Tute Genomics was an American genomics startup that provided a cloud-based web application for rapid and accurate annotation of human genomic data. It was built on the expertise of ANNOVAR. Tute Genomics assisted researchers in identifying disease genes and biomarkers, and assisted clinicians/labs in performing genetic diagnosis. Based in Provo, Utah, Tute was co-founded by Dr. Kai Wang, an assistant professor at the University of Southern California (USC); and Dr. Reid J. Robison, a board-certified psychiatrist with fellowship training in both neurodevelopmental genetics and bioinformatics. Tute Genomics was acquired by PierianDX in 2016. == History == The word "tute" means "personal" in the Na’vi language created for the 2009 film Avatar by Paul Frommer, a linguist and communications professor at the USC Marshall School of Business. === Timeline === 2013 Tute Genomics launched in 2013 and entered the accelerator, BoomStartup. By "demo day" of BoomStartup, Tute had raised their seed round of funding and expanded the round to include angel investors from SLC Angels, Park City Angels, Life Science Angels. Tute was the tenth ever online syndicate for AngelList and in all raised a seed round of $1.5 million. 2014 In March 2014, the company announced that Affiliated Genetics, a Utah-based CLIA-certified laboratory, selected Tute Genomics for its next-generation sequencing (NGS) analytics pipeline. In May 2014, the company announced joining the Global Alliance for Genomics and Health. In June 2014, Advanced Biological Laboratories (ABL), S.A., announced a licensing and collaboration agreement with Tute Genomics and the commercial launch of OncoChek for managing and analysing genomics data in the field of oncology. In July 2014, the company announced an agreement with Lineagen, Inc., to provide next-generation sequencing analytics for Lineagen’s NextStepDx Plus assay. Also, Brigham Young University selected the Tute Genomics genome annotation and discovery platform for analysis and interpretation of 1,000 exomes and genomes. In November 2014, the company announced addition of the Tute platform to Illumina’s BaseSpace. The company announced a Series A1 funding round of $2.3 million in December 2014. The round was led by UK-based Eurovestech. Peak Ventures and a number of angel investors also participated in this round. 2015 Tute recruits David Mittelman, founder of Arpeggi, Inc. and former CSO at FamilyTreeDNA, to Tute Genomics as Chief Scientific Officer. Tute acquires Knome and integrates the KnoSys platform into its software product. 2016 Reid Robison, Tute CEO, launches a Kickstarter campaign to sell Tute interpreted whole genome and whole exome sequencing directly to consumers. The campaign was suspended within the same month after receiving a letter from the United States Food and Drug Administration. Tute is acquired by PierianDX.
Connectionist expert system
Connectionist expert systems are artificial neural network (ANN) based expert systems where the ANN generates inferencing rules e.g., fuzzy-multi layer perceptron where linguistic and natural form of inputs are used. Apart from that, rough set theory may be used for encoding knowledge in the weights better and also genetic algorithms may be used to optimize the search solutions better. Symbolic reasoning methods may also be incorporated (see hybrid intelligent system). (Also see expert system, neural network, clinical decision support system.)
Generalized iterative scaling
In statistics, generalized iterative scaling (GIS) and improved iterative scaling (IIS) are two early algorithms used to fit log-linear models, notably multinomial logistic regression (MaxEnt) classifiers and extensions of it such as MaxEnt Markov models and conditional random fields. These algorithms have been largely surpassed by gradient-based methods such as L-BFGS and coordinate descent algorithms.
Random projection
In mathematics and statistics, random projection is a technique used to reduce the dimensionality of a set of points which lie in Euclidean space. According to theoretical results, random projection preserves distances well, but empirical results are sparse. They have been applied to many natural language tasks under the name random indexing. == Dimensionality reduction == Dimensionality reduction, as the name suggests, is reducing the number of random variables using various mathematical methods from statistics and machine learning. Dimensionality reduction is often used to reduce the problem of managing and manipulating large data sets. Dimensionality reduction techniques generally use linear transformations in determining the intrinsic dimensionality of the manifold as well as extracting its principal directions. For this purpose there are various related techniques, including: principal component analysis, linear discriminant analysis, canonical correlation analysis, discrete cosine transform, random projection, etc. Random projection is a simple and computationally efficient way to reduce the dimensionality of data by trading a controlled amount of error for faster processing times and smaller model sizes. The dimensions and distribution of random projection matrices are controlled so as to approximately preserve the pairwise distances between any two samples of the dataset. == Method == The core idea behind random projection is given in the Johnson-Lindenstrauss lemma, which states that if points in a vector space are of sufficiently high dimension, then they may be projected into a suitable lower-dimensional space in a way which approximately preserves pairwise distances between the points with high probability. In random projection, the original d {\displaystyle d} -dimensional data is projected to a k {\displaystyle k} -dimensional subspace, by multiplying on the left by a random matrix R ∈ R k × d {\displaystyle R\in \mathbb {R} ^{k\times d}} . Using matrix notation: If X d × N {\displaystyle X_{d\times N}} is the original set of N d-dimensional observations, then X k × N R P = R k × d X d × N {\displaystyle X_{k\times N}^{RP}=R_{k\times d}X_{d\times N}} is the projection of the data onto a lower k-dimensional subspace. Random projection is computationally simple: form the random matrix "R" and project the d × N {\displaystyle d\times N} data matrix X onto K dimensions of order O ( d k N ) {\displaystyle O(dkN)} . If the data matrix X is sparse with about c nonzero entries per column, then the complexity of this operation is of order O ( c k N ) {\displaystyle O(ckN)} . === Orthogonal random projection === A unit vector can be orthogonally projected to a random subspace. Let u {\displaystyle u} be the original unit vector, and let v {\displaystyle v} be its projection. The norm-squared ‖ v ‖ 2 2 {\displaystyle \|v\|_{2}^{2}} has the same distribution as projecting a random point, uniformly sampled on the unit sphere, to its first k {\displaystyle k} coordinates. This is equivalent to sampling a random point in the multivariate gaussian distribution x ∼ N ( 0 , I d × d ) {\displaystyle x\sim {\mathcal {N}}(0,I_{d\times d})} , then normalizing it. Therefore, ‖ v ‖ 2 2 {\displaystyle \|v\|_{2}^{2}} has the same distribution as ∑ i = 1 k x i 2 ∑ i = 1 k x i 2 + ∑ i = k + 1 d x i 2 {\displaystyle {\frac {\sum _{i=1}^{k}x_{i}^{2}}{\sum _{i=1}^{k}x_{i}^{2}+\sum _{i=k+1}^{d}x_{i}^{2}}}} , which by the chi-squared construction of the Beta distribution, has distribution Beta ( k / 2 , ( d − k ) / 2 ) {\displaystyle \operatorname {Beta} (k/2,(d-k)/2)} , with mean k / d {\displaystyle k/d} . We have a concentration inequality P r [ | ‖ v ‖ 2 − k d | ≥ ϵ k d ] ≤ 3 exp ( − k ϵ 2 / 64 ) {\displaystyle Pr\left[\left|\|v\|_{2}-{\frac {k}{d}}\right|\geq \epsilon {\sqrt {\frac {k}{d}}}\right]\leq 3\exp \left(-k\epsilon ^{2}/64\right)} for any ϵ ∈ ( 0 , 1 ) {\displaystyle \epsilon \in (0,1)} . === Gaussian random projection === The random matrix R can be generated using a Gaussian distribution. The first row is a random unit vector uniformly chosen from S d − 1 {\displaystyle S^{d-1}} . The second row is a random unit vector from the space orthogonal to the first row, the third row is a random unit vector from the space orthogonal to the first two rows, and so on. In this way of choosing R, and the following properties are satisfied: Spherical symmetry: For any orthogonal matrix A ∈ O ( d ) {\displaystyle A\in O(d)} , RA and R have the same distribution. Orthogonality: The rows of R are orthogonal to each other. Normality: The rows of R are unit-length vectors. === More computationally efficient random projections === Achlioptas has shown that the random matrix can be sampled more efficiently. Either the full matrix can be sampled IID according to R i , j = 3 / k × { + 1 with probability 1 6 0 with probability 2 3 − 1 with probability 1 6 {\displaystyle R_{i,j}={\sqrt {3/k}}\times {\begin{cases}+1&{\text{with probability }}{\frac {1}{6}}\\0&{\text{with probability }}{\frac {2}{3}}\\-1&{\text{with probability }}{\frac {1}{6}}\end{cases}}} or the full matrix can be sampled IID according to R i , j = 1 / k × { + 1 with probability 1 2 − 1 with probability 1 2 {\displaystyle R_{i,j}={\sqrt {1/k}}\times {\begin{cases}+1&{\text{with probability }}{\frac {1}{2}}\\-1&{\text{with probability }}{\frac {1}{2}}\end{cases}}} Both are efficient for database applications because the computations can be performed using integer arithmetic. More related study is conducted in. It was later shown how to use integer arithmetic while making the distribution even sparser, having very few nonzeroes per column, in work on the Sparse JL Transform. This is advantageous since a sparse embedding matrix means being able to project the data to lower dimension even faster. === Random Projection with Quantization === Random projection can be further condensed by quantization (discretization), with 1-bit (sign random projection) or multi-bits. It is the building block of SimHash, RP tree, and other memory efficient estimation and learning methods. == Large quasiorthogonal bases == The Johnson-Lindenstrauss lemma states that large sets of vectors in a high-dimensional space can be linearly mapped in a space of much lower (but still high) dimension n with approximate preservation of distances. One of the explanations of this effect is the exponentially high quasiorthogonal dimension of n-dimensional Euclidean space. There are exponentially large (in dimension n) sets of almost orthogonal vectors (with small value of inner products) in n–dimensional Euclidean space. This observation is useful in indexing of high-dimensional data. Quasiorthogonality of large random sets is important for methods of random approximation in machine learning. In high dimensions, exponentially large numbers of randomly and independently chosen vectors from equidistribution on a sphere (and from many other distributions) are almost orthogonal with probability close to one. This implies that in order to represent an element of such a high-dimensional space by linear combinations of randomly and independently chosen vectors, it may often be necessary to generate samples of exponentially large length if we use bounded coefficients in linear combinations. On the other hand, if coefficients with arbitrarily large values are allowed, the number of randomly generated elements that are sufficient for approximation is even less than dimension of the data space. == Implementations == RandPro - An R package for random projection sklearn.random_projection - A module for random projection from the scikit-learn Python library Weka implementation [1]
Clustering illusion
The clustering illusion is the tendency to erroneously consider the inevitable "streaks" or "clusters" arising in small samples from random distributions to be non-random. The illusion is caused by a human tendency to underpredict the amount of variability likely to appear in a small sample of random or pseudorandom data. Thomas Gilovich, an early author on the subject, argued that the effect occurs for different types of random dispersions. Some might perceive patterns in stock market price fluctuations over time, or clusters in two-dimensional data such as the locations of impact of World War II V-1 flying bombs on maps of London. Although Londoners developed specific theories about the pattern of impacts within London, a statistical analysis by R. D. Clarke originally published in 1946 showed that the impacts of V-2 rockets on London were a close fit to a random distribution. == Similar biases == Using this cognitive bias in causal reasoning may result in the Texas sharpshooter fallacy, in which differences in data are ignored and similarities are overemphasized. More general forms of erroneous pattern recognition are pareidolia and apophenia. Related biases are the illusion of control which the clustering illusion could contribute to, and insensitivity to sample size in which people don't expect greater variation in smaller samples. A different cognitive bias involving misunderstanding of chance streams is the gambler's fallacy. == Possible causes == Daniel Kahneman and Amos Tversky explained this kind of misprediction as being caused by the representativeness heuristic (which itself they also first proposed).
Visual temporal attention
Visual temporal attention is a special case of visual attention that involves directing attention to specific instant of time. Similar to its spatial counterpart visual spatial attention, these attention modules have been widely implemented in video analytics in computer vision to provide enhanced performance and human interpretable explanation of deep learning models. As visual spatial attention mechanism allows human and/or computer vision systems to focus more on semantically more substantial regions in space, visual temporal attention modules enable machine learning algorithms to emphasize more on critical video frames in video analytics tasks, such as human action recognition. In convolutional neural network-based systems, the prioritization introduced by the attention mechanism is regularly implemented as a linear weighting layer with parameters determined by labeled training data. == Application in Action Recognition == Recent video segmentation algorithms often exploits both spatial and temporal attention mechanisms. Research in human action recognition has accelerated significantly since the introduction of powerful tools such as Convolutional Neural Networks (CNNs). However, effective methods for incorporation of temporal information into CNNs are still being actively explored. Motivated by the popular recurrent attention models in natural language processing, the Attention-aware Temporal Weighted CNN (ATW CNN) is proposed in videos, which embeds a visual attention model into a temporal weighted multi-stream CNN. This attention model is implemented as temporal weighting and it effectively boosts the recognition performance of video representations. Besides, each stream in the proposed ATW CNN framework is capable of end-to-end training, with both network parameters and temporal weights optimized by stochastic gradient descent (SGD) with back-propagation. Experimental results show that the ATW CNN attention mechanism contributes substantially to the performance gains with the more discriminative snippets by focusing on more relevant video segments. == Literature == Seibold VC, Balke J and Rolke B (2023): Temporal attention. Front. Cognit. 2:1168320. doi: 10.3389/fcogn.2023.1168320.
Arabic Speech Corpus
The Arabic Speech Corpus is a Modern Standard Arabic (MSA) speech corpus for speech synthesis. The corpus contains phonetic and orthographic transcriptions of more than 3.7 hours of MSA speech aligned with recorded speech on the phoneme level. The annotations include word stress marks on the individual phonemes. The Arabic Speech Corpus was built as part of a doctoral project by Nawar Halabi at the University of Southampton funded by MicroLinkPC who own an exclusive license to commercialise the corpus, but the corpus is available for strictly non-commercial purposes through the official Arabic Speech Corpus website. It is distributed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. == Purpose == The corpus was mainly built for speech synthesis purposes, specifically Speech Synthesis, but the corpus has been used for building HMM based voices in Arabic. It was also used to automatically align other speech corpora with their phonetic transcript and could be used as part of a larger corpus for training speech recognition systems. == Contents == The package contains the following: 1813 .wav files containing spoken utterances. 1813 .lab files containing text utterances. 1813 .TextGrid files containing the phoneme labels with time stamps of the boundaries where these occur in the .wav files. phonetic-transcript.txt which has the form "[wav_filename]" "[Phoneme Sequence]" in every line. orthographic-transcript.txt which has the form "[wav_filename]" "[Orthographic Transcript]" in every line. Orthography is in Buckwalter Format which is friendlier where there is software that does not read Arabic script. It can be easily converted back to Arabic. There is an extra 18 minutes of fully annotated corpus (separate from above but with the same structure as above) which was used to evaluated the corpus (see PhD thesis). The corpus was also used to prove that using automatically extracted, orthography-based stress marks improve the quality of speech synthesis in MSA.