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Differential co-expression analysis has been widely applied by scientists in understanding the biological mechanisms of diseases. However, the unknown differential patterns are often complicated; thus, models based on simplified parametric…
The modified Gerchberg-Saxton algorithm (MGSA) is one of the standard methods for phase retrieval. In this work we apply the MGSA in the paraxial domain. For three given physical parameters - i.e. wavelength, propagation distance and pixel…
Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…
Phase-rectified signal averaging (PRSA) is a widely used algorithm to analyze nonstationary biomedical time series. The method operates by identifying hinge points in the time series according to prescribed rules, extracting segments…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…
Recent advancements in protein design have leveraged diffusion models to generate structural scaffolds, followed by a process known as protein inverse folding, which involves sequence inference on these scaffolds. However, these…
This paper focuses on an improved Gaussian approximation (GA) based construction of polar codes with successive cancellation (SC) decoding over an additive white Gaussian noise (AWGN) channel. Arikan has proven that polar codes with…
The precision of synchronization algorithms based on the theory of pulse-coupled oscillators is evaluated on FPGA-based radios for the first time. Measurements show that such algorithms can reach precision in the low microsecond range when…
Advances in compressive sensing provided reconstruction algorithms of sparse signals from linear measurements with optimal sample complexity, but natural extensions of this methodology to nonlinear inverse problems have been met with…
Phase retrieval with prior information can be cast as a nonsmooth and nonconvex optimization problem. We solve the problem by graph projection splitting (GPS), where the two proximity subproblems and the graph projection step can be solved…
We numerically and experimentally investigate the laser phase noise tolerance of probabilistically shaped (PS) and uniformly shaped (US) quadrature amplitude modulation (QAM) signals. In the simulations, we compare PS-64QAM to US-16QAM,…
A phase detection sequence is a length-$n$ cyclic sequence, such that the location of any length-$k$ contiguous subsequence can be determined from a noisy observation of that subsequence. In this paper, we derive bounds on the minimal…
AlphaFold2 (AF2) has transformed protein structure prediction by harnessing co-evolutionary constraints embedded in multiple sequence alignments (MSAs). MSAs not only encode static structural information, but also hold critical details…
In this paper, we propose a novel pulse shaping design for single-carrier integrated sensing and communication (ISAC) transmission. Due to the communication information embedded in the ISAC signal, the resulting auto-correlation function…
This letter proposes a novel hybrid automatic repeat request with chase combining assisted sparse code multiple access (HARQ-CC-SCMA) scheme. Depending on whether the same superimposed packet are retransmitted, synchronous and asynchronous…
Motivated by the ideal peak-to-average-power ratio and radar sensing capability of traditional frequency-coded radar waveforms, this paper considers the frequency shift keying (FSK) based waveform for joint communications and radar (JCR).…
This paper compares the performance of conventional radix-2 program counters with program counters based on Feedback Shift Registers (FSRs), a class of cyclic sequence generator. FSR counters have constant time scaling with bit-width, $N$,…
Retrieval-Augmented Generation (RAG) enhances coding tasks by incorporating retrieved code examples into prompts. However, lengthy prompts, often exceeding tens of thousands of tokens, introduce challenges related to limited context windows…
We address the problem of signal reconstruction from intensity measurements with respect to a measurement frame. This non-convex inverse problem is known as phase retrieval. The case considered in this paper concerns phaseless measurements…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…