How Data Happened: A History from the Age of Reason to the Age of Algorithms is a 2023 non-fiction book written by Columbia University professors Chris Wiggins and Matthew L. Jones. The book explores the history of data and statistics from the end of the 18th century to the present day. == Content == The book starts at the end of the 18th century, when European states began tabulating physical resources, and ends at the present day, when algorithms manipulate our personal information as a commodity. It looks at the rise of data and statistics, and how early statistical methods were used to justify eugenics, quantify supposed racial differences, and develop military and industrial applications. The authors also discuss the impact of the internet and e-commerce on data collection, the rise of data science, and the consequences of government-run surveillance systems collecting vast amounts of personal data for customized, targeted advertising. They emphasize the importance of privacy and democracy and propose remedies to the problems caused by mass data collection, including stronger regulation of the tech industry and collective action by its employees. The book is a historical analysis that provides context for understanding the debates surrounding data and its control. The book has 336 pages and was published in 2023 by W. W. Norton & Company.
GeneRIF
A GeneRIF or Gene Reference Into Function is a short (255 characters or fewer) statement about the function of a gene. GeneRIFs provide a simple mechanism for allowing scientists to add to the functional annotation of genes described in the Entrez Gene database. In practice, function is constructed quite broadly. For example, there are GeneRIFs that discuss the role of a gene in a disease, GeneRIFs that point the viewer towards a review article about the gene, and GeneRIFs that discuss the structure of a gene. However, the stated intent is for GeneRIFs to be about gene function. Currently over half a million geneRIFs have been created for genes from almost 1000 different species. GeneRIFs are always associated with specific entries in the Entrez Gene database. Each GeneRIF has a pointer to the PubMed ID (a type of document identifier) of a scientific publication that provides evidence for the statement made by the GeneRIF. GeneRIFs are often extracted directly from the document that is identified by the PubMed ID, very frequently from its title or from its final sentence. GeneRIFs are usually produced by NCBI indexers, but anyone may submit a GeneRIF. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the species. The latter case is implemented via records in Gene with the symbol NEWENTRY. Once the Gene ID is identified, only three types of information are required to complete a submission: a concise phrase describing a function or functions (less than 255 characters in length, preferably more than a restatement of the title of the paper); a published paper describing that function, implemented by supplying the PubMed ID of a citation in PubMed; a valid e-mail address (which will remain confidential). == Example == Here are some GeneRIFs taken from Entrez Gene for GeneID 7157, the human gene TP53. The PubMed document identifiers have been omitted from the examples. Note the wide variability with respect to the presence or absence of punctuation and of sentence-initial capital letters. p53 and c-erbB-2 may have independent role in carcinogenesis of gall bladder cancer Degradation of endogenous HIPK2 depends on the presence of a functional p53 protein. p53 codon 72 alleles influence the response to anticancer drugs in cells from aged people by regulating the cell cycle inhibitor p21WAF1 Logistic regression analysis showed p53 and COX-2 as dependent predictors in pancreatic carcinogenesis, and a reciprocal relationship to neoplastic progression between p53 and COX-2. GeneRIFs are an unusual type of textual genre, and they have recently been the subject of a number of articles from the natural language processing community.
Knowledge graph embedding
In representation learning, knowledge graph embedding (KGE), also called knowledge representation learning (KRL), or multi-relation learning, is a machine learning task of learning a low-dimensional representation of a knowledge graph's entities and relations while preserving their semantic meaning. Leveraging their embedded representation, knowledge graphs can be used for various applications such as link prediction, triple classification, entity recognition, clustering, and relation extraction. == Definition == A knowledge graph G = { E , R , F } {\displaystyle {\mathcal {G}}=\{E,R,F\}} is a collection of entities E {\displaystyle E} , relations R {\displaystyle R} , and facts F {\displaystyle F} . A fact is a triple ( h , r , t ) ∈ F {\displaystyle (h,r,t)\in F} that denotes a link r ∈ R {\displaystyle r\in R} between the head h ∈ E {\displaystyle h\in E} and the tail t ∈ E {\displaystyle t\in E} of the triple. Another notation that is often used in the literature to represent a triple (or fact) is ⟨ head , relation , tail ⟩ {\displaystyle \langle {\text{head}},{\text{relation}},{\text{tail}}\rangle } . This notation is called the Resource Description Framework (RDF). A knowledge graph represents the knowledge related to a specific domain; leveraging this structured representation, it is possible to infer a piece of new knowledge from it after some refinement steps. However, nowadays, people have to deal with the sparsity of data and the computational inefficiency to use them in a real-world application. The embedding of a knowledge graph is a function that translates each entity and each relation into a vector of a given dimension d {\displaystyle d} , called embedding dimension. It is even possible to embed the entities and relations with different dimensions. The embedding vectors can then be used for other tasks. A knowledge graph embedding is characterized by four aspects: Representation space: The low-dimensional space in which the entities and relations are represented. Scoring function: A measure of the goodness of a triple-embedded representation. Encoding models: The modality in which the embedded representation of the entities and relations interact with each other. Additional information: Any additional information coming from the knowledge graph that can enrich the embedded representation. Usually, an ad hoc scoring function is integrated into the general scoring function for each additional piece of information. == Embedding procedure == All algorithms for creating a knowledge graph embedding follow the same approach. First, the embedding vectors are initialized to random values. Then, they are iteratively optimized using a training set of triples. In each iteration, a batch of size b {\displaystyle b} triples is sampled from the training set, and a triple from it is sampled and corrupted—i.e., a triple that does not represent a true fact in the knowledge graph. The corruption of a triple involves substituting the head or the tail (or both) of the triple with another entity that makes the fact false. The original triple and the corrupted triple are added in the training batch, and then the embeddings are updated, optimizing a scoring function. Iteration stops when a stop condition is reached. Usually, the stop condition depends on the overfitting of the training set. At the end, the learned embeddings should have extracted semantic meaning from the training triples and should correctly predict unseen true facts in the knowledge graph. === Pseudocode === The following is the pseudocode for the general embedding procedure. algorithm Compute entity and relation embeddings input: The training set S = { ( h , r , t ) } {\displaystyle S=\{(h,r,t)\}} , entity set E {\displaystyle E} , relation set R {\displaystyle R} , embedding dimension k {\displaystyle k} output: Entity and relation embeddings initialization: the entities e {\displaystyle e} and relations r {\displaystyle r} embeddings (vectors) are randomly initialized while stop condition do S b a t c h ← s a m p l e ( S , b ) {\displaystyle S_{batch}\leftarrow sample(S,b)} // Sample a batch from the training set for each ( h , r , t ) {\displaystyle (h,r,t)} in S b a t c h {\displaystyle S_{batch}} do ( h ′ , r , t ′ ) ← s a m p l e ( S ′ ) {\displaystyle (h',r,t')\leftarrow sample(S')} // Sample a corrupted fact T b a t c h ← T b a t c h ∪ { ( ( h , r , t ) , ( h ′ , r , t ′ ) ) } {\displaystyle T_{batch}\leftarrow T_{batch}\cup \{((h,r,t),(h',r,t'))\}} end for Update embeddings by minimizing the loss function end while == Performance indicators == These indexes are often used to measure the embedding quality of a model. The simplicity of the indexes makes them very suitable for evaluating the performance of an embedding algorithm even on a large scale. Given Q {\displaystyle {\ce {Q}}} as the set of all ranked predictions of a model, it is possible to define three different performance indexes: Hits@K, MR, and MRR. === Hits@K === Hits@K or in short, H@K, is a performance index that measures the probability to find the correct prediction in the first top K model predictions. Usually, it is used k = 10 {\displaystyle k=10} . Hits@K reflects the accuracy of an embedding model to predict the relation between two given triples correctly. Hits@K = | { q ∈ Q : q < k } | | Q | ∈ [ 0 , 1 ] {\displaystyle ={\frac {|\{q\in Q:q Automation in construction is the combination of methods, processes, and systems that allow for greater machine autonomy in construction activities. Construction automation may have multiple goals, including but not limited to, reducing jobsite injuries, decreasing activity completion times, and assisting with quality control and quality assurance. Some systems may be fielded as a direct response to increasing skilled labor shortages in some countries. Opponents claim that increased automation may lead to less construction jobs and that software leaves heavy equipment vulnerable to hackers. Research insights on this subject are today published in several journals such as Automation in Construction by Elsevier. == Uses of automation in construction == Equipment control and management: Automation can be used to control and monitor construction equipment, such as cranes, excavators, and bulldozers. Material handling: Automated systems can be used to handle, transport, and place materials such as concrete, bricks, and stones. Surveying: Automated survey equipment and drones can be used to collect and analyze data on construction sites. Quality control: Automated systems can be used to monitor and control the quality of materials and construction processes. Safety management: Automated systems can be used to monitor and control safety conditions on construction sites. Scheduling and planning: Automated systems can be used to manage schedules, resources, and costs. Waste management: Automated systems can be used to manage and dispose of waste materials generated during construction. 3D printing: Automated 3D printing can be used to create prototypes, models, and even full-scale building components. == Autonomous heavy equipment == Advances in sensors, machine learning, and autonomous vehicle technology have led to the development of self-operating construction equipment and retrofit systems designed to automate excavators, bulldozers, tracked loaders, skid steer loaders, and haul trucks, allowing them to perform tasks with limited human supervision. Since 2017, tech companies have developed autonomous or semi-autonomous retrofit kits that can be installed on existing construction machinery. Examples include Bedrock Robotics, Built Robotics, and SafeAI, which develop sensor and software systems that enable excavators and other earthmoving machines to operate with varying degrees of autonomy. Major equipment manufacturers have also introduced autonomous capabilities: Caterpillar and John Deere have developed autonomous or semi-autonomous systems for construction and mining equipment, including haul trucks and earthmoving machines. == Transportation сonstruction == Kratos Defense & Security Solutions fielded the world’s first Autonomous Truck-Mounted Attenuator (ATMA) in 2017, in conjunction with Royal Truck & Equipment. == Benefits of automation in construction == The use of automation in construction has become increasingly prevalent in recent years due to its numerous benefits. Automation in construction refers to the use of machinery, software, and other technologies to perform tasks that were previously done manually by workers. One of the most significant benefits of automation in construction is increased productivity. Automation can help speed up construction processes, reduce project completion times, and improve overall efficiency. For example, using automated machinery for tasks such as concrete pouring, bricklaying, and welding can significantly increase the speed and accuracy of these tasks, allowing for more work to be completed in a shorter amount of time. Another benefit of automation in construction is improved safety. By automating tasks that are hazardous to workers, such as demolition or working at height, companies can reduce the risk of accidents and injuries on site. Automation can also help to reduce worker fatigue, which can be a significant factor in accidents and mistakes. Overall, the use of automation in construction can improve productivity, reduce costs, increase safety, and improve the quality of construction projects. As technology continues to advance, the use of automation is likely to become even more prevalent in the construction industry. Model compression is a machine learning technique for reducing the size of trained models. Large models can achieve high accuracy, but often at the cost of significant resource requirements. Compression techniques aim to compress models without significant performance reduction. Smaller models require less storage space, and consume less memory and compute during inference. Compressed models enable deployment on resource-constrained devices such as smartphones, embedded systems, edge computing devices, and consumer electronics computers. Efficient inference is also valuable for large corporations that serve large model inference over an API, allowing them to reduce computational costs and improve response times for users. Model compression is not to be confused with knowledge distillation, in which a smaller "student" model is trained to imitate the input-output behavior of a larger "teacher" model (as opposed to using the "teacher"'s trained parameters or the "teacher"'s training targets). == Techniques == Several techniques are employed for model compression. === Pruning === Pruning sparsifies a large model by setting some parameters to exactly zero. This effectively reduces the number of parameters. This allows the use of sparse matrix operations, which are faster than dense matrix operations. Pruning criteria can be based on magnitudes of parameters, the statistical pattern of neural activations, Hessian values, etc. === Quantization === Quantization reduces the numerical precision of weights and activations. For example, instead of storing weights as 32-bit floating-point numbers, they can be represented using 8-bit integers. Low-precision parameters take up less space, and takes less compute to perform arithmetic with. It is also possible to quantize some parameters more aggressively than others, so for example, a less important parameter can have 8-bit precision while another, more important parameter, can have 16-bit precision. Inference with such models requires mixed-precision arithmetic. Quantized models can also be used during training (rather than after training). PyTorch implements automatic mixed-precision (AMP), which performs autocasting, gradient scaling, and loss scaling. === Low-rank factorization === Weight matrices can be approximated by low-rank matrices. Let W {\displaystyle W} be a weight matrix of shape m × n {\displaystyle m\times n} . A low-rank approximation is W ≈ U V T {\displaystyle W\approx UV^{T}} , where U {\displaystyle U} and V {\displaystyle V} are matrices of shapes m × k , n × k {\displaystyle m\times k,n\times k} . When k {\displaystyle k} is small, this both reduces the number of parameters needed to represent W {\displaystyle W} approximately, and accelerates matrix multiplication by W {\displaystyle W} . Low-rank approximations can be found by singular value decomposition (SVD). The choice of rank for each weight matrix is a hyperparameter, and jointly optimized as a mixed discrete-continuous optimization problem. The rank of weight matrices may also be pruned after training, taking into account the effect of activation functions like ReLU on the implicit rank of the weight matrices. == Training == Model compression may be decoupled from training, that is, a model is first trained without regard for how it might be compressed, then it is compressed. However, it may also be combined with training. The "train big, then compress" method trains a large model for a small number of training steps (less than it would be if it were trained to convergence), then heavily compress the model. It is found that at the same compute budget, this method results in a better model than lightly compressed, small models. In Deep Compression, the compression has three steps. First loop (pruning): prune all weights lower than a threshold, then finetune the network, then prune again, etc. Second loop (quantization): cluster weights, then enforce weight sharing among all weights in each cluster, then finetune the network, then cluster again, etc. Third step: Use Huffman coding to losslessly compress the model. The SqueezeNet paper reported that Deep Compression achieved a compression ratio of 35 on AlexNet, and a ratio of ~10 on SqueezeNets. BeHafizh is a mobile application to assist in the effort to memorize Qur'anic verses. The software runs on the Android operating system. This application was made by a team from Gadjah Mada University (UGM) consisting of Farid Amin Ridwanto, Rian Adam Rajagede and Alfian Try Putranto in order to participate in the National Student Musabaqoh Tilawatil Quran (MTQ) held at University of Indonesia (UI) on 1- August 8, 2015. This application then won a gold medal in the branch of Computer Application Design in the competition. == Features == === Audio Player === Audio player, paragraph can be played repeatedly, with pause, and can be done on a certain range of Quranic verses. === Memorization Test === Memorization testing continues users to improve their memorization. Memorization Recorders improves user's ability to recite Quran. === Colour indicators === === Achievements === === Reminders === In statistics, EM (expectation maximization) algorithm handles latent variables, while GMM is the Gaussian mixture model. == Background == In the picture below, are shown the red blood cell hemoglobin concentration and the red blood cell volume data of two groups of people, the Anemia group and the control group (i.e. the group of people without Anemia). As expected, people with Anemia have lower red blood cell volume and lower red blood cell hemoglobin concentration than those without Anemia. x {\displaystyle x} is a random vector such as x := ( red blood cell volume , red blood cell hemoglobin concentration ) {\displaystyle x:={\big (}{\text{red blood cell volume}},{\text{red blood cell hemoglobin concentration}}{\big )}} , and from medical studies it is known that x {\displaystyle x} are normally distributed in each group, i.e. x ∼ N ( μ , Σ ) {\displaystyle x\sim {\mathcal {N}}(\mu ,\Sigma )} . z {\displaystyle z} is denoted as the group where x {\displaystyle x} belongs, with z i = 0 {\displaystyle z_{i}=0} when x i {\displaystyle x_{i}} belongs to the Anemia group and z i = 1 {\displaystyle z_{i}=1} when x i {\displaystyle x_{i}} belongs to the control group. Also z ∼ Categorical ( k , ϕ ) {\displaystyle z\sim \operatorname {Categorical} (k,\phi )} where k = 2 {\displaystyle k=2} , ϕ j ≥ 0 , {\displaystyle \phi _{j}\geq 0,} and ∑ j = 1 k ϕ j = 1 {\displaystyle \sum _{j=1}^{k}\phi _{j}=1} . See Categorical distribution. The following procedure can be used to estimate ϕ , μ , Σ {\displaystyle \phi ,\mu ,\Sigma } . A maximum likelihood estimation can be applied: ℓ ( ϕ , μ , Σ ) = ∑ i = 1 m log ( p ( x ( i ) ; ϕ , μ , Σ ) ) = ∑ i = 1 m log ∑ z ( i ) = 1 k p ( x ( i ) ∣ z ( i ) ; μ , Σ ) p ( z ( i ) ; ϕ ) {\displaystyle \ell (\phi ,\mu ,\Sigma )=\sum _{i=1}^{m}\log(p(x^{(i)};\phi ,\mu ,\Sigma ))=\sum _{i=1}^{m}\log \sum _{z^{(i)}=1}^{k}p\left(x^{(i)}\mid z^{(i)};\mu ,\Sigma \right)p(z^{(i)};\phi )} As the z i {\displaystyle z_{i}} for each x i {\displaystyle x_{i}} are known, the log likelihood function can be simplified as below: ℓ ( ϕ , μ , Σ ) = ∑ i = 1 m log p ( x ( i ) ∣ z ( i ) ; μ , Σ ) + log p ( z ( i ) ; ϕ ) {\displaystyle \ell (\phi ,\mu ,\Sigma )=\sum _{i=1}^{m}\log p\left(x^{(i)}\mid z^{(i)};\mu ,\Sigma \right)+\log p\left(z^{(i)};\phi \right)} Now the likelihood function can be maximized by making partial derivative over μ , Σ , ϕ {\displaystyle \mu ,\Sigma ,\phi } , obtaining: ϕ j = 1 m ∑ i = 1 m 1 { z ( i ) = j } {\displaystyle \phi _{j}={\frac {1}{m}}\sum _{i=1}^{m}1\{z^{(i)}=j\}} μ j = ∑ i = 1 m 1 { z ( i ) = j } x ( i ) ∑ i = 1 m 1 { z ( i ) = j } {\displaystyle \mu _{j}={\frac {\sum _{i=1}^{m}1\{z^{(i)}=j\}x^{(i)}}{\sum _{i=1}^{m}1\left\{z^{(i)}=j\right\}}}} Σ j = ∑ i = 1 m 1 { z ( i ) = j } ( x ( i ) − μ j ) ( x ( i ) − μ j ) T ∑ i = 1 m 1 { z ( i ) = j } {\displaystyle \Sigma _{j}={\frac {\sum _{i=1}^{m}1\{z^{(i)}=j\}(x^{(i)}-\mu _{j})(x^{(i)}-\mu _{j})^{T}}{\sum _{i=1}^{m}1\{z^{(i)}=j\}}}} If z i {\displaystyle z_{i}} is known, the estimation of the parameters results to be quite simple with maximum likelihood estimation. But if z i {\displaystyle z_{i}} is unknown it is much more complicated. Being z {\displaystyle z} a latent variable (i.e. not observed), with unlabeled scenario, the expectation maximization algorithm is needed to estimate z {\displaystyle z} as well as other parameters. Generally, this problem is set as a GMM since the data in each group is normally distributed. In machine learning, the latent variable z {\displaystyle z} is considered as a latent pattern lying under the data, which the observer is not able to see very directly. x i {\displaystyle x_{i}} is the known data, while ϕ , μ , Σ {\displaystyle \phi ,\mu ,\Sigma } are the parameter of the model. With the EM algorithm, some underlying pattern z {\displaystyle z} in the data x i {\displaystyle x_{i}} can be found, along with the estimation of the parameters. The wide application of this circumstance in machine learning is what makes EM algorithm so important. == EM algorithm in GMM == The EM algorithm consists of two steps: the E-step and the M-step. Firstly, the model parameters and the z ( i ) {\displaystyle z^{(i)}} can be randomly initialized. In the E-step, the algorithm tries to guess the value of z ( i ) {\displaystyle z^{(i)}} based on the parameters, while in the M-step, the algorithm updates the value of the model parameters based on the guess of z ( i ) {\displaystyle z^{(i)}} of the E-step. These two steps are repeated until convergence is reached. The algorithm in GMM is: Repeat until convergence: 1. (E-step) For each i , j {\displaystyle i,j} , set w j ( i ) := p ( z ( i ) = j | x ( i ) ; ϕ , μ , Σ ) {\displaystyle w_{j}^{(i)}:=p\left(z^{(i)}=j|x^{(i)};\phi ,\mu ,\Sigma \right)} 2. (M-step) Update the parameters ϕ j := 1 m ∑ i = 1 m w j ( i ) {\displaystyle \phi _{j}:={\frac {1}{m}}\sum _{i=1}^{m}w_{j}^{(i)}} μ j := ∑ i = 1 m w j ( i ) x ( i ) ∑ i = 1 m w j ( i ) {\displaystyle \mu _{j}:={\frac {\sum _{i=1}^{m}w_{j}^{(i)}x^{(i)}}{\sum _{i=1}^{m}w_{j}^{(i)}}}} Σ j := ∑ i = 1 m w j ( i ) ( x ( i ) − μ j ) ( x ( i ) − μ j ) T ∑ i = 1 m w j ( i ) {\displaystyle \Sigma _{j}:={\frac {\sum _{i=1}^{m}w_{j}^{(i)}\left(x^{(i)}-\mu _{j}\right)\left(x^{(i)}-\mu _{j}\right)^{T}}{\sum _{i=1}^{m}w_{j}^{(i)}}}} With Bayes' rule, the following result is obtained by the E-step: p ( z ( i ) = j | x ( i ) ; ϕ , μ , Σ ) = p ( x ( i ) | z ( i ) = j ; μ , Σ ) p ( z ( i ) = j ; ϕ ) ∑ l = 1 k p ( x ( i ) | z ( i ) = l ; μ , Σ ) p ( z ( i ) = l ; ϕ ) {\displaystyle p\left(z^{(i)}=j|x^{(i)};\phi ,\mu ,\Sigma \right)={\frac {p\left(x^{(i)}|z^{(i)}=j;\mu ,\Sigma \right)p\left(z^{(i)}=j;\phi \right)}{\sum _{l=1}^{k}p\left(x^{(i)}|z^{(i)}=l;\mu ,\Sigma \right)p\left(z^{(i)}=l;\phi \right)}}} According to GMM setting, these following formulas are obtained: p ( x ( i ) | z ( i ) = j ; μ , Σ ) = 1 ( 2 π ) n / 2 | Σ j | 1 / 2 exp ( − 1 2 ( x ( i ) − μ j ) T Σ j − 1 ( x ( i ) − μ j ) ) {\displaystyle p\left(x^{(i)}|z^{(i)}=j;\mu ,\Sigma \right)={\frac {1}{(2\pi )^{n/2}\left|\Sigma _{j}\right|^{1/2}}}\exp \left(-{\frac {1}{2}}\left(x^{(i)}-\mu _{j}\right)^{T}\Sigma _{j}^{-1}\left(x^{(i)}-\mu _{j}\right)\right)} p ( z ( i ) = j ; ϕ ) = ϕ j {\displaystyle p\left(z^{(i)}=j;\phi \right)=\phi _{j}} In this way, a switch between the E-step and the M-step is possible, according to the randomly initialized parameters.Automation in construction
Model compression
BeHafizh
EM algorithm and GMM model