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Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering Laboratory Electrical and Computer Engineering Department University of Florida www.cnel.ufl.edu [email protected]

Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

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Page 1: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing

Jose C. Principe, Ph.D.Distinguished Professor ECE, BME

Computational NeuroEngineering Laboratory

Electrical and Computer Engineering Department

University of Florida

www.cnel.ufl.edu

[email protected]

Page 2: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Brain Machine Interfaces (BMI)

A man made device that either substitutes a sensory input to the brain, repairs functional communication between brain regions or translates intention of movement.

Page 3: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Types of BMIsSensory (Input BMI): Providing sensory input to form percepts when natural systems are damaged.

Ex: Visual, Auditory Prosthesis

Motor (Output BMI): Converting motor intent to a command output (physical device, damaged limbs)

Ex: Prosthetic Arm Control

Cognitive BMI: Interpret internal neuronal state to deliever feedback to the neural population.

Ex: Epilepsy, DBS Prosthesis

Computational Neuroscience and Technology developments are playing a larger role in the development of each of these areas.

Page 4: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

J.R. Wolpaw et al. 2002

BCI (BMI) bypasses the brain’s normal pathways of peripheral nerves (and muscles)

General Architecture

Page 5: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

INTENT

PERCEPT

ACTION

STIMULUS

Decoding

Coding

BRAIN MACHINE

Neural Interface Physical Interface

The Fundamental Concept

Stimulus Neural Response

Coding Given To be inferred

Decoding To be inferred Given

Need to understand how brain processes information.

Page 6: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Levels of Abstraction for Neurotechnology

Brain is an extremely complex system

1012 neurons

1015 synapses

Specific interconnectivity

Page 7: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Tapping into the Nervous System

The choice and availability of brain signals and recording methods can greatly influence the ultimate performance of the BMI.

The level of BMI performance may be attributed to selection of electrode technology, choice of model, and methods for extracting rate, frequency, or timing codes.

Page 8: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

http://ida.first.fhg.de/projects/bci/bbci_official/

Coarse(mm)

Page 9: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Choice of Scale for Neuroprosthetics

Bandwidth (approximate)

Localization

Scalp Electrodes

0 ~ 80 Hz Volume Conduction Cortical Surface

Electro-corticogram (ECoG)

0 ~ 500Hz Cortical Surface

Implanted Electrodes

0 ~ 7kHz Single Neuron

Page 10: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Spatial Resolution of Recordings

Moran

Page 11: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Florida Multiscale Signal Acquisition

EEG

ECoG

Microelectrodes

Least Invasive

Highest Resolution

NRG IRB Approval for

Human Studies

NRG IACUC

Approval for Animal Studies

Develop a experimental paradigm with a nested hierarchy for studying neural population dynamics.

Page 12: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Common BMI-BCI Methods

BMIs --- Invasive, work with intention of movement• Spike trains, field potentials, ECoG• Very specific, potentially better performance

BCIs --- Noninvasive, subjects must learn how to control their brain activity

• EEG• Very small bandwidth

Page 13: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Computational NeuroScience

Integration of probabilistic models of information processing with the neurophysiological reality of brain anatomy, physiology and purpose.

Need to abstract the details of the “wetware” and ask what is the purpose of the function. Then quantify it in mathematical terms.

Difficult but very promising. One issue is that biological evolution is a legacy system!

BMI research is an example of a computational neuroscience approach.

Page 14: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

How to put it together?

NeoCortical Brain Areas Related to Movement

Posterior Parietal (PP) – Visual to motor transformation

Premotor (PM) and Dorsal Premotor (PMD) -

Planning and guidance (visual inputs)

Primary Motor (M1) – Initiates muscle contraction

Page 15: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Ensemble Correlations – Local in Time – are Averaged with

Global Models

Page 16: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Computational Models of Neural Intent

Two different levels of neurophysiology realism

Black Box models – no realism, function relation between input desired response

Generative Models – minimal realism, state space models using neuroscience elements

Page 17: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Signal Processing Approaches with Black Box Modeling

Accessing 2 types of signals (cortical activity and behavior) leads us to a general class of I/O models.

Data for these models are rate codes obtained by binning spikes on 100 msec windows.

Optimal FIR Filter – linear, feedforwardTDNN – nonlinear, feedforwardMultiple FIR filters – mixture of expertsRMLP – nonlinear, dynamic

Page 18: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Linear Model (Wiener-Hopf solution)

Consider a set of spike counts from M neurons, and a hand position vector dC (C is the output dimension, C = 2 or 3). The spike count of each neuron is embedded by an L-tap discrete time-delay line. Then, the input vector for a linear model at a given time instance n is composed as x(n) = [x1(n), x1(n-1) … x1(n-L+1), x2(n) … xM(n-L+1)]T, xLM, where xi(n-j) denotes the spike count of neuron i at a time instance n-j.

A linear model estimating hand position at time instance n from the embedded spike counts can be described as

where yc is the c-coordinate of the estimated hand position by the model, wji is a weight on the connection from xi(n-j) to yc, and bc is a bias for the c-coordinate.

cL

i

M

j

cjii

c bwjnxy

1

0 1

)(

Page 19: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Linear Model (Wiener-Hopf solution)

In a matrix form, we can rewrite the previous equation as

where y is a C-dimensional output vector, and W is a weight matrix of dimension (LM+1)C. Each column of W consists of [w10

c, w11c, w12

c…, w1L-

1c, w20

c, w21c…, wM0

c, …, wML-1c]T.

xWy T

x1(n)

xM(n)

z-1

z-1

z-1

z-1

yx(n)

yy(n)

yz(n)

Page 20: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Linear Model (Wiener-Hopf solution)

For the MIMO case, the weight matrix in the Wiener filter system is estimated by

R is the correlation matrix of neural spike inputs with the dimension of (LM)(LM),

where rij is the LL cross-correlation matrix between neurons i and j (i ≠ j), and rii is the LL autocorrelation matrix of neuron i.

P is the (LM)C cross-correlation matrix between the neuronal bin count and hand position, where pic is the cross-correlation vector between neuron i and the c-coordinate of hand position. The estimated weights WWiener are optimal based on the assumption that the error is drawn from white Gaussian distribution and the data are stationary.

PRW 1Wiener

MMMM

M

M

rrr

rrr

rrr

R

21

22221

11211

MCM

C

C

pp

pp

pp

P

1

221

111

Page 21: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Linear Model (Wiener-Hopf solution)

The predictor WWiener minimizes the mean square error (MSE) cost function,

Each sub-block matrix rij can be further decomposed as

where rij() represents the correlation between neurons i and j with time lag . Assuming that the random process xi(k) is ergodic for all i, we can utilize the time average operator to estimate the correlation function. In this case, the estimate of correlation between two neurons, rij(m-k), can be obtained by

ydee ],[2

EJ

)0()2()1(

)2()0()1(

)1()1()0(

rLrLr

Lrrr

Lrrr

ij

ijijij

ijijij

ij

r

)()(1

1)]()([)(

1

knxmnxN

kxmxEkmr j

N

nijiij

Page 22: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Linear Model (Wiener-Hopf solution)

The cross-correlation vector pic can be decomposed and estimated in the same way, substituting xj by the desired signal cj.

From the equations, it can be seen that rij(m-k) is equal to rji(k-m). Since these two correlation estimates are positioned at the opposite side of the diagonal entries of R, the equality leads to a symmetric R.

The symmetric matrix R, then, can be inverted effectively by using the Cholesky factorization. This factorization reduces the computational complexity for the inverse of R from O(N3) using Gaussian elimination to O(N2) where N is the number of parameters.

)()(1

1)]()([)(

1

kncmnxN

kcmxEkmp j

N

nijiij

Page 23: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Optimal Linear Model

Normalized LMS with weight decay is a simple starting point.

Four multiplies, one divide and two adds per weight update

Ten tap embedding with 105 neurons

For 1-D topology contains 1,050 parameters (3,150)

Alternatively, the Wiener solution

)()()(

)()1( 2 nxnenx

nwnw

pw 1)( IR

Page 24: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Time-Delay Neural Network (TDNN)

The first layer is a bank of linear filters followed by a nonlinearity.The number of delays to span I secondy(n)= Σ wf(Σwx(n))Trained with backpropagationTopology contains a ten tap embedding and five hidden PEs– 5,255 weights (1-D)

Principe, UF

Page 25: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Multiple Switching Local Models

Multiple adaptive filters that compete to win the modeling of a signal segment. Structure is trained all together with normalized LMS/weight decay Needs to be adapted for input-output modeling.We selected 10 FIR experts of order 10 (105 input channels)

d(n)

Page 26: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Recurrent Multilayer Perceptron (RMLP) – Nonlinear “Black Box”

Spatially recurrent dynamical systems Memory is created by feeding back the states of the hidden PEs. Feedback allows for continuous representations on multiple timescales. If unfolded into a TDNN it can be shown to be a universal mapper in Rn

Trained with backpropagation through time

))1()(()( 1111 byWxWy ttft f

2122 )()( byWy tt

Page 27: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Motor Tasks Performed

-40 -30 -20 -10 0 10 20 30 40-40

-30

-20

-10

0

10

20

30

40

Tas

k 1

Tas

k 2

Data• 2 Owl monkeys – Belle, Carmen

• 2 Rhesus monkeys – Aurora, Ivy

• 54-192 sorted cells

• Cortices sampled: PP, M1, PMd, S1, SMA

• Neuronal activity rate and behavior is time synchronized and downsampled to 10Hz

Page 28: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Model Building Techniques

Train the adaptive system with neuronal firing rates (100 msec) as the input and hand position as the desired signal.Training - 20,000 samples (~33 minutes of neuronal firing) Freeze weights and present novel neuronal data.Testing - 3,000 samples – (5 minutes of neuronal firing)

Page 29: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Results (Belle)

  Signal to error ratio (dB) Correlation Coefficient

  (average) (max) (average) (max)

LMS 0.8706 7.5097 0.6373 0.9528

Kalman 0.8987 8.8942 0.6137 0.9442

TDNN 1.1270 3.6090 0.4723 0.8525

Local Linear 1.4489 23.0830 0.7443 0.9748

RNN 1.6101 32.3934 0.6483 0.9852

 

Based on 5 minutes of test data, computed over 4 sec windows (training on 30 minutes)

Page 30: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Physiologic Interpretation

When the fitting error is above chance, a sensitivity analysis can be performed by computing the Jacobian of the output vector with respect to each neuronal input i

This calculation indicates which inputs (neurons) are most important for modulating the output/trajectory of the model.

Page 31: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Computing Sensitivities Through the Models

T

iit

Tft

T

t

t1

12

2

)(

)(WDWDW

x

y

))1()(()( 1111 byWxWy ttft f

2122 )()( byWy tt

Feedforward RMLP Eqs.

General form of RMLP Sensitivity

Feedforward Linear Eq.

General form of Linear Sensitivity

Wx

y

)(

)(

t

t

)()( tt Wxy

Identify the neurons that affect the output the most.

Page 32: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Data Analysis : The Effect of Sensitive Neurons on Performance

0 20 40 60

-20

0

20

40

60

Hightest Sensitivity Neurons

0 20 40 60

-20

0

20

40

60

Middle Sensitivity Neurons

0 20 40 60

-20

0

20

40

60

Lowest Sensitivity Neurons

0 20 40 60 800

0.2

0.4

0.6

0.8

1

Pro

babi

lity

3D Error Radius (mm)

Movements (hits) of Test Trajectory

10 Highest Sensitivity

84 Intermediate Sensitivity

10 Low est Sensitivity

All Neurons

0 20 40 60 80 100 1200

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

Se

nsi

tivity

Primate 1, Session 1

Neurons

93

19 29 5 4

84 7

26 45

104

Decay trend appears in all animals and behavioral

paradigms

Page 33: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Directional Tuning vs. Sensitivity of ranked cells

Tuning Sensitivity

Significance: Sensitivity analysis through trained models automatically delivers deeply tuned cells that span the space.

Page 34: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Reaching Movement Segmentation

0 10 20 30 40 50 60 70-30

-20

-10

0

10

20

30

40

50

60

70XYZ

Food to Mouth Mouth to RestRest to Food

How does each cortical area contribute to the reconstruction of this movement?

Page 35: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Cortical Contributions Belle Day 2

0 20 40

-20

0

20

40

60

Area 1

0 20 40

-20

0

20

40

60

Area 2

0 20 40

-20

0

20

40

60

Area 3

0 20 40

-20

0

20

40

60

Area 4

0 20 40

-20

0

20

40

60

Areas 12

0 20 40

-20

0

20

40

60

Areas 13

0 20 40

-20

0

20

40

60

Areas 14

0 20 40

-20

0

20

40

60

Areas 23

0 20 40

-20

0

20

40

60

Areas 24

0 20 40

-20

0

20

40

60

Areas 34

0 20 40

-20

0

20

40

60

Areas 123

0 20 40

-20

0

20

40

60

Areas 124

0 20 40

-20

0

20

40

60

Areas 134

0 20 40

-20

0

20

40

60

Areas 234

0 20 40

-20

0

20

40

60

Areas 1234

Area 1 PP

Area 2 M1

Area 3 PMd

Area 4 M1 (right)

Train 15 separate RMLPs with every combination of cortical input.

Page 36: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Is there enough information in spike trains for modeling movement?

Analysis is based on the time embedded modelCorrelation with desired is based on a linear filter output for each neuron

Utilize a non-stationary tracking algorithmParameters are updated by LMS

Build a spatial filterAdaptive in real timeSparse structure based on regularization for enables selection

Page 37: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Adapted by LMS Adapted by on-line LAR(Kim et. al., MLSP, 2004)

Architecture

x1(n)z-1

z-1

y1(n)

w11

w1L

//

xM(n)z-1

z-1

yM(n)

wM1

wML

//

… y2(n)

c1

cM

)(ˆ ndc2

Page 38: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Training Algorithms

Tap weights for every time lag is updated by LMS

Then, the spatial filter coefficients are obtained by on-line version of least angle regression (LAR) (Efron et. al. 2004)

i=0 r = y-X = yFind argmaxi |xi

Tr|xj

jr = y-X = y-xjj

Adjust j s.t.k, |xk

Tr|=|xiTr|

. . .

x1

xk

yxj

jr = y-(xjj+ xkk)Adjust j & k s.t.q, |xq

Tr|=|xkTr|=|xi

Tr|k

)()(2)()1( nxnenwnw ijijij

Page 39: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Application to BMI Data – Tracking Performance

Page 40: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Application to BMI Data – Neuronal Subset Selection

Hand Trajectory

(z)

Neuronal Channel

Index

EarlyPart

LatePart

Page 41: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Generative Models for BMIs

Use partial information about the physiological system, normally in the form of states.

They can be either applied to binned data or to spike trains directly.

Here we will only cover the spike train implementations.

Difficulty of spike train Analysis: Spike trains are point processes, i.e. all the information is

contained in the timing of events, not in the amplitude fo the signals!

Page 42: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Build an adaptive signal processing framework for BMI decoding in the spike domain.

Features of Spike domain analysisBinning window size is not a concernPreserve the randomness of the neuron behavior. Provide more understanding of neuron physiology (tuning) and interactions at the cell assembly levelInfer kinematics onlineDeal with nonstationaryMore computation with millisecond time resolution

Goal

Page 43: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Recursive Bayesian Approach

),~

(~

tt nXHZ tt

State Time-series model cont.

observ.

Prediction

),(~

11 tttt vXFX

Updating

tZ

P(state|observation)

Page 44: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Recursive Bayesian approach

State space representation

First equation (system model) defines a first order Markov process.

Second equation (observation model) defines the likelihood of the observations p(zt|xt) . The problem is completely defined by the prior distribution p(x0).

Although the posterior distribution p(x0:t|u1:t,z1:t) constitutes the complete solution, the filtering density p(xt|u1:t, z1:t) is normally used for on-line problems.

The general solution methodology is to integrate over the unknown variables (marginalization).

ttttt

ttt

nxuhz

vxfx

),(

)(1

Page 45: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Recursive Bayesian approach

There are two stages to update the filtering density: Prediction (Chapman Kolmogorov)

System model p(xt|xt-1) propagates into the future the posterior density

Update

Uses Bayes rule to update the filtering density. The following equations are needed in the solution.

11:11:1111:11:1 ),|()|(),|( ttttttttt dxzuxpxxpzuxp

),|(

),|(),|(),|(

1:1

1:11:1:1:1

ttt

ttttttttt zuup

zxxpuxzpzuxp

1111111111 )()()|(),|()|( ttttttttttttt dvvpxvxdvxvpxvxpxxp

ttttttttt dnnpnxuhzuxzp )()),((),|(

tttttttttt dxuzxpuxzpuzzp ),|(),|(),|( 1:11:11:1

Page 46: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Kalman filter for BMI decoding

Kinematic State

Neuron tuning function Firing rate

Continuous Observation

P(state|observation)Prediction

Updating

Gaussian

Linear

Linear

[Wu et al. 2006]

For Gaussian noises and linear prediction and observation models, there

is an analytic solution called the Kalman Filter.

Page 47: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Particle Filter for BMI decoding

Kinematic State

Neuron tuning function Firing rate

Continuous Observation

P(state|observation)Prediction

Updating

nonGaussianLinear

Exponential

[Brockwell et al. 2004]

In general the integrals need to be approximated by sums using Monte Carlo integration with a set of samples drawn from the

posterior distribution of the model parameters.

Page 48: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

State estimation framework for BMI decoding in spike domain

Tuning function

Kinematics

state

Neural Tuning function

Multi-spike trains observation

xk k-1xkF k-1v= ( ),

kx

kz

kH

kn= )( ,

0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2

x 105

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

time

spike

0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2

x 105

-1.5

-1

-0.5

0

0.5

1

1.5

time (ms)

ve

loc

ity

Decoding

Kinematic dynamic model

Key Idea: work with the probability of spike firing which is a

continuous random variable

Page 49: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Adaptive algorithm for point processes

Kinematic State

Neuron tuning function spike train

Point process

P(state|observation)Prediction

Updating

GaussianLinear

nonlinear

[Brown et al. 2001]

Poisson Model

Page 50: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Monte Carlo Sequential estimation for point process

Kinematic State

Neuron tuning function spike train

Point process

P(state|observation)Prediction

Updating

nonGaussiannonLinear

nonlinear

[Wang et al. 2006]

Sequential Estimate PDF

Page 51: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Monte Carlo sequential estimation framework for BMI decoding in spike domain

STEP 1. Preprocessing1. Generate spike trains from stored spike times 10ms interval, (99.62%

binary train)

2. Synchronize all the kinetics with the spike trains.

3. Assign the kinematic vector to reconstruct.

X=[position velocity acceleration]’

(more information, instantaneous state avoid error accumulation,

less computation)

x

Page 52: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

STEP 2- Neural tuning analysis

Encoding

(Tuning)

kinematics Neural spike trains

A example of a tuned neuron

Metric: Tuning depth:

how differently does a neuron fire across directions?

D=(max-min)/std (firing rate)

0.05

0.1

0.15

0.2

0.25

30

210

60

240

90

270

120

300

150

330

180 0

neuron No. 72 TuningDepth: 1

Neuron 72: Tuning Depth 1

)arg(N

iN

Nermeancircular

Page 53: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 2- Information Theoretic Metric of Tuning

1,0

2 ))(

)|((log)|()();(

spikeangle spikep

anglespikepanglespikepanglepanglespikeI

kinematics direction angle

neural spikesInformation

)(

),1()|1(

anglep

anglespikepanglespikep

Page 54: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 2- Information theoretic Tuning depths for 3 kinds of kinematics (log axis)

Page 55: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 2- Tuning Function Estimation

Neural firing Model

Assumption :

generation of the spikes depends only on the kinematic vector we choose.

Linear filter

nonlinear f Poisson model

velocity spikes

)( tt vkf )( tt Poissonspike

Page 56: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 2- Linear Filter Estimation

• Spike Triggered Average (STA)

• Geometry interpretation

][)][(|

1 vEIvvEkspikev

T

-30 -20 -10 0 10 20 30-25

-20

-15

-10

-5

0

5

10

15

20

25

1st Principal Component

2nd

Prin

cipa

l Com

pone

nt

neuron 72: VpS PCA

Vp

VpS

1st Principal component2nd P

rincipal com

ponent

Page 57: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 2- Nonlinear f estimation

Page 58: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 2- Diversity of neural nonlinear properties

Ref: Paradoxical cold [Hensel et al. 1959]

Page 59: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 2- Estimated firing probability and generated spikes

Page 60: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 3: Sequential Estimation Algorithm for Point Process Filtering

• Consider the neuron as an inhomogenous Poisson point process

• Observing N(t) spikes in an interval T, the posterior of the spike

model is

• The probability of observing an event in t is

• And the one step prediction density (Chapman-Kolmogorov)

The posterior of the state vector, given an observation N

}exp{)( kkk vkt

t

ttttNttNtttt

t

))(),(),(|1)()(Pr(lim))(),(),(|(

0

HθxHθx

)),|(exp()),|((),|( ttttNP kkkN

kkkkkkk HxHxHx

)|(

)|(),|(),|(

kk

kkkkkkkk Np

pNPNp

H

HxHxHx

11111 ),|(),|()|( kkkkkkkkk dNppp xHxHxxHx

Page 61: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 3: Sequential Estimation Algorithm for Point Process Filtering

• Monte Carlo Methods are used to estimate the integral. Let

represent a random measure on the posterior density, and represent

the proposed density by

• The posterior density can then be approximated by

• Generating samples from using the principle of Importance

sampling

• By MLE we can find the maximum or use direct estimation with kernels

of mean and variance

)|( :1:0 kk Nq x

N

i

itt

ittt xxkwNxp

1:0:0:1:0 ),()|(

SNi

ik

ik w 1:0 },{ x SN

iik

ik w 1:0 },{ x SN

iik

ik w 1:0 },{ x SN

iik

ik w 1:0 },{ x

SNi

ik

ik w 1:0 },{ x

),|(

)|()|(

)|(

)|(

1

11

:1:0

:1:0

kik

ik

ik

ik

ikki

kk

ik

ki

kik Nq

pNpw

Nq

Npw

xx

xxx

x

x

SN

i

ik

ikkk Np

1

~)|( xxx ))()(()|(

~

1

~T

kik

N

i

kik

ikkk

S

NpV xxxxx

)|( :1:0 kk Nq x

Page 62: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Posterior density at a time index

-2.5 -2 -1.5 -1 -0.5 0 0.50

0.05

0.1

0.15

0.2

0.25

0.3

0.35

velocity

prob

abili

typdf at time index 45.092s

posterior density

desired velocity

velocity by seq. estimation (collapse)velocity by seq. estimation (MLE)

velocity by adaptive filtering

Page 63: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 3: Causality concerns

1,0

2);( ))(

))(|((log))(|())(()(

spikeXKXspike spikep

lagKXspikeplagKXspikeplagKXplagI

lag

Page 64: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

For 185 neurons, average delay is 220.108 ms

0 50 100 150 200 250 300 350 400 450 5000.4

0.6

0.8

1

1.2

1.4

1.6

1.8

2

2.2

2.4

time delay (ms)

I (spk

,KX

)(Tim

eD

ela

y)

I(spk,KX) as function of time delay

neuron 80

neuron 72

neuron 99neruon 108

neruon 77

Figure 3-14 Mutual information as function of time delay for 5 neurons.

Step 3: Information Estimated Delays

Page 65: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Step 4: Monte Carlo sequential kinematics estimation

)(i

itt

Xkf

Kinematic State

Neural Tuning function spike trains

Prediction

it

itt

it vXFX 11

Updating

)|( )(1

it

jt

it

it Npww

)( jtN

NonGaussian

P(state|observation)

N

i

itt

it

jtt xxkwNxp

1:0:0

)(:1:0 )()|(

N

i

i

kki

kkk kWNp1

:1 )()|( xxx

Page 66: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Reconstruct the kinematics from neuron spike trains

650 700 750 800-30

-20

-10

0

10

t

Px

650 700 750 800-40

-20

0

20

40

t

Py

650 700 750 800-2

-1

0

1

t

Vx

650 700 750 800-2

0

2

t

Vy

650 700 750 800-0.1

0

0.1

0.2

0.3

t

Ax

650 700 750 800-0.1

0

0.1

0.2

0.3

t

Ay

desired

ccexp

=0.7002

ccMLE

=0.69188

desired

ccexp

=0.015071

ccMLE

=0.040027

desiredcc

exp=0.91319

ccMLE

=0.91162

desiredcc

exp=0.81539

ccMLE

=0.8151

desired

ccexp

=0.97445

ccMLE

=0.95376

desired

ccexp

=0.80243

ccMLE

=0.67264

Page 67: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Table 3-2 Correlation Coefficients between the Desired Kinematics and the Reconstructions

CC

Position Velocity Acceleration

x y x y x y

Expectation 0.8161 0.8730 0.7856 0.8133 0.5066 0.4851

MLE 0.7750 0.8512 0.7707 0.7901 0.4795 0.4775

Table 3-3 Correlation Coefficient Evaluated by the Sliding Window

CC

Position Velocity Acceleration

x y x y x y

Expectation0.84010 0.0738

0.89450.0477

0.79440.0578

0.81420.0658

0.52560.0658

0.44600.1495

MLE0.79840.0963

0.87210.0675

0.78050.0491

0.79180.0710

0.49500.0430

0.44710.1399

Results comparison

[Sanchez, 2004]

Page 68: Brain Machine Interfaces: Modeling Strategies for Neural Signal Processing Jose C. Principe, Ph.D. Distinguished Professor ECE, BME Computational NeuroEngineering

Conclusion

• Our results and those from other laboratories show it is possible to extract intent of movement for trajectories from multielectrode array data.

• The current results are very promising, but the setups have limited difficulty, and the performance seems to have reached a ceiling at an uncomfortable CC < 0.9

• Recently, spike based methods are being developed in the hope of improving performance. But difficulties in these models are many.

• Experimental paradigms to move the field from the present level need to address issues of: Training (no desired response in paraplegic) How to cope with coarse sampling of the neural population How to include more neurophysiology knowledge in the design