Signal Processing for Biologically Inspired Sensors P. Sattigeri, J. J. Thiagarajan, K. N. Ramamurthy, B. Konnanath, T. Mathew, A. Spanias, M. Goryll, T. Thornton, S. Prasad and S. Phillips SenSIP and CSSER Centers, School of ECEE, Arizona State University, Tempe, USA Abstract—Pores or channels with diameters in the range of nanometers up to micrometers can be used as Coulter counting apertures to detect particles and organic molecules such as proteins. Coulter counting is performed by applying a constant potential across a nano- or micropore while recording the drop in ionic current upon passage of a molecule. Looking at the shape and duration of these current pulses enables us to estimate the size as well as the concentration of these molecules. Discrimination between different analytes can be performed by extracting appropriate features from the Coulter signals (events) and using them for classification. The challenge in being able to identify particular analytes is that a drop in current can also be caused by a molecule bouncing off the pore wall rather than moving through the micropore. Such drops are called non- events and can be discriminated from the events using Support Vector Machines. In this paper, we consider the amplitude of the current drop and the duration of the current pulse as features to determine if an event occurred. The proposed approach uses the Dirichlet process mixture model to cluster the data in the feature domain as the type of the events in the signal record is unknown. Results obtained show that the Dirichlet process mixture model accurately finds the types of events and their count for each signal record. Index Terms—Silicon pore, Wavelet transforms, Feature ex- traction, Clustering, Dirichlet process mixture model. I. I NTRODUCTION The use of semiconductor nanostructures and novel nano- materials such as conducting polymers for building biosensors is gaining popularity, since they can enable single molecule detection [1]. A silicon nanopore, for example, behaves like a protein channel and allows selective analyte transport [2], [3]. The ability to fabricate structures ranging from micrometers down to a few nanometers has led to the re-discovery of the Coulter counting principle. In Coulter counting experiments, the drop in ionic current through a micron-sized aperture is recorded upon passage of a particle, such as a blood cell. The shape and amplitude of the current signal then enables a discrimination between different cells, allowing for example a complete blood cell count to be generated. For a Coulter counter to be most efficient in discriminating between different particle sizes, the aperture through which the particles flow has to be on the same order of magnitude as the particles themselves. Thus, nanoscale particles are best detected using a nanopore. Using nanopores, however, restricts the range of particle sizes significantly. Moreover nanopores tend to become irreversibly blocked by larger particles or molecules, rendering them useless. Thus, in our experiments, we decided to use a micron-sized silicon pore, since it offers the best trade- off between sensitivity and detection range and is significantly easier to fabricate compared to a silicon nanopore. The silicon micropore is setup to act as a Coulter count- ing device [4] with the silicon micropore chip itself be- ing sandwiched between two chambers containing electrolyte solution, typically physiologically buffered saline (PBS). A constant voltage is applied across the silicon micropore using reversible Ag/AgCl reference electrodes. Since the current flowing through the aperture at the applied bias is on the order of a few nA, no separate counter and working electrodes are necessary to pass the current. To observe Coulter transloca- tion events, silica microbeads were added to the electrolyte solution. Since the silica beads carry a surface charge, the applied bias causes the silica microbeads to enter the pore resulting in a drop in the value of the baseline current. By functionalizing the silica beads with biotin using amine linker chemistry, an immunoassay can be performed using the beads. By adding avidin to the solution, the beads will agglomerate and cause a drop in Coulter current that is proportional to that of a single silica bead passing through the micropore. The amount of drop in current and the corresponding increase in resistance can be used to detect and identify the presence of bead agglomeration, which can be extended to provide a direct biomolecule detection capability [5]. Previous experiments with signals originating from nanopore Coulter counting [6] and electromigration of beads through silicon nanopores [7] show the wide range of applicability of particle classifica- tion using ionic current drop measurements. The ability to employ signal processing to discriminate between different biochemical entities has been reported in prior work by the authors, including extracting features for ion-channel devices [8], classifying ion-channel signals using HMMs [5] as well as using neural networks [9] and SVM [10] to characterize and detect the presence of analytes in ion-channel signals. In this paper, we explore two features of the current drop to classify the object that is passing through the micropore: the amplitude of the drop and the time duration of the event. We discriminate between an event and a non-event based on the amplitude of the drop. The problem we are facing in the experiments when basing the event/non-event classification on the amplitude is that the signals obtained from the setup are inherently noisy. This is due to the noise sources being present, which is primarily the thermal noise of the aperture resistance itself. Since a lower resistance creates a higher thermal current noise, this limits the minimal achievable noise level of the system. Since the spectrum of the thermal noise is white, the only way to reduce the root-mean-square (rms) value of the noise is to limit the recording bandwidth. In a purely analog signal chain, this can be accomplished using higher