FROM COMPRESSIVE TO ADAPTIVE SAMPLING OF NEURAL AND ECG RECORDINGS
Alexander Singh Alvarado and José C. Prı́ncipe
University of Florida, Electrical and Computer Engineering Department
Gainesville, Florida, 32611
ABSTRACT
The miniaturization required for interfacing with the brain
demands new methods of transforming neuron responses
(spikes) into digital representations. The sparse nature of neu-
ral recordings is evident when represented in a shift invariant
basis. Although a compressive sensing (CS) framework may
seem suitable in reducing the data rates, we show that the
time varying sparsity in the signals makes it difficult to apply.
Furthermore, we present an adaptive sampling scheme which
takes advantage of the local characteristics of the neural spike
trains and electrocardiograms (ECG). In contrast to the global
constraints imposed in CS our solution is sensitive to the local
time structure of the input. The simplicity in the design of
the integrate-and-fire (IF) make it a viable solution in cur-
rent brain machine interfaces (BMI) and ambulatory cardiac
monitoring.
Index Terms— Adaptive sampling, brain-machine inter-
face, non-uniform sampling, integrate-and-fire model, ECG
1. INTRODUCTION
Information in the brain is encoded in the stereotypical out-
put of neurons known as action potentials (AP) that stand out
above a noisy background. The goal of BMIs is to extract
meaningful information from these neural recordings, in or-
der to take future actions. The first stage in any BMI is to
capture the behavior of the hundreds of neurons and reliably
transmit APs to the external world.
Cortical neurons spike at rates of 5-100 AP per second,
the upper limit when they form neural assemblies that are
related to behavioral tasks. The algorithms used in conven-
tional BMIs require that the AP be catalogued by neuron and
assume the rest of the signal as featureless. It is evident that
the regions of interest in neural recordings are localized in
time and amplitude. The only information that must be pre-
served is the shape of each action potential, in order to guaran-
tee discriminability. The recording of the electrocardiogram
(ECG) presents a very similar structure and there is a great
need to compress ECG for ambulatory, 24 hour monitoring.
The sparse events immediately suggest the use of a CS ap-
proach.
The authors acknowledge NINDS Grant Number: NS053561.
978-1-4577-0539-7/11/$26.00 ©2011 IEEE 633
Although the approach seems reasonable, a number of dif-
ficulties arise. First, the CS framework assumes the sparsity
of the input is known and constant. This does not hold for
neural recordings, since the firing patterns may change dras-
tically. Specially when neurons are involved in neural assem-
blies. Furthermore, measurements in CS are created based on
projections on the entire sparse feature. Although this may
reduce the data rates in comparison to conventional analog to
digital converters (ADC), the time structure of the signal is
being ignored. In contrast we propose an adaptive sampling
scheme that can be tuned to the specific features of the in-
put. Instead of imposing global sparseness constraints, we ex-
ploit the local structure of the signal. The adaptive sampling
scheme proposed is based on the integrate-and-fire model [1].
The sampler is asynchronous and will generate samples based
on level crossings of the integral of the signal. Therefore, the
resulting sample sets are nonuniformly spaced and clustered
in the vicinity of the action potentials, given their prominent
amplitude.
Recently a variety of adaptive sampling schemes have
been implemented, mostly in wireless sensor networks [2].
Other approaches also include information about the specific
task in the design of the sampler [3], these are related to ac-
tive learning in the machine learning context. In this case, the
sample locations and values are determined based on the final
goal and the available information. Given the abstract nature
of the problem, it is difficult to describe a general framework
for all adaptive sampling schemes.
In this paper we focus on the IF sampler which is a spe-
cial case of a large class of asynchronous Σ − Δ modulators
[4]. These samplers are typically designed such that they os-
cillate in an autonomous mode. The oscillation frequency is
analogous to the clock period in their discrete counterparts.
These modulators encode the input into the output sample
rate, which is typically hundreds of times the Nyquist rate.
Nevertheless, they are attractive since coarse quantization of
the amplitude still provides an accurate representation. The
input can be recovered using a simple low pass filter. In con-
trast, the IF sampler is used to sub-sample the input. When
used to encode neural recordings or ECG we can still accu-
rately recover the APs and QRS complexes at sub-Nyquist
rates. Nevertheless, the recovery algorithms are nonlinear and
the compression depends on the signal characteristics.
ICASSP 2011
 The paper is organized as follows. We describe both CS
and IF sampling schemes and their corresponding recovery
algorithms. Both approaches are then compared in terms of
the data rates and the recovery accuracy when applied to neu-
ral recordings and ECG. Since BMI algorithms are designed
on conventional digital systems, we must also consider the ef-
fects of quantization under both schemes. In the case of CS
sample amplitudes are quantized assuming a constant sam-
pling period while the IF events are quantized in time and
consider a coarse amplitude range.
2. A CS APPROACH FOR ANALOG SIGNALS
Compressive sensing literature [5], was initially framed in
terms of discrete finite length signals. The basic framework
exploits the fact that given an appropriate representation most
signals can be considered sparse. Therefore a relatively small
number of measurements is necessary to ensure recovery. It
is crucial to define the necessary and sufficient conditions un-
der which a feasible recovery is possible, i.e. constraints on
the projection matrix must be imposed. Most authors refer
to the sufficient conditions as the coherence measure or the
Uniform Uncertainty Principle (UUP) otherwise known as the
restricted isometry property (RIP).
In recent years, compressive sensing has been extended
to the analog signal class providing reconstruction algorithms
and hardware implementations. We have identified at least
three different trends in the implementation of compressive
sampling algorithms for streaming data. The first, consists of
using finite length random filters [6]. The measurements are
the convolution of the finite response filter and the input. The
process can be translated into a linear system of equations
y = Φx where y are the measurements, x is the sparse input
and Φ is a banded projection matrix for which each row has
no more than b nonzero elements, where b is the length of the
filter. In this paper we use a similar implementation assuming
we have access to the entire sparse signal. The integrate and
fire, although a nonlinear system can also be framed in terms
of linear constraints but the matrix rows are built from ones
with a varying number of nonzero elements which depend on
the distance between consecutive samples. On the other hand
the measurement vector would only consist of ±θ.
Other approaches, such as the random analog demodula-
tor proposed in [7, 8] mix the sparse components directly in
the continuous time domain. These are then uniformly sam-
pled presumably at sub-Nyquist rates. A third class of im-
plementations combines traditional frequency based analysis
and CS proposed in [9]. Other alternatives that assume spar-
sity constraints on the input include the work on finite rate of
innovation [10]. The reconstruction algorithms separate the
problem in two stages the first uses Prony’s method (a.k.a an-
nihilation filter) to determine the location of the sparse com-
ponents. The second determines the sample values at these
locations by least squares.
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Fig. 1. Bi-phasic integrate-and-fire block diagram.
3. THE BI-PHASIC INTEGRATE-AND-FIRE
SAMPLER
Since the inter-spike activity is mostly noise, an appropriate
sampler should exploit the sparse nature of the APs. A simi-
lar case occurs in ECG, where the most relevant feature is the
QRS complex. The IF model takes advantage of these fea-
tures, Figure 1 shows the basic components. The continuous
input x(t) is convolved with an “averaging function” uk (t),
the result is compared against two fixed thresholds, when ei-
ther of these is reached, a pulse is created at time tk repre-
senting the threshold value. The integrator is reset and held
at this state depending on the refractory period specified by
τ ; the process then repeats. Note that samples are bi-polar,
which is one of the differences when compared to other ap-
proaches using these type of models as sampling devices [11].
The output pulse train is defined over a discrete set of nonuni-
formly spaced time stamps. Here we assume uk (t) is constant
between two samples. Other averaging functions have been
considered in [12]. Therefore, the IF samples satisfy:
 tk+1
θk = x(t)dt (1)
tk +τ
The input is modeled in a shift invariant spaces (SIS), a nat-
ural representation for the action potentials. These spaces are
well known in approximation theory, nonuniform sampling
and compressive sensing. In this case, the input is defined in
a M dimensional space:
M

x(t) = ck φ(t − T k) (2)
k=1
Where φ(t) are known as the generators of the space and T is
the underlying period. Which is determined in relation to the
Nyquist period. The generator is chosen to be a cubic B(asis)-
spline defined over a uniform knot sequence. The samples
generated by the IF provide a system of equations from which
we can determine the sparse coefficients, θ = Sc, where the
elements in S are defined by:
 ti+1
Si,k = φ(t − T k)dt (3)
ti +τ
The vector 
θ contains the threshold values and c are the coeffi-
cients. Note that the size and elements of the matrix are signal
dependent and since the basis are compactly supported most but then grows slowly, while CS soars to nearly 100 dB. The
of the non zero elements are near the diagonal. In this case low SNR reconstruction in the IF is due to the low amplitude
we can ensure perfect recovery as long as, one sample falls details in the AP as seen in Figure 2(a), in order to reproduce
in the support of each basis. Nevertheless, we are not con- these small variations we would need to select the threshold
cerned with full recovery of the signal, but rather the spike extremely low. In contrast, CS only assumes a sparse sig-
regions [12]. We have also presented recovery algorithms in nal and does not constrain the amplitude of these elements,
the typical bandlimited space, along with the corresponding therefore the conditions are exactly satisfied. Nevertheless,
error bounds [13]. these small details are in the range of the noise for this appli-
cation and are not crucial. This trend does not extend to real
4. RESULTS

We show results both on neural and ECG recordings. The 120

IF
50

neural data used has been recorded from a behaving animal. 100
CS
40
IF
CS

Average spike SER [dB]

Average spike SER [dB]

This data was provided by the Neuro-prosthetics Research 80

60
30

Group at the University of Florida. We also use synthetic 40

20
Nyquist Rate

data in order to satisfy the sparsity constraints imposed by 20

10

CS. The synthetic data was created by placing synthetic APs 0

0 100 200 300 400
Number of samples
500 600 700
0
0 100 200 300 400 500
Number of samples
600 700 800

and forcing the inter-spike regions to zero. Figure 2(a) shows
the reconstruction for this type of signals using the IF and CS
approaches. The insert shows the complete signal consisting
of three APs. Since the IF assumes an analog input, the pre-
cise timings for the samples are determined based on an over-
sampled version of the input. The measurements in the CS
case, were determined by projections of the input with a ran-
dom matrix whose elements are instances of a zero mean unit
variance gaussian random variable. We use the optimization
methods proposed in [5], based on an interior point method
to determine the sparse vector. As mentioned earlier BMIs
−5
x 10
6
6
original
(a) Neural simulator. (b) Real data.
Fig. 3. Variation in the reconstruction accuracy in relation to
the number of samples.
recordings, as seen in Figure 2(b). Here we show a zoomed in
version of the last AP, these have amplitudes near 50μV and
a bandwidth of 5KHz. Since they are no longer strictly sparse
the performance using CS deteriorates as seen in Figure 3(b).
−5
The IF outperforms the conventional CS approach, and pro-
vides a feasible representation even at sub-Nyquist rates. In
x 10

4
rec−CS
rec−IF
4

2
this case the Nyquist rate is 10Khz and the signal duration
Amplitude [Volts]

2 0
is 37ms which translates into 368 samples. We have also
Amplitude [Volts]

−2
0 −4 extended our results to ECG recordings, which share simi-
lar time structure with neural signals. Here we used the QT
−6 original
−2 rec−CS
−8 rec−IF

−4
5
−9
x 10 database available at PhysioBank [14]. The recordings have
Threshold

−6

0.01 0.011 0.012 0.013 0.014 0.015 0.016

0

−5
0.02 0.022 0.024 0.026 0.028
been sampled at 250Hz. Figure 4 shows the original and re-
Time [s] Time [s]
covered signals, as well as the variation of the reconstruction
(a) Neural simulator. (b) Real data on the entire window in relation to the number of samples.
The entire signal has a duration of approximately 4s therefore
Fig. 2. Data recovered using CS and IF. The underline defines the number of samples equivalent to the Nyquist rate would
the AP region. be 1024. These results are comparable to those in [15] based
on a CS approach using wavelet decompositions. Although
require knowledge of the precise timings of the APs for each the SER seems to be low, sufficient information of the signal
neuron. Therefore, we are only concerned with the recon- is preserved to make reliable estimates on cardiac features.
struction accuracy in the vicinity of the AP. The recovery er- Since the data must eventually be processed by a digital sys-
ror is measured in terms of the signal to error ratio (SER) tem we also show the variation in the recovery based on the
(10 log(power signal/power error)) within a window around quantization. In CS the amplitudes of the measurements are
the AP, where the error is simply given by the difference be- quantized, while in the IF the sample time instants are quan-
tween both signals. Figure 3(a) shows the average variation tized to a specific clock as seen in Figure 4. These results were
of the SER around the three AP regions for both approaches obtained using the synthetic data. In the case of the IF we
in relation to the number of samples. In the case of the IF the require at least 1μs resolution at the receiver side, this does
samples were increased by reducing the threshold, keeping not imply we need to transmit the quantized time. In con-
the refractory period at zero. Note that the reconstruction per- trast, each measurement transmitted using the CS approach
formance of the IF outperforms the CS for very few samples requires at least 10 bits.

635
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