The Human Gene Mutation Database (HGMD
®
) constitutes a comprehensive collection of published germline mutations in nuclear genes that are thought to underlie, or are closely associated with human ...inherited disease. At the time of writing (June 2020), the database contains in excess of 289,000 different gene lesions identified in over 11,100 genes manually curated from 72,987 articles published in over 3100 peer-reviewed journals. There are primarily two main groups of users who utilise HGMD on a regular basis; research scientists and clinical diagnosticians. This review aims to highlight how to make the most out of HGMD data in each setting.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Multiset-Partition Distribution Matching Fehenberger, Tobias; Millar, David S.; Koike-Akino, Toshiaki ...
IEEE transactions on communications,
03/2019, Volume:
67, Issue:
3
Journal Article
Peer reviewed
Open access
Distribution matching is a fixed-length invertible mapping from a uniformly distributed bit sequence to shaped amplitudes and plays an important role in the probabilistic amplitude shaping framework. ...With conventional constant-composition distribution matching (CCDM), all output sequences have identical composition. In this paper, we propose multiset-partition distribution matching (MPDM), where the composition is constant over all output sequences. When considering the desired distribution as a multiset, MPDM corresponds to partitioning this multiset into equal-sized subsets. We show that MPDM allows addressing more output sequences and, thus, has a lower rate loss than CCDM in all nontrivial cases. By imposing some constraints on the partitioning, a constructive MPDM algorithm is proposed which comprises two parts. A variable-length prefix of the binary data word determines the composition to be used, and the remainder of the input word is mapped with a conventional CCDM algorithm, such as arithmetic coding, according to the chosen composition. Simulations of 64-ary quadrature amplitude modulation over the additive white Gaussian noise channel demonstrate that the block-length saving of MPDM over CCDM for a fixed gap to capacity is approximately a factor of 2.5-5 at medium to high signal-to-noise ratios.
Recently, data-driven approaches motivated by modern deep learning have been applied to optical communications in place of traditional model-based counterparts. The application of deep neural ...networks (DNN) allows flexible statistical analysis of complicated fiber-optic systems without relying on any specific physical models. Due to the inherent nonlinearity in DNN, various equalizers based on DNN have shown significant potential to mitigate fiber nonlinearity. In this paper, we propose turbo equalization (TEQ) based on DNN as a new alternative framework to deal with nonlinear fiber impairments. The proposed DNN-TEQ is constructed with nested deep residual networks (ResNet) to train extrinsic likelihood given soft-information feedback from channel decoding. Through extrinsic information transfer (EXIT) analysis, we verify that our DNN-TEQ can accelerate decoding convergence to achieve a significant gain in achievable throughput by 0.61 b/s/Hz. We also demonstrate that optimizing irregular low-density parity-check (LDPC) codes based on the EXIT chart of the DNN-TEQ can improve achievable rates by up to 0.12 b/s/Hz.
In order to realize probabilistically shaped signaling within the probabilistic amplitude shaping (PAS) framework, a shaping device outputs sequences that follow a certain nonuniform distribution. In ...case of constant-composition (CC) distribution matching (CCDM), the sequences differ only in the ordering of their constituent symbols, whereas the number of occurrences of each symbol is constant in every output block. Recent results by Amari et al. have shown that the CCDM block length can have a considerable impact on the effective signal-to-noise ratio (SNR) after fiber transmission. So far, no explanation for this behavior has been presented. Furthermore, the block-length dependence of the SNR seems not to be fully aligned with previous results in the literature. This paper is devoted to a detailed analysis of the nonlinear fiber interactions for CC sequences. We confirm in fiber simulations the inverse proportionality of SNR with CCDM block length and present two explanations. The first one, which only holds in the short-length regime, is based on how two-dimensional symbols are generated from shaped amplitudes in the PAS framework. The second, more general explanation relates to an induced shuffling within a sequence, or equivalently a limited concentration of identical symbols, that is an inherent property for short CC blocks, yet not necessarily present in case of long blocks. This temporal property results in weaker nonlinear interactions, and thus higher SNR, for short CC sequences. For a typical multi-span fiber setup, the SNR difference is numerically demonstrated to be up to 0.7 dB. Finally, we evaluate a heuristic figure of merit that captures the number of runs of identical symbols in a concatenation of several CC sequences. For moderate block lengths up to approximately 100 symbols, this metric suggests that limiting the number identical-symbol runs can be beneficial for reducing fiber nonlinearities and thus, for increasing SNR.
We propose the use of dual coding concatenation for mitigation of post-shaping burst errors in probabilistic amplitude shaping (PAS) architectures. The proposed dual coding concatenation for PAS is a ...hybrid integration of conventional reverse concatenation and forward concatenation, i.e., post-shaping forward error correction (FEC) layer and pre-shaping FEC layer, respectively. A low-complexity architecture based on parallel Bose-Chaudhuri-Hocquenghem (BCH) codes is introduced for the pre-shaping FEC layer. Proposed dual coding concatenation can relax bit error rate (BER) requirement after post-shaping soft-decision (SD) FEC codes by an order of magnitude, resulting in a gain of up to 0.25 dB depending on the complexity of post-shaping FEC. Also, combined shaping and coding performance was analyzed based on sphere shaping and the impact of shaping length on coding performance was demonstrated.
A distribution matcher (DM) maps a binary input sequence into a block of nonuniformly distributed symbols. To facilitate the implementation of shaped signaling, fast DM solutions with high throughput ...and low serialism are required. We propose a novel DM architecture with parallel amplitudes (PA-DM) for which <inline-formula> <tex-math notation="LaTeX">m-1 </tex-math></inline-formula> component DMs, each with a different binary output alphabet, are operated in parallel in order to generate a shaped sequence with <inline-formula> <tex-math notation="LaTeX">m </tex-math></inline-formula> amplitudes. With negligible rate loss compared to a single nonbinary DM, PA-DM has a parallelization factor that grows linearly with <inline-formula> <tex-math notation="LaTeX">m </tex-math></inline-formula>, and the component DMs have reduced output lengths. For such binary-output DMs, a novel constant-composition DM (CCDM) algorithm based on subset ranking (SR) is proposed. We present SR-CCDM algorithms that are serial in the minimum number of occurrences of either binary symbol for mapping, and fully parallel for demapping. For distributions that are optimized for the additive white Gaussian noise (AWGN) channel, we numerically show that PA-DM combined with SR-CCDM can reduce the number of sequential processing steps by more than an order of magnitude, while having a rate loss that is comparable to conventional nonbinary CCDM with arithmetic coding.
In this article, we study amplitude shaping schemes for the probabilistic amplitude shaping (PAS) framework as well as algorithms for constant-composition distribution matching (CCDM). Huffman-coded ...sphere shaping (HCSS) is discussed in detail, which internally uses Huffman coding to determine the composition to be used and relies on conventional CCDM algorithms for mapping and demapping. Numerical simulations show that HCSS closes the performance gap between distribution matching schemes and sphere shaping techniques such as enumerative sphere shaping (ESS). HCSS is based on an architecture that is different from the trellis-based setup of ESS. It allows to tailor the used HCSS compositions to the transmission channel and to take into account complexity constraints. We further discuss in detail multiset ranking (MR) and subset ranking (SR) as alternatives to arithmetic-coding (AC) CCDM. The advantage of MR over AC is that it requires less sequential operations for mapping. SR operates on binary alphabets only, which can introduce some additional rate loss when a nonbinary-to-binary transformation is required. However, the binomial coefficients required for SR can be precomputed and stored in a lookup table (LUT). We perform an analysis of rate loss and decoding performance for the proposed techniques and compare them to other prominent amplitude shaping schemes. For medium to long block lengths, MR-HCSS and SR-HCSS are shown to have similar performance to ESS. SR-HCSS and uniform 64QAM are compared in additive white Gaussian noise simulations and shaping gains of 0.5 dB and 1 dB are demonstrated with 1 kbit and 100 kbit LUT size, respectively.
In this paper, we examine the performance of several modulation formats in more than four dimensions for coherent optical communications systems. We compare two high-dimensional modulation design ...methodologies based on spherical cutting of lattices and block coding of a 'base constellation' of binary phase shift keying (BPSK) on each dimension. The performances of modulation formats generated with these methodologies is analyzed in the asymptotic signal-to-noise ratio regime and for an additive white Gaussian noise (AWGN) channel. We then study the application of both types of high-dimensional modulation formats to standard single-mode fiber (SSMF) transmission systems. For modulation with spectral efficiencies comparable to dual-polarization (DP-) BPSK, polarization-switched quaternary phase shift keying (PS-QPSK) and DP-QPSK, we demonstrate SNR gains of up to 3 dB, 0.9 dB and 1 dB respectively, at a BER of 10(-3).
In this paper, we review the concept of multiset-partition-based distribution matching. We then characterize performance over short block lengths of 20, 40, and 80 symbols, and with 16QAM, 64QAM, and ...256QAM modulation formats. We note that a 40 symbol distribution matcher length can obtain better than uniform performance, while an 80 symbol distribution matcher can utilize most of the available gain over a wide range of signal-to-noise ratios.
The study and manipulation of T cell receptors (TCRs) is central to multiple fields across basic and translational immunology research. Produced by V(D)J recombination, TCRs are often only recorded ...in the literature and data repositories as a combination of their V and J gene symbols, plus their hypervariable CDR3 amino acid sequence. However, numerous applications require full-length coding nucleotide sequences. Here we present Stitchr, a software tool developed to specifically address this limitation. Given minimal V/J/CDR3 information, Stitchr produces complete coding sequences representing a fully spliced TCR cDNA. Due to its modular design, Stitchr can be used for TCR engineering using either published germline or novel/modified variable and constant region sequences. Sequences produced by Stitchr were validated by synthesizing and transducing TCR sequences into Jurkat cells, recapitulating the expected antigen specificity of the parental TCR. Using a companion script, Thimble, we demonstrate that Stitchr can process a million TCRs in under ten minutes using a standard desktop personal computer. By systematizing the production and modification of TCR sequences, we propose that Stitchr will increase the speed, repeatability, and reproducibility of TCR research. Stitchr is available on GitHub.
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