Abstract: Disclosed herein include systems, devices, and methods for grouping sequence reads and collapsing families of sequence reads that originate from the same DNA molecules using UMIs.

Abstract: Methods, systems, and apparatuses, including computer programs for identifying a gene fusion in a biological sample is disclosed. The method can include actions of obtaining first data that represents a plurality of aligned reads, identifying a plurality of fusion candidates included within the obtained first data, filtering the plurality of fusion candidates to determine a filtered set of fusion candidates, for each particular fusion candidate of the filtered set of fusion candidates: generating, by one or more computers, input data for input to a machine learning model that includes extracted feature data that to represents the particular fusion candidate, providing the generated input data as an input to the machine learning model that has been trained to generate output data representing a likelihood that a fusion candidate is a valid gene fusion, and determining whether the particular fusion candidate corresponds to a valid gene fusion based on the output data.

Abstract: Systems, methods, and computer programs for analyzing genetic sequence data is disclosed. In one aspect, the system can include one or more of a first integrated circuit, with each first integrated circuit forming a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of a sequence analysis pipeline. Additionally, the system can include one or more second integrated circuits, with each second integrated circuit forming a field programmable gate array (FPGA). The FPGA can be configured by firmware to arrange a set of hardwired digital logic circuits to perform a second set of genomic processing stages of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing stages.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A method for adjusting power in a mobile terminal is disclosed and may include determining a total transmit power control (TPC) command for a downlink channel based on a plurality of TPC commands. The plurality of TPC commands may be calculated based on a plurality of control channels. The transmit power may be adjusted based on the determined total TPC command. The plurality of control channels may include a dedicated physical channel and a common pilot channel. Noise power may be determined for each of the plurality of control channels. A TPC command may be determined based on the plurality of control channels. A reliability weight value may be determined for each of the plurality of TPC commands, based on the determined noise power for each of the plurality of control channels.

Abstract: Disclosed are various embodiments involving a two-step searcher for cell discovery. Multiple scrambling codes associated with multiple neighboring cells are obtained. Slot timing is obtained for a received signal based at least in part on a detection of primary synchronization peak energy in the received signal. One of the scrambling codes for decoding the received signal is identified based at least in part on testing multiple scrambling code hypotheses in parallel during an accumulation time period of the received signal in response to obtaining the slot timing.

Abstract: A system and method for generating weight values based on maximum data rate for weighting elements included within signal weighting and combining arrangements used in various multi-antenna transmitter and receiver structures is disclosed herein. Weighting values for a given signal combining arrangement are set so as to maximize an output data rate of the applicable multi-antenna system in the presence of adaptive bit loading of the subcarriers of a transmitted signal. The disclosed techniques may be employed to maximize a data rate of a multi-antenna communication system by using adaptive bit loading and RF and baseband weighting schemes. In this case a search is conducted over various combinations of RF and baseband weights in order to find the weight combination which, when adaptive bit loading is also employed, maximizes the data rate.

Abstract: Methods and systems for processing signals in a receiver are disclosed herein and may include updating a plurality of filter taps utilizing at least one channel response vector and at least one correlation vector, for a plurality of received clusters, based on initialized values related to the at least one channel response vector and the at least one correlation vector. At least a portion of the received signal clusters may be filtered utilizing at least a portion of the updated plurality of filter taps. The update may be repeated whenever a specified signal-to-noise ratio (SNR) for the received signal clusters is reached. The initialized values may be updated during a plurality of iterations, and the update may be repeated whenever a specified number of the plurality of iterations is reached.

Abstract: A method for communication includes performing by one or more processors and/or circuits in a communication device functions including determining transmit power weights, which are to be utilized for communicating one or more wireless signals via a wireless channel, as a function of frequency of a wireless signal communicated via the wireless channel. The determining may be based on a transmission mode of the wireless signal and a state of the wireless communication channel. Transmit antenna spatial weights may be determined for communicating the one or more wireless signals via a plurality of antennas. The one or more wireless signals may be weighted with the transmit power weights and/or one of the transmit antenna spatial weights. The weighted one or more wireless signals may be transmitted via one of a plurality of antennas in accordance with the transmission mode.

Abstract: Method and apparatus for computing a noise power estimate in a wideband CDMA (WCDMA) network are disclosed and may include calculating a noise power estimate for a downlink channel based on an orthogonal sequence generated for a transmitted signal. The orthogonal sequence may be generated based on a slot number of the transmitted signal and/or a transmit diversity mode used for the transmitted signal. A portion of a plurality of dedicated physical channel (DPCH) pilot bits for the downlink channel may be summed to generate an in-phase (I) component and a quadrature (Q) component. The generated I component and the generated Q component may be multiplied by the orthogonal sequence to generate at least one noise I component and at least one noise Q component.

Abstract: Various aspects of a method and a system for finding a threshold for semi-orthogonal user group selection in multiuser MIMO downlink transmission are presented. Aspects of a system for semi-orthogonal user group selection may include a processor that computes an orthogonality measurement between one of a plurality of signals and at least one of a remaining portion of the plurality of signals. The processor may compare each of the orthogonality measurements to a threshold orthogonality value based on a computed probability. The processor may select a user group, based on the threshold orthogonality value, including one of the plurality of signals and one or more signals selected from the remaining portion of the plurality of signals.

Abstract: Method and apparatus for processing transmit power control (TPC) commands in a wideband CDMA (WCDMA) network are disclosed and may include calculating a signal-to-noise ratio (SNR) of a downlink dedicated physical channel (DPCH) based on a plurality of transmit power control (TPC) bits received via the downlink DPCH. A value of at least one of said plurality of TPC bits is not known when said at least one of said plurality of TPC bits is received. Transmit power for at least one uplink communication path may be adjusted based on the calculated SNR of the downlink dedicated physical channel. At least one reliability weight value may be calculated for at least a portion of the received TCP bits, based on the calculated SNR.

Abstract: Systems and methods that provide channel-adaptive antenna selection in multi-antenna element communication systems are provided. In one embodiment, a method that selects a subset of receive antennas of a receiver to receive a transmitted RF signal may include, for example, one or more of the following: establishing possible subsets of the receive antennas; determining sets of channel parameter statistics corresponding to the possible subsets of the receive antennas; computing output bit error rates of the receiver, each output bit error rate being computed based on at least one set of channel parameter statistics; selecting a particular possible subset of the receive antennas based upon a criterion predicated on the computed output bit error rates; and connecting one or more RF chains of the receiver to the receive antennas of the selected particular possible subset.

Abstract: A receiver operatively coupled to an antenna structure capable of receiving a first plurality of RF signals is disclosed herein. The receiver includes an RF processing network operative to perform weighting and combining operations within the RF domain using the first plurality of RF signals so as to produce a second plurality of RF signals. Also provided is a downconverter configured to downconvert the second plurality of RF signals into a second plurality of down-converted signals. In alternate implementations certain of the weighting and combining operations are performed at baseband and the remainder effected within the RF domain. A transmitter of corresponding architecture is also disclosed.

Abstract: Methods and systems for processing signals in a wireless communication system are disclosed. Aspects of the method may include calculating at a receiver, a plurality of energy values corresponding to a plurality of signal paths detected within a communication channel. At least one of the plurality of detected signal paths may be selected for processing based on a pre-defined threshold and a dynamic threshold, in order to achieve a desired probability of misdetection and a desired probability of false alarm. The probability of misdetection is a probability that a real signal path is missed, and the probability of false alarm is a probability of detecting a false signal path. A slot boundary, a frame boundary, and/or a scrambling code may be determined for signals communicated via said plurality of signal paths.

Abstract: Adaptive path selection for interference cancellation is provided for wireless communication devices. Signal strength metrics are obtained for each of multiple signal paths. One or more of the signal paths are selected as cancellation candidates in response to determining that the signal paths are associated with a strong interfering path based at least in part on the signal strength metrics for the signal paths and threshold criteria. Cancellation is enabled for an estimated signal generated using the signal paths in response to the signal paths being selected as cancellation candidates.

Abstract: A method and system for determining synchronization status in a wide band CDMA (WCDMA) network may comprise calculating a signal to noise ratio (SNR) of a downlink dedicated physical channel (DPCH) based on a plurality of transmit power control (TPC) bits received via the downlink dedicated physical channel (DPCH), wherein the value of at least one of the plurality of TPC bits is not known when at least one of the plurality of TPC bits is received. The transmit circuitry may be controlled based on the calculated signal to noise ratio. The transmit circuitry may be disabled if the calculated SNR of the plurality of TPC bits is below a first channel threshold. The transmit circuitry may be enabled if the calculated SNR of the plurality of TPC bits is above a second channel threshold.

Abstract: A wireless system may receive a plurality of multipath signals from a plurality of transmitters and allocate per-cell modules for generating an interference suppressed signal from the multipath signals. Data symbols may be sequentially processed in the received multipath signals utilizing the per-cell modules and subtracting the processed symbols from a residual buffer storing the received multipath signals. Desired information received from one or more of the transmitters may be recovered utilizing the interference suppressed signal. Timing of the data symbols may be correlated utilizing a cell chip combiner. The data symbols may be descrambled utilizing conjugated scrambling codes associated with one of the plurality of transmitters. Orthogonal variable spreading factor (OVSF) codes may be generated utilizing a Walsh transform on the data symbols. Power levels of the OVSF codes may be estimated and estimated signals may be generated based on the OVSF codes and the estimated power levels.

Abstract: Disclosed are various embodiments providing processor configured to determine a received signal strength indication (RSSI) value for each of the plurality of channel taps. The processing circuitry identifies a maximum RSSI value among the RSSI values and may adjust a variable threshold range according to the maximum RSSI value. The RSSI value for each channel tap may be scaled according to a corresponding per tap noise power.

Abstract: Aspects of a method and system for a programmable interference suppression module may include receiving a communication signal comprising one or more desired signal, and one or more undesired signals. The communication signal may be utilized to generate estimated channel state information. The estimated channel state information may be formatted for use in interference suppression. A reduced interference signal may be generated from a delayed version of said communications signal and the estimated channel state information, wherein the one or more undesired signals may be attenuated. The reduced interference signal may be formatted for post-processing. The desired signals may comprise WCDMA and/or HSDPA signals, and the undesired signals may be inter-cell and/or intra-cell interference. Further processing may comprise HSDPA processing and/or RAKE finger processing. The communication signal may be a Universal Mobile Telecommunication System (UMTS) compliant signal.