n)
Similarly for n occurrences of state 'i', and there are no probability splitting ambiguities upon exiting state 'e' as there is only one state to exit to in the twostate system (and there are no differences in the Viterbi and Forward/Backward transition probability alterations).
Consider, as an example, a simple extension of our twostate notation to cover N + 1 states: {e, i^{1},...,i^{N}}. Suppose we are interested in the probability of an 'i' after seeing a length 4 segment of estates:
P(ieeee) = 1  P(eeeee) = 1  P(L_{e} = 5)/P(L_{e} = 4)
There are two types of transition rule that appear to result, one for Viterbi, with its maximum operation on paths, and one for Forward/Backward, with its sum operation. For the twostate case, N = 1, and these update rules involving "splitting" factors all become the same (see Results):
Viterbi update

(1)
Difference splitting: p(i^{k}eeee) = [1  P(L_{e} = 5)/P(L_{e} = 4)] * [1 + P(i^{k}e)  Avg_{z}P(Ze)]

(2)
Ratio splitting: p(i^{k}eeee) = [1  P(L_{e} = 5)/P(L_{e} = 4)] * P(i^{k}e)/[Avg_{z}P(Ze)]
In this situation we are not maintaining a sum rule on probabilities, here we are viewing each path through the table in a manner consistent with the maxprob evaluation.
Forward/Backward update

(1)
Difference splitting: p(i^{k}eeee) = [1  P(L_{e} = 5)/P(L_{e} = 4)] * [1 + P(i^{k}e)  Avg_{z}P(Ze)]/N

(2)
Ratio splitting: p(i^{k}eeee) = [1  P(L_{e} = 5)/P(L_{e} = 4)] * P(i^{k}e)/[N*Avg_{z}P(Ze)]
The equation above with the factor [1 + P(i^{k}e)  Avg_{z}P(Ze)]/N provides a suitable "splitting factor", as i^{k} and 'e' probabilities sum to one, remain positive, and have other nice properties. The splitting factor is not unique, however, as case (2) makes clear.
It is important to note that we appear to have some freedom on splittings of probabilities upon exiting a state (when we are using the length distribution cumulants to describe transition probabilities, etc.). This is merely an associated effect of that length distribution incorporation – now upon exiting that length distribution our main factor is P(i^{k}some prior length of e), that factor is blind to the appropriate splittings amongst the "not e" states, and we must incorporate another factor to deal with the probability splitting – in the case of forward/backward, this is chosen to obey a prob sum to 1 on all cases, on Viterbi this must maintain each path's probability with proper weighting with respect to the others (consistent with the maxpath operation).
Realtime processing hardware/software setup
The server was able to concurrently perform the following using a single 1.5 GHz processor with no hyperthreading:

1.
Acquire data from the DAQ buffer at 50 KHz sample rate.

2.
Update the server GUI screen with the acquired data – though a 10× data decimation was required in order to avoid irrevocable delays in reading from the DAQ buffer

3.
Perform tFSA logic to screen for signals resulting from molecular capture events at the nanopore channel

4.
Send capturesignals as long as 100 ms in duration at a rate 10 per second to a waiting 1.5 GHz processor, Linuxbased TCP/IP client for HMMbased feature extraction

5.
Receive extracted HMM features from the TCP/IP client

6.
Compute the classification of the HMM features with tolerance via a binary SVM previously trained on 9gc and 9at bphp signals.

7.
According to the user's preset preference, issue a control signal to the DAQ resulting in ejection of the undesirable molecule so determined from the nanopore channel site.
References
WintersHilt S, Vercoutere W, DeGuzman VS, Deamer DW, Akeson M, Haussler D: Highly Accurate Classification of WatsonCrick Basepairs on Termini of Single DNA Molecules. Biophys J. 2003, 84: 967976.
Vercoutere W, WintersHilt S, Olsen H, Deamer DW, Haussler D, Akeson M: Rapid discrimination among individual DNA hairpin molecules at singlenucleotide resolution using an ion channel. Nat Biotechnol. 2001, 19 (3): 248252.
Vercoutere W, WintersHilt S, DeGuzman VS, Deamer D, Ridino S, Rogers JT, Olsen HE, Marziali A, Akeson M: Discrimination Among Individual WatsonCrick BasePairs at the Termini of Single DNA Hairpin Molecules. Nucl Acids Res. 2003, 31: 13111318.
WintersHilt S: Hidden Markov Model Variants and their Application. BMC Bioinformatics. 7 (Suppl 2): S142006, Sept. 26
Durbin R: Biological sequence analysis: probalistic models of proteins and nucleic acids. 1998, Cambridge, UK New York: Cambridge University Press, xi: 356
Koski T: Hidden Markov Models for Bioinformatics. 2001, Kluwer Academic Publishers
Churbanov A, Baribault C, WintersHilt S: Duration learning for nanopore ionic flow blockade analysis. BMC Bioinformatics. 2007, 8 (Suppl 7): S14
Osuna E, Freund R, Girosi F: An improved training algorithm for support vector machines. Neural Networks for Signal Processing VII. Edited by: Principe J, Gile L, Morgan N, Wilson E. 1997, IEEE, New York, 27685.
WintersHilt S: Nanopore detection using channel current cheminformatics. SPIE Second International Symposium on Fluctuations and Noise, 25–28 May. 2004
WintersHilt S, Akeson M: Nanopore cheminformatics. DNA and Cell Biology. 2004
WintersHilt S: Highly Accurate RealTime Classification of ChannelCaptured DNA Termini. Third International Conference on Unsolved Problems of Noise and Fluctuations in Physics, Biology, and High Technology. 2003, 355368.
WintersHilt S, Landry M, Akeson M, Tanase M, Amin I, Coombs A, Morales E, Millet J, Baribault C, Sendamangalam S: Cheminformatics Methods for Novel Nanopore analysis of HIV DNA termini. BMC Bioinformatics. 7 (Suppl 2): S222006, Sept. 26
WintersHilt S, Davis A, Amin I, Morales E: Nanopore current transduction analysis of protein binding to nonterminal and terminal DNA regions: analysis of transcription factor binding, retroviral DNA terminus dynamics, and retroviral integraseDNA binding. BMC Bioinformatics. 2007, 8 (Suppl 7): S10
Ken Healy K: NanoporeBased DNA Analysis. PhD Thesis. 2006, The National University of Ireland – University College Cork
Bezrukov SM, Vodyanoy I, Parsegian VA: Counting polymers moving through a single ion channel. Nature. 1994, 370 (6457): 279281.
Bezrukov SM: Ion Channels as Molecular Coulter Counters to Probe Metabolite Transport. J Membr Biol. 2000, 174: 113.
Kasianowicz JJ, Brandin E, Branton D, Deamer DW: Characterization of Individual Polynucleotide Molecules Using a Membrane Channel. Proc Natl Acad Sci USA. 1996, 93 (24): 1377073.
Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW: Microsecond timescale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys J. 1999, 77 (6): 32273233.
Meller A, Nivon L, Brandin E, Golovchenko J, Branton D: Rapid nanopore discrimination between single polynucleotide molecules. Proc Natl Acad Sci USA. 2000, 97 (3): 10791084.
Meller A, Branton D: Single molecule measurements of DNA transport through a nanopore. Electrophoresis. 2002, 23 (16): 25832591.
Henrickson SE, Misakian M, Robertson B, Kasianowicz JJ: Driven DNA transport into an asymmetric nanometerscale pore. Phys Rev Lett. 2000, 85 (14): 30573060.
Meller A, Nivon L, Branton D: Voltagedriven DNA translocations through a nanopore. Phys Rev Lett. 2001, 86 (15): 34353438.
Howorka S, Cheley S, Bayley H: Sequencespecific detection of individual DNA strands using engineered nanopores. Nat Biotechnol. 2001, 19 (7): 636639.
Deamer DW, Akeson M: Nanopores and nucleic acids: prospects for ultrarapid sequencing. Trends Biotechnol. 2000, 18: 147151.
Branton D, Meller A: Using nanopores to discriminate between single molecules of DNA. Structure and Dynamics of Confined Polymers. Edited by: Kasianowicz JJ. 2002, Kluwer Acad Pub, 177185.
Heins E, Albertorio F, Yang T, Siwy Z, Baker L, Cheley S, Bayley HP, Cremer PS, Martin CR: Development of a supported lipid bilayer on porous polymeric support. presented at the 49th Biophysical Society Meeting, Long Beach, CA, USA. 2005
Li J, Stein D, M C, Branton D, Aziz M, Golovchenko J: Ion beam sculpting on the nanoscale. Nature. 2001, 412: 166169.
Stein D, Li J, Golovchenko JA: Ionbeam sculpting time scales. Phys Rev Lett. 2002, 89 (27): 276106
Stein DM, McMullan CJ, Li J, Golovchenko JA: Feedbackcontrolled ion beam sculpting apparatus. Rev Sci Instrum. 2004, 75 (4): 900905.
Mitsui T, Stein D, Kim YR, Hoogerheide D, Golovchenko JA: Nanoscale volcanoes: accretion of matter at ionsculpted nanopores. Phys Rev Lett. 2006, 96 (3): 036102
Chen P, Mitsui T, Farmer DB, Golovchenko J, Gordon RG, Branton D: Atomic layer deposition to finetune the surface properties and diameters of fabricated nanopores. Nano Lett. 2004, 4 (7): 13331337.
Storm AJ, Chen JH, Ling XS, Zandbergen HW, Dekker C: Fabrication of solidstate nanopores with singlenanometre precision. Nat Mater. 2003, 2 (8): 537540.
Heng J, Dimitrov V, Grinkova Y, Ho C, Kim T, Muller D, Sligar S, Sorsch T, Twesten R, Timp R, Timp G: The detection of DNA using a silicon nanopore. Proc IEDM. 32.2.132.2.4. 8–10 Dec 2003
Siwy Z, Dobrev D, Neumann R, Trautmann C, Voss K: Electroresponsive asymmetric nanopores in polyimide with stable ioncurrent signal. Appl Phys A. 2003, 76: 781785.
Mara A, Siwy Z, Trautmann C, Wan J, Kamme F: An asymmetric polymer nanopore for single molecule detection. Nano Lett. 2004, 4 (3): 497501.
Apel PY, Korchev YE, Siwy Z, Spohr R, Yoshida M: Diodelike singleion track membrane prepared by electrostopping. Nucl Instrum Methods Phys Res, Sect B. 2001, 184: 337346.
Cormen TH, Leiserson CE, Rivest RL: Introduction to Algorithms. 1989, MITPress, Cambridge, USA
Vapnik VN: The Nature of Statistical Learning Theory. 1998, SpringerVerlag, New York, 2
Burges CJC: A tutorial on support vector machines for pattern recognition. Data Min Knowl Discov. 1998, 2: 12167.
WintersHilt S, Yelundur A, McChesney C, Landry M: Support Vector Machine Implementations for Classification & Clustering. BMC Bioinformatics. 7 (Suppl 2): S42006, Sept. 26
Johnson M: Capacity and Complexity of HMM Duration Modeling Techniques. IEEE Signal Processing Letters. 2005, 12 (5): 407410.
Ferguson J: Variable duration models for speech. Proc Symp App Hidden Markov Models Text Speech. 1980
Levinson S: Continuously variable duration hidden Markov models for speech analysis. Proc Int Conf Acoust, Speech, Signal Process. 1986, 12411244.
Ramesh P, Wilpon J: Modeling state durations in hidden Markov models for automatic speech recognition. Proc Int Conf Acoust, Speech, Signal Process. 1992, 381384.
Mitchell C, Harper M, Jamieson L, Helzerman R: A Parallel Implementation of a Hidden Markov Model with Duration Modeling for Speech Recognition. Dig Sig Proc. 1995, 5: 4357.
Vaseghi S: State duration modeling in hidden Markov models. Signal Process. 1995, 41: 3141.
Sin B, Kim J: Nonstationary hidden Markov model. Signal Process. 1995, 46: 3146.
YK Park, Un CK, Kwon OW: Modeling acoustic transitions in speech by modified hidden Markov models with state duration and state durationdependent observation probabilities. IEEE Trans Speech Audio Process. 1996, 4 (5): 389392.
Yoma N, McInnes F, Jack M, Stump S, Ling L: On including temporal constraints in viterbi alignment for speech recognition in noise. IEEE Trans Speech Audio Process. 2001, 9 (2): 179182.
Acknowledgements
Federal funding was provided by NIH K22 (PI, 5K22LM008794), NIH NNBM R21 (coPI), and NIH R01 (subaward). State funding was provided from a LaBOR Enhancement (PI), a LaBOR Research Competitiveness Subcontract (PI), and a LaBOR/NASA LaSPACE Grant (PI). Thanks to Eric Morales and Iftekhar Amin for gathering data. Thanks to Matthew Landry for establishing the feature vector test sets from data from the nanopore detector. Thanks to A. Murat Eren for work updating the webinterfaces. Funding also provided by New Orleans Children's Hospital and the University of New Orleans Computer Science Department.
This article has been published as part of BMC Bioinformatics Volume 8 Supplement 7, 2007: Proceedings of the Fourth Annual MCBIOS Conference. Computational Frontiers in Biomedicine. The full contents of the supplement are available online at http://www.biomedcentral.com/14712105/8?issue=S7.
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The authors declare that they have no competing interests.
Authors' contributions
The paper was written by SWH. The HMM with Duration method was developed by SWH and implemented by CB and SWH. The PRI feedback experimental approach was implemented by CB under the supervision of SWH. The dataruns for both the HMMwithDuration results and the PRIfeedback results were performed by CB.
Electronic supplementary material
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Additional file 1: Further Results for with the new HMMwithduration formalism (see Fig. 7), with only 1 step used in the Viterbi decoding HMM’s approximation of the 1kstep generating HMM’s Poisson durations. (DOC 26 KB)
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Additional file 2: Further Results for with the new HMMwithduration formalism (see Fig. 7), with 10 steps used in the Viterbi decoding HMM’s approximation of the 1kstep generating HMM’s Poisson durations. (DOC 26 KB)
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Additional file 3: Further Results for with the new HMMwithduration formalism (see Fig. 7), with 100 steps used in the Viterbi decoding HMM’s approximation of the 1kstep generating HMM’s Poisson durations. (DOC 26 KB)
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Additional file 4: Results on a 3state system, showing the strong performance of the new HMMwithDuration method is demonstrated (see Figures 8 and 9 for other results on this system). (DOC 72 KB)
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Additional file 6: A real time 9AT vs 9GC DNA hairpin classification (with 9AT identification indicated by the LED light flashing on). (DOC 114 KB)
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Additional file 8: A 50state genericHMM (typically) is used to obtain feature vectors, a webinterfaces for this tool is shown. (DOC 566 KB)
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WintersHilt, S., Baribault, C. A novel, fast, HMMwithDuration implementation – for application with a new, pattern recognition informed, nanopore detector. BMC Bioinformatics 8 (Suppl 7), S19 (2007). https://doi.org/10.1186/147121058S7S19
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DOI: https://doi.org/10.1186/147121058S7S19