Model-X Sequential Testing for Conditional Independence via Testing by Betting Shalev Shaer1Gal Maman1Yaniv Romano12

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Model-X Sequential Testing for Conditional Independence
via Testing by Betting
Shalev Shaer,1Gal Maman,1Yaniv Romano1,2
1Department of Electrical and Computer Engineering, Technion–Israel Institute of Technology
2Department of Computer Science, Technion–Israel Institute of Technology
Abstract
This paper develops a model-free sequential test
for conditional independence. The proposed test
allows researchers to analyze an incoming i.i.d.
data stream with any arbitrary dependency struc-
ture, and safely conclude whether a feature is
conditionally associated with the response under
study. We allow the processing of data points on-
line, as soon as they arrive, and stop data acqui-
sition once significant results are detected, rigor-
ously controlling the type-I error rate. Our test
can work with any sophisticated machine learn-
ing algorithm to enhance data efficiency to the
extent possible. The developed method is in-
spired by two statistical frameworks. The first
is the model-X conditional randomization test,
a test for conditional independence that is valid
in offline settings where the sample size is fixed
in advance. The second is testing by betting,
a “game-theoretic” approach for sequential hy-
pothesis testing. We conduct synthetic experi-
ments to demonstrate the advantage of our test
over out-of-the-box sequential tests that account
for the multiplicity of tests in the time horizon,
and demonstrate the practicality of our proposal
by applying it to real-world tasks.
1 INTRODUCTION
A central problem in data analysis is to rigorously find con-
ditional associations in complex data sets with nonlinear
dependencies. This problem lies at the heart of causal dis-
covery (Pearl et al., 2000; Peters et al., 2017), variable se-
lection (Barber and Cand`
es, 2015; Candes et al., 2018), ma-
chine learning interpretability (Burns et al., 2020; Lu et al.,
*Equal contribution.
2018), economics (Angrist and Kuersteiner, 2011; Wang
and Hong, 2018), and genetics studies (Sesia et al., 2019;
Bates et al., 2020), to name a few. In such applications, the
data are often collected online, and, naturally, researchers
are interested in analyzing the data points immediately af-
ter they are observed so that further data acquisition can be
terminated as soon as significant results are detected. This
experimental setting, for example, is typical in decision-
making (Nikolakopoulou et al., 2018; Bhui, 2019) and clin-
ical trials (Park et al., 2018), where the need for additional
samples to obtain accurate statistical inference must fre-
quently be balanced with experimental costs.
To formalize the problem, suppose we are given a stream of
data points (Xt, Yt, Zt)for tN= 1,2, . . . , where each
triplet contains a response YtR, a feature XtR, and
a vector of covariates ZtRd. We assume the observa-
tions are sampled i.i.d. from PY XZ =PY|XZ PXZ , where
PY|XZ is unknown. Given such an online data stream, our
goal is to test for conditional independence (CI), where the
null hypothesis is given by
H0:XtYt|Ztfor all tN.
In words, we say that H0is true if Xtis independent of the
response Ytafter accounting for the effect of the covariates
Zt,simultaneously for all time steps t. We refer to Xtthat
satisfies H0as an ‘unimportant’ feature. Analogously, the
alternative hypothesis implies that Xtcarries new informa-
tion on the response Ytbeyond what is already contained
in Zt, i.e., Xt6⊥Yt|Zt. Therefore, we say that such a
feature Xtis ‘important’.
The goal of sequential hypothesis testing is to formulate a
concrete decision rule on whether we can confidently reject
the null at each time step t, by monitoring and accumulat-
ing the evidence collected at each step against the null us-
ing past data {(Xs, Ys, Zs)}t
s=1 (Wald, 1945). This allows
the analyst great flexibility, as she can decide, at each step,
whether new data should be collected to support the ques-
tion under study. Key to this setting is the need to provide
the analyst with a tool that rigorously controls the type-I
error rate—defined as the probability of rejecting the null
when it is in fact true—at any given desired level α, simul-
arXiv:2210.00354v2 [stat.ME] 19 Feb 2023
Model-X Sequential Testing for Conditional Independence via Testing by Betting
taneously for all time steps t. This requirement should not
be confused with the premise of classic offline tests for CI
that attain type-I error rate control only when the sample
size is fixed in advance. We refer to these as offline tests,
emphasizing that one cannot naively monitor the outcome
of a classic test—a p-value—and reject the null at an op-
tional time step twithout accounting for the multiplicity of
the tests across the time horizon; this strategy would result
in inflation of the type-I error rate. Beyond online type-I
error rate control, ideally, we wish to have a powerful test
that would reject the null when it is false, and we want it to
do so as early as possible.
Our contribution
In this paper, we develop a novel sequential test for CI.
Our proposal takes inspiration from two powerful and at-
tractive statistical tools that are gaining increasing atten-
tion in recent years. The first is the model-X conditional
randomization test (CRT) by Candes et al. (2018), an of-
fline test for CI. The second is testing by betting (Shafer
and Vovk, 2019; Gr¨
unwald et al., 2020), a “game-theoretic”
approach for sequential hypothesis testing, where our pro-
posal is very much inspired by the line of work reported
in (Ramdas and Wenbe, 2020; Ramdas et al., 2022). The
method we introduce in this paper, presented in Section 4,
generalizes the offline CRT to the challenging online set-
ting, resulting in a new test with the following features.
Safe testing with early stopping: building on recent ad-
vances in sequential testing using e-values and martingales,
detailed in Section 3, the proposed CI test is guaranteed to
control the type-I error rate at any time step. In particular,
the analyst is allowed to track the outcome of the test over
time, and safely reject the null if it exceeds a user-defined
significance level, preventing a wasteful collection of un-
necessary new data points.
Model-X setting: similar to the offline CRT method, de-
scribed in Section 2, the online test we propose does not
make any assumptions on the conditional distribution of
Y|X, Z. For instance, we do not make unrealistic as-
sumptions that the relationship between Yand (X, Z)is
linear, or that Y|X, Z is Gaussian. However, this advan-
tage comes at the cost of assuming that the distribution of
X|Zis known. This assumption is common to all tests be-
longing to the family of model-X knockoffs, including the
CRT, and it is manageable when (i) large unlabeled data are
available in contrast to labeled data, or (ii) when we have
good prior knowledge about the distribution of X|Z(Can-
des et al., 2018; Sesia et al., 2019; Romano et al., 2020).
We discuss this in more detail in Section 4.2.
Online learning from past experience: the proposed test
can leverage any machine learning algorithm to powerfully
discover violations of the CI null. In particular, when a
new triplet (Yt, Xt, Zt)is observed, we use online learn-
ing techniques to efficiently update the running predictive
model, instead of fitting a new model from scratch. This
way, the whole data stream is used for training in a compu-
tationally efficient manner. The proposed framework also
falls under the umbrella of interactive tests (Lei and Fithian,
2018; Lei et al., 2021; Duan et al., 2022), providing the an-
alyst the liberty to look at past data and decide how to mod-
ify the learning algorithm at any time step—e.g., to switch
to a model that is more robust to outliers—to better dis-
criminate the null and alternative hypotheses when applied
to future test points.
Optimized software package: we provide a python code
that implements our testing framework, is available at
https://github.com/shaersh/ecrt. The pack-
age includes important design principles: an automatic
hyper-parameter tuning that does not require fitting the ma-
chine learning model from scratch (Supplementary Sec-
tion E); an ensemble procedure for improving the power
of the test by averaging multiple martingales (Section 4.2);
and a de-randomization procedure that also improves
power by reducing inherent algorithmic randomness due to
a sampling mechanism that is necessary to formulate the
test (Section 4.2).
2 MODEL-X CI TESTING
The CRT, developed by Candes et al. (2018), is an offline
test for CI that we build upon in this work. A key advan-
tage of the CRT is that it assumes nothing on the condi-
tional distributions of Y|X, Z and Y|Z. This test, how-
ever, assumes that the conditional distribution of X|Zis
known. The CRT procedure, described in Algorithm 3 in
Supplementary Section B, resembles classic permutation
tests and has two key components: a test statistic func-
tion T(·)and a function that samples dummy features ˜
X
from PX|Z. Since ˜
Xis sampled without looking at Y, the
dummy triplets (˜
X, Y, Z)satisfy ˜
XY|Zby construc-
tion. Hence, by comparing the test statistic evaluated on the
original {(Xi, Yi, Zi)}n
i=1 and dummy {(˜
Xi, Yi, Zi)}}n
i=1
triplets, the CRT generates a valid p-value pn, controlling
the CI null at level αwhen the sample size nis fixed in
advance (Candes et al., 2018), i.e.,
P[pnα|the null is true]αfor a fixed n. (1)
Put differently, when all nobservations are available be-
fore testing, one can use pnto rigorously control the type-I
error. However, future observations cannot be utilized to
generate a new p-value (e.g., in cases where the null is not
rejected) without a proper correction that ensures the valid-
ity of the sequential test. To see this, suppose for simplicity
that under the null pnUniform(0,1) is distributed uni-
formly over the [0,1] interval for any fixed n, satisfying (1).
Next, let τbe a data-dependent stopping time, given by
τ={min n:pnα, n N}.
Shalev Shaer, Gal Maman, Yaniv Romano
Now, observe that with this choice of stopping time,
P[pτα|the null is true]cannot be bounded by αany-
more: there exists τsuch that a rejection rule pταwould
result in an invalid α-level test.
In many applications, however, one is interested in apply-
ing the test online to obtain reliable data-driven conclusions
as soon as possible. This motivates us to adopt a fresh sta-
tistical approach for hypothesis testing, called testing by
betting, briefly described in the next section.
3 TESTING BY BETTING
Before diving into the mathematical principles of the test-
ing by betting approach, we follow Shafer and Vovk (2019)
and Shafer (2021) and present an intuitive interpretation of
this framework. Imagine we are playing a game, in which
we start with initial toy money. At each time step, we place
a bet against the null hypothesis, and then reality reveals
the truth. If this bet turns out to be correct, our wealth is
increased by the money we risk in the bet; otherwise, we
lose and the wealth is decreased accordingly. If our wealth
at time tis at least 1times as large as the initial toy
money we started with (e.g., we have managed to multiply
our initial money by a factor of 1/0.05 = 20 for α= 0.05)
we can confidently reject the null, knowing that the type-I
error is guaranteed to be controlled at level α. A property
important to the formulation of the above game is this: if
the null is true, the game must be fair in the sense that it is
unlikely we will be able to significantly increase our initial
toy money, no matter how sophisticated our betting strategy
is.
A mathematical object that is crucial to formalize a fair
game is a test martingale, defined below.
Definition 1. A random process {St:tN0}is a test
martingale for a given null hypothesis H0if it satisfies the
following conditions: (i) S0= 1, (ii) St0,tN0,
and (iii) {St:tN0}is a supermartingale under H0.
In the view of testing by betting, the initial value of the test
martingale S0represents the initial toy money in the game,
and Stcorresponds to our wealth at time t. Now, suppose
we are handed a valid test martingale {St:tN0}, and
let τ1be a data-dependent optional stopping time. By
invoking the optional stopping theorem we get
EH0[Sτ]EH0[S0]=1,(2)
meaning that Sτis a non-negative random variable whose
expected value is bounded by one for any stopping time
τ1. In the literature on testing by betting, Sτis often
referred to as an e-value (Vovk and Wang, 2021; Wang and
Ramdas, 2022; Gr¨
unwald et al., 2020). Importantly, the
consequence of (2) is that, under the null, the game is fair
since the expected value of our wealth Stat any time step
tis bounded by the initial toy money S0. Moreover, since
{St:tN0}is a non-negative supermartingale under H0,
we can apply Ville’s inequality (Ville, 1939) and get
PH0(t1 : St1)αEH0[S0] = α, (3)
for any α(0,1). Therefore, the ability to form a valid test
martingale allows us to rigorously test for H0and reject the
null if St1at any time step, with the premise that the
type-I error would not exceed the level α. Crucially, when
the null is false, Stcan largely grow depending on how suc-
cessful our betting strategy is. In Section 4 we formulate a
valid test martingale and design a powerful betting strategy.
Related work. Sequential testing has a long standing his-
tory (Wald, 1945; Lai, 1984; Naghshvar and Javidi, 2013;
Lh´
eritier and Cazals, 2018), where the sequential probabil-
ity ratio test of Wald (1945) is perhaps one of the first se-
quential hypothesis tests. More recently, the testing by bet-
ting methodology (Shafer and Vovk, 2019; Shafer, 2021)
has led to the design of new powerful nonparametric ap-
proaches for constructing confidence sequences, e.g., (Jun
and Orabona, 2019; Waudby-Smith and Ramdas, 2023), for
testing a single hypothesis, as well as for testing multiple
hypotheses; see (Waudby-Smith and Ramdas, 2023, Sec-
tion 6) for a detailed summary.
Related methods to our proposal are offline and online
two-sample tests that are based on martingales (Balsub-
ramani and Ramdas, 2016; Turner et al., 2021; Shekhar
and Ramdas, 2021; Duan et al., 2022). Specifically,
Shekhar and Ramdas (2021) studied the problem of design-
ing martingale-based sequential nonparametric one- and
two-sample tests that are consistent, i.e., these sequential
tests can attain power one under certain conditions. In our
work, we build on the foundations of Shekhar and Ram-
das (2021), and extend this framework to CI testing. Re-
cently, Ren and Barber (2022) suggested using e-values to
de-randomize the outcome of the knockoff filter—a sister
method to the CRT that focuses on false discovery rate con-
trol (FDR) in an offline setting. In our work, we aggregate
e-values to de-randomize our test, where the e-values we
define take a different form than those proposed by Ren
and Barber (2022), as we focus on sequential testing of
a single feature. Lastly, independent work by Gr¨
unwald
et al. (2022), which has been developed and posted in par-
allel to ours, also offers a martingale-based sequential test
under the model-X setting, although suggesting a different
test martingale. In Supplementary Section D we provide a
more detailed discussion about the relation of our proposal
to that of Gr¨
unwald et al. (2022), along with empirical com-
parisons.
4 THE PROPOSED e-CRT
In this section, we introduce e-CRT: a sequential test for CI
based on martingales and e-values. Suppose we are given a
Model-X Sequential Testing for Conditional Independence via Testing by Betting
Figure 1: Illustration of the test martingale (wealth) St
as a function of t. The blue (resp. green) curve represents
the test martingale evaluated on simulated null data
(resp. non-null data).
machine learning model ˆ
ft, fitted on an initial batch of la-
beled data {(Xs, Ys, Zs) : st1}to provide an estimate
of Ygiven (X, Z). At a high level, the test is initialized
with toy money S0= 1 and proceeds as follows.
1. Collect a fresh test triplet (Xt, Yt, Zt).
2. Generate a dummy feature ˜
XtPX|Z(Xt|Zt), and
form the dummy triplet (˜
Xt, Yt, Zt).
3. Compute a betting score Wt. Use ˆ
ftto bet against the
null, where the bet is that the prediction error of ˆ
ft(or
any other test statistic), evaluated on the dummy triplet
(˜
Xt, Yt, Zt), would be higher than that of the original
triplet (Xt, Yt, Zt). A positive (resp. negative) score
indicates that our bet is successful (resp. unsuccessful).
4. Update the current wealth (test martingale) St: if the
betting score is positive, the previous St1is increased
by the money we risked on placing the bet; otherwise,
the previous wealth St1is decreased analogously.
5. Update the predictive model ˆ
ftand get ˆ
ft+1, e.g., by
taking one (or more) gradient steps to minimize a loss
evaluated on {(Xs, Ys, Zs) : st}.
6. If St1reject H0and stop. Otherwise, increase t
and return to step (1).
In what follows, we describe each of the above components
in depth, define the proposed test martingale, and prove its
validity. Later, in Section 4.2, we provide additional design
principles that improve the power of the test.
Before doing so, we pause to provide a small synthetic ex-
periment that showcases how the wealth process Stbe-
haves under the null and the alternative. To this end,
we generate two different data sets. The first satisfies
H0, which we refer to as null data in which Xis
unimportant. The second satisfies the alternative, which we
call non-null data in which Xis important. The data
generation process for each case and the implementation
details are described in Section 5.1. Next, we apply e-CRT
on each data set, and present in Figure 1 the wealth pro-
cess Stas a function of t. When the test is applied to the
null data, the value of Stremains close to the initial
wealth S0= 1 for all presented time steps t. In particu-
lar, Stdoes not exceed the value 1= 20, and thus H0
cannot be rejected. By contrast, when the test is applied
to the non-null data, the wealth process grows as the
testing procedure proceeds, until reaching a target value of
1= 20. In this case, we reject the null and report that X
is indeed important. This experiment illustrates the advan-
tage of monitoring the value of Stover time: we can safely
terminate the test after collecting 300 samples and avoid a
wasteful collection of new data.
4.1 Formulating the Test Martingale
Our procedure exploits the dummy feature ˜
Xt, sampled
from the conditional distribution of X|Zto form a fair
game. In the sequel, we state key properties of the dum-
mies, which we will use to define our test. The proofs of
all statements given in this section are provided in Supple-
mentary Section A. We start by emphasizing that we sam-
ple ˜
XtPX|Z(Xt|Zt)without looking at Yt, and so
˜
XtXt|Ztfor all tNby construction. Therefore,
Xtand its dummy ˜
Xtare exchangeable conditional on Zt;
that is, (Xt,˜
Xt)|Zt
d
= ( ˜
Xt, Xt)|Zt, where d
=reads as
‘equal in distribution’. This implies that it is impossible to
distinguish between Xtand its dummy ˜
Xtwhen viewing
Zt, for any time step t. Furthermore, under the null, this ex-
changeability property holds not only conditionally on Zt
but also on Yt.
Lemma 1. Take (Xt, Yt, Zt)PXY Z , and let ˜
Xtbe
drawn independently from PX|Zwithout looking at Yt. If
YtXt|Zt, then (Xt,˜
Xt, Yt, Zt)d
= ( ˜
Xt, Xt, Yt, Zt).
The above result lies at the heart of the knockoff and CRT
frameworks, and its proof follows (Candes et al., 2018,
Lemma 3.2), (Barber et al., 2020, Lemma 1). Lemma 1
implies that, if the null is true, it is impossible to tell which
is the original feature and which is the dummy when view-
ing the full observation, at any time step t. This result is
essential for proving the validity of the CRT p-value, as
well as for formulating our test martingale, as we do next.
Denote by Ft=σ({Xs, Ys, Zs}t
s=1)the sigma-algebra
generated by observations collected up to time t, where F0
is the trivial sigma-algebra. Let qt=T(Xt, Yt, Zt;ˆ
ft)R
and ˜qt=T(˜
Xt, Yt, Zt;ˆ
ft)Rbe the test statistics evalu-
ated on the original and dummy triplets, respectively. Im-
portantly, T(·;ˆ
ft)can be any function, and its choice may
affect the power of the test. For instance, one can define
T(·;ˆ
ft)as the squared prediction error evaluated on the
current sample T(x, y, z;ˆ
ft) = ( ˆ
ft(x, z)y)2using a
model ˆ
fttrained on past data {Xs, Ys, Zs}t1
s=1. Observe
that ˆ
ftis not fitted on the new triplet (Xt, Yt, Zt), thus it is
considered as a fixed function once conditioning on Ft1.
We then proceed by evaluating a betting score
Wt=g(qt,˜qt),(4)
Shalev Shaer, Gal Maman, Yaniv Romano
where the function g(a, b)[m, m]is antisymmetric
g(a, b) = g(b, a), satisfying g(a, b)>0if b > a and
g(a, b1)g(a, b2)for b1b2. For example, g(a, b) =
m·sign(ba). The hyper-parameter 0< m 1controls
the magnitude of the score. As in the knockoff filter, our
design of gensures it follows the flip sign property, requir-
ing that a swap of the original feature Xtand its dummy
˜
Xtwill flip the sign of Wt(Candes et al., 2018).
Under the alternative, one should interpret a strictly posi-
tive betting score Wt>0as a successful bet, which will
increase our wealth. This means that we gain some evi-
dence that Xtcarries extra predictive power about Ytbe-
yond what is already known in Zt. Analogously, a strictly
negative Wt<0indicates an erroneous bet, which will
reduce our wealth even though the null is false. Crucially,
under the null, Wtwill be zero on average, no matter how
accurate ˆ
ftis. In other words, it is impossible to have a
systematically positive Wtwhen H0is true.
Lemma 2. Under the same conditions as in Lemma 1, if
H0is true then EH0[Wt| Ft1]=0for all tN.
The core idea behind the proof of the above lemma is that,
under the null, Wthas a symmetric distribution about zero
conditional on Ft1, and thereby its expected value is zero;
see (Ramdas et al., 2020) for a related property of symmet-
ric distributions. In particular, Wtis equally likely to have
positive and negative values, which is a well-known result
in the knockoff literature with the important difference that
in our case we show it holds conditionally on Ft1.
Armed with the betting score Wtat time t, we turn to define
a test martingale {St:tN0}for H0. The martingale
can be thought of as the wealth process, initialized by toy
money S0= 1, and our ultimate goal is to maximize it. We
begin with defining the base martingale as follows:
Sv
t:=
t
Y
j=1
(1 + v·Wj),(5)
where v[0,1] is a fixed amount of toy money that we are
willing to risk at step t.1Proposition 2 in Supplementary
Section C.1 shows that {Sv
t:tN0}in (5) is a valid test
martingale. As a result, following Ville’s inequality in (3),
one can monitor Sv
tand control the type-I error for any
choice of v[0,1]. Importantly, the amount of toy money
vthat we risk when placing the bet affects the power.
The above immediately raises the question of how should
we choose v? Ideally, we want to set the best constant
vso that Sv
tis maximized under the alternative. The
problem is that we are not allowed to look at the current
1We can set a different vtfor each time step, yet vtmust be
chosen without looking at the current (Xt, Yt, Zt)as otherwise
the test will cease to be valid. Intuitively, in such a case one can
always set vt= 0 when Wtis negative and vt= 1 otherwise, and
increase the wealth regardless on whether the null is true or false.
betting score Wt, so it is impossible to find such an ideal
data-dependent vin foresight. As a thought experiment,
consider the simplest choice for gas the sign function for
which Wt∈ {+1,1}, and suppose we adopt an aggres-
sive betting strategy with v= 1. With this choice, when
we win a bet we will increase Sv
tby the maximal amount
possible at step t. However, if we lose a bet even once, we
will have Sv
t= 0, resulting in a powerless test; to see this,
assign Wt=1in (5). We give a concrete example that
visualizes this discussion in Supplementary Section C.2.
As a way out, we formulate a powerful betting strategy us-
ing the mixture-method of Shekhar and Ramdas (2021),
which is intimately connected to universal portfolio opti-
mization (Cover, 2011). The mixture-method is defined as
the average over Sv
tfor all v[0,1]:
St=Z1
0
Sv
t·h(v)dv, (6)
where h(v)is a probability density function (pdf) whose
support is on the [0,1] interval, e.g., a uniform distribution.
We adopt the mixture method betting strategy to formu-
late our test martingale since it has appealing power prop-
erties, which we discuss soon. Before doing so, however,
we shall first prove that the test martingale in (6) is valid.
The theorem presented below states that by monitoring St
one can safely reject the null the first time Stexceeds 1,
while rigorously controlling the type-I error simultaneously
for all optional stopping times. This result holds in finite
samples, without making any modeling assumptions on the
conditional distribution of Y|X, and for any machine
learning model ˆ
ft, which we use to bet against the null. The
proof follows (Shekhar and Ramdas, 2021, Section 2.2).
Theorem 1. Under the same conditions as in Lemma 1, if
the null hypothesis H0is true then for any α(0,1),
PH0(t:St1)α.
Having established the validity of the test, we turn to dis-
cuss the key advantage of the mixture method betting strat-
egy. The idea behind this approach is that one of the base
martingales Sv
tin (6) must hit the best constant v, which,
in turn, drives the average martingale Stupwards. We
demonstrate this visually in Supplementary Section C.2. In
fact, Shekhar and Ramdas (2021) proved that Stis not only
dominated by Sv
t, but can also provably form a consistent
test that achieves power one in the limit of infinite data.
Proposition 1 (Shekhar and Ramdas (2021)).If
lim inft→∞ 1
tPt
s=1 Ws>0under the alternative
H1. Then, PH1(t:St1) = 1 for any α(0,1).
The condition of lim inft→∞ 1
tPt
s=1 Ws>0implies that
it suffices that only on average the predictive model will be
able to tell apart the original and dummy triplets, so at the
limit of infinite data we will attain a consistent test.
摘要:

Model-XSequentialTestingforConditionalIndependenceviaTestingbyBettingShalevShaer;1GalMaman;1YanivRomano1;21DepartmentofElectricalandComputerEngineering,Technion–IsraelInstituteofTechnology2DepartmentofComputerScience,Technion–IsraelInstituteofTechnologyAbstractThispaperdevelopsamodel-freesequentia...

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