Mattias Wahde

Coarse-grained reverse engineering of genetic regulatory networks

We have modeled genetic regulatory networks in the framework of continuous-time recurrent neural networks. A method for determining the parameters of such networks, given expression level time series data, is introduced and evaluated using artificial data. The method is also applied to a set of actual expression data from the development of rat central nervous system.

Modeling genetic regulatory dynamics in neural development.

We model genetic regulatory networks in the framework of continuous-time recurrent networks. The network parameters are determined from gene expression level time series data using genetic algorithms. We have applied the method to expression data from the development of rat central nervous system, where the active genes cluster into four groups, within which the temporal expression patterns are similar. The data permit us to identify approximately the interactions between these groups of genes. We find that generally a single time series is of limited value in determining the interactions in the network, but multiple time series collected in related tissues or under treatment with different drugs can fix their values much more precisely.

Reaction of sleepiness indicators to partial sleep deprivation, time of day and time on task in a driving simulator : the DROWSI project

Studies of driving and sleepiness indicators have mainly focused on prior sleep reduction. The present study sought to identify sleepiness indicators responsive to several potential regulators of sleepiness: sleep loss, time of day (TOD) and time on task (TOT) during simulator driving. Thirteen subjects drove a high‐fidelity moving base simulator in six 1‐h sessions across a 24‐h period, after normal sleep duration (8 h) and after partial sleep deprivation (PSD; 4 h). The results showed clear main effects of TOD (night) and TOT but not for PSD, although the latter strongly interacted with TOD. The most sensitive variable was subjective sleepiness, the standard deviation of lateral position (SDLAT) and measures of eye closure [duration, speed (slow), amplitude (low)]. Measures of electroencephalography and line crossings (LCs) showed only modest responses. For most variables individual differences vastly exceeded those of the fixed effects, except for subjective sleepiness and SDLAT. In a multiple regression analysis, SDLAT, amplitude/peak eye‐lid closing velocity and blink duration predicted subjective sleepiness bouts with a sensitivity and specificity of about 70%, but were mutually redundant. The prediction of LCs gave considerably weaker, but similar results. In summary, SDLAT and eye closure variables could be candidates for use in sleepiness‐monitoring devices. However, individual differences are considerable and there is need for research on how to identify and predict individual differences in susceptibility to sleepiness.

Sleepy driving on the real road and in the simulator - A comparison

Sleepiness has been identified as one of the most important factors contributing to road crashes. However, almost all work on the detailed changes in behavior and physiology leading up to sleep related crashes has been carried out in driving simulators. It is not clear, however, to what extent simulator results can be generalized to real driving. This study compared real driving with driving in a high fidelity, moving base, driving simulator with respect to driving performance, sleep related physiology (using electroencephalography and electrooculography) and subjective sleepiness during night and day driving for 10 participants. The real road was emulated in the simulator. The results show that the simulator was associated with higher levels of subjective and physiological sleepiness than real driving. However, both for real and simulated driving, the response to night driving appears to be rather similar for subjective sleepiness and sleep physiology. Lateral variability was more responsive to night driving in the simulator, while real driving at night involved a movement to the left in the lane and a reduction of speed, both of which effects were absent in the simulator. It was concluded that the relative validity of simulators is acceptable for many variables, but that in absolute terms simulators cause higher sleepiness levels than real driving. Thus, generalizations from simulators to real driving must be made with great caution.

The Characteristics of Sleepiness During Real Driving at Night - A Study of Driving Performance, Physiology and Subjective Experience

STUDY OBJECTIVES Most studies of sleepy driving have been carried out in driving simulators. A few studies of real driving are available, but these have used only a few sleepiness indicators. The purpose of the present study was to characterize sleepiness in several indicators during real driving at night, compared with daytime driving. DESIGN Participants drove 55 km (at 90 km/h) on a 9-m-wide rural highway in southern Sweden. Daytime driving started at 09:00 or 11:00 (2 groups) and night driving at 01:00 or 03:00 (balanced design). SETTING Instrumented car on a real road in normal traffic. PARTICIPANTS Eighteen participants drawn from the local driving license register. INTERVENTIONS Daytime and nighttime drives. MEASUREMENT AND RESULTS The vehicle was an instrumented car with video monitoring of the edge of the road and recording of the lateral position and speed. Electroencephalography and electrooculography were recorded, together with ratings of sleepiness every 5 minutes. Pronounced effects of night driving were seen for subjective sleepiness, electroencephalographic indicators of sleepiness, blink duration, and speed. Also, time on task showed significant effects for subjective sleepiness, blink duration, lane position, and speed. Sleepiness was highest toward the end of the nighttime drive. Night driving caused a leftward shift in lateral position and a reduction of speed. The latter two findings, as well as the overall pattern of sleepiness indicators, provide new insights into the effects of night driving. CONCLUSION Night driving is associated with high levels of subjective, electrophysiologic, and behavioral sleepiness.

Detecting Driver Sleepiness Using Optimized Nonlinear Combinations of Sleepiness Indicators

This paper addresses the problem of detecting sleepiness in car drivers. First, a variety of sleepiness indicators (based on driving behavior) proposed in the literature were evaluated. These indicators were then subjected to parametric optimization using stochastic optimization methods. To improve performance, the functional form of some of the indicators was generalized before optimization. Next, using a neural network, the best performing sleepiness indicators were combined with a mathematical model of sleepiness, i.e., the sleep/wake predictor (SWP). The analyses were based on data obtained from a study that involved 12 test subjects at the moving-base driving simulator at the Swedish National Road and Transportation Research Institute (VTI), Linköping, Sweden. The data were derived from 12 1-h driving sessions for each test subject, with varying degrees of sleepiness. The performance measure (range [0,1]) for indicators was taken as the average of sensitivity and specificity. Starting with indicators proposed in the literature, the best such indicator, i.e., the standard deviation of the yaw angle, reached a performance score of 0.72 on previously unseen test data. It was found that indicators based on a given signal gave essentially equal performance after parametric optimization, but in no case was it better than 0.72. The best generalized indicator (the generic variability indicator) obtained a performance score of 0.74. SWP achieved a score of 0.78. However, by nonlinearly combining SWP with the generic variability indicator, a score of 0.83 was obtained. Thus, the results imply that a nonlinear combination of a measure based on driving behavior with a model of sleepiness significantly improves driver sleepiness detection.

A Review of Near-Collision Driver Behavior Models

Objective: This article provides a review of recent models of driver behavior in on-road collision situations. Background: In efforts to improve traffic safety, computer simulation of accident situations holds promise as a valuable tool, for both academia and industry. However, to ensure the validity of simulations, models are needed that accurately capture near-crash driver behavior, as observed in real traffic or driving experiments. Method: Scientific articles were identified by a systematic approach, including extensive database searches. Criteria for inclusion were defined and applied, including the requirement that models should have been previously applied to simulate on-road collision avoidance behavior. Several selected models were implemented and tested in selected scenarios. Results: The reviewed articles were grouped according to a rough taxonomy based on main emphasis, namely avoidance by braking, avoidance by steering, avoidance by a combination of braking and steering, effects of driver states and characteristics on avoidance, and simulation platforms. Conclusion: A large number of near-collision driver behavior models have been proposed. Validation using human driving data has often been limited, but exceptions exist. The research field appears fragmented, but simulation-based comparison indicates that there may be more similarity between models than what is apparent from the model equations. Further comparison of models is recommended. Application: This review provides traffic safety researchers with an overview of the field of driver models for collision situations. Specifically, researchers aiming to develop simulations of on-road collision accident situations can use this review to find suitable starting points for their work.

Effective dimensionality of large-scale expression data using principal component analysis.

Large-scale expression data are today measured for thousands of genes simultaneously. This development is followed by an exploration of theoretical tools to get as much information out of these data as possible. One line is to try to extract the underlying regulatory network. The models used thus far, however, contain many parameters, and a careful investigation is necessary in order not to over-fit the models. We employ principal component analysis to show how, in the context of linear additive models, one can get a rough estimate of the effective dimensionality (the number of information-carrying dimensions) of large-scale gene expression datasets. We treat both the lack of independence of different measurements in a time series and the fact that that measurements are subject to some level of noise, both of which reduce the effective dimensionality and thereby constrain the complexity of models which can be built from the data.

Structural Evolution of Central Pattern Generators for Bipedal Walking in 3D Simulation

Anthropomorphic walking for a simulated bipedal robot has been realized by means of artificial evolution of central pattern generator (CPG) networks. The approach has been investigated through full rigid-body dynamics simulations in 3D of a bipedal robot with 14 degrees of freedom. The half-center CPG model has been used as an oscillator unit, with interconnection paths between oscillators undergoing structural modifications using a genetic algorithm. In addition, the connection weights in a feedback network of predefined structure were evolved. Furthermore, a supporting structure was added to the robot in order to guide the evolutionary process towards natural, human-like gaits. Subsequently, this structure was removed, and the ability of the best evolved controller to generate a bipedal gait without the help of the supporting structure was verified. Stable, natural gait patterns were obtained, with a maximum walking speed of around 0.9 m/s.

Comparing and validating models of driver steering behaviour in collision avoidance and vehicle stabilisation

A number of driver models were fitted to a large data set of human truck driving, from a simulated near-crash, low-friction scenario, yielding two main insights: steering to avoid a collision was best described as an open-loop manoeuvre of predetermined duration, but with situation-adapted amplitude, and subsequent vehicle stabilisation could to a large extent be accounted for by a simple yaw rate nulling control law. These two phenomena, which could be hypothesised to generalise to passenger car driving, were found to determine the ability of four driver models adopted from the literature to fit the human data. Based on the obtained results, it is argued that the concept of internal vehicle models may be less valuable when modelling driver behaviour in non-routine situations such as near-crashes, where behaviour may be better described as direct responses to salient perceptual cues. Some methodological issues in comparing and validating driver models are also discussed.