Feature learningIn machine learning, feature learning or representation learning is a set of techniques that allows a system to automatically discover the representations needed for feature detection or classification from raw data. This replaces manual feature engineering and allows a machine to both learn the features and use them to perform a specific task. Feature learning is motivated by the fact that machine learning tasks such as classification often require input that is mathematically and computationally convenient to process.
Artificial neural networkArtificial neural networks (ANNs, also shortened to neural networks (NNs) or neural nets) are a branch of machine learning models that are built using principles of neuronal organization discovered by connectionism in the biological neural networks constituting animal brains. An ANN is based on a collection of connected units or nodes called artificial neurons, which loosely model the neurons in a biological brain. Each connection, like the synapses in a biological brain, can transmit a signal to other neurons.
Transformer (machine learning model)A transformer is a deep learning architecture that relies on the parallel multi-head attention mechanism. The modern transformer was proposed in the 2017 paper titled 'Attention Is All You Need' by Ashish Vaswani et al., Google Brain team. It is notable for requiring less training time than previous recurrent neural architectures, such as long short-term memory (LSTM), and its later variation has been prevalently adopted for training large language models on large (language) datasets, such as the Wikipedia corpus and Common Crawl, by virtue of the parallelized processing of input sequence.
Deep learningDeep learning is part of a broader family of machine learning methods, which is based on artificial neural networks with representation learning. The adjective "deep" in deep learning refers to the use of multiple layers in the network. Methods used can be either supervised, semi-supervised or unsupervised.
Recurrent neural networkA recurrent neural network (RNN) is one of the two broad types of artificial neural network, characterized by direction of the flow of information between its layers. In contrast to uni-directional feedforward neural network, it is a bi-directional artificial neural network, meaning that it allows the output from some nodes to affect subsequent input to the same nodes. Their ability to use internal state (memory) to process arbitrary sequences of inputs makes them applicable to tasks such as unsegmented, connected handwriting recognition or speech recognition.
Generative pre-trained transformerGenerative pre-trained transformers (GPT) are a type of large language model (LLM) and a prominent framework for generative artificial intelligence. The first GPT was introduced in 2018 by OpenAI. GPT models are artificial neural networks that are based on the transformer architecture, pre-trained on large data sets of unlabelled text, and able to generate novel human-like content. As of 2023, most LLMs have these characteristics and are sometimes referred to broadly as GPTs.
TreebankIn linguistics, a treebank is a parsed text corpus that annotates syntactic or semantic sentence structure. The construction of parsed corpora in the early 1990s revolutionized computational linguistics, which benefitted from large-scale empirical data. The term treebank was coined by linguist Geoffrey Leech in the 1980s, by analogy to other repositories such as a seedbank or bloodbank. This is because both syntactic and semantic structure are commonly represented compositionally as a tree structure.
Protein structure predictionProtein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).
Semantic parsingSemantic parsing is the task of converting a natural language utterance to a logical form: a machine-understandable representation of its meaning. Semantic parsing can thus be understood as extracting the precise meaning of an utterance. Applications of semantic parsing include machine translation, question answering, ontology induction, automated reasoning, and code generation. The phrase was first used in the 1970s by Yorick Wilks as the basis for machine translation programs working with only semantic representations.
Protein function predictionProtein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. These predictions are often driven by data-intensive computational procedures. Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of publications, phylogenetic profiles, phenotypic profiles, and protein-protein interaction.
Protein–protein interaction predictionProtein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical processes.
TransformerA transformer is a passive component that transfers electrical energy from one electrical circuit to another circuit, or multiple circuits. A varying current in any coil of the transformer produces a varying magnetic flux in the transformer's core, which induces a varying electromotive force (EMF) across any other coils wound around the same core. Electrical energy can be transferred between separate coils without a metallic (conductive) connection between the two circuits.
Gene predictionIn computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced. In its earliest days, "gene finding" was based on painstaking experimentation on living cells and organisms.
Symbolic artificial intelligenceIn artificial intelligence, symbolic artificial intelligence is the term for the collection of all methods in artificial intelligence research that are based on high-level symbolic (human-readable) representations of problems, logic and search. Symbolic AI used tools such as logic programming, production rules, semantic nets and frames, and it developed applications such as knowledge-based systems (in particular, expert systems), symbolic mathematics, automated theorem provers, ontologies, the semantic web, and automated planning and scheduling systems.
Circuit topology (electrical)The circuit topology of an electronic circuit is the form taken by the network of interconnections of the circuit components. Different specific values or ratings of the components are regarded as being the same topology. Topology is not concerned with the physical layout of components in a circuit, nor with their positions on a circuit diagram; similarly to the mathematical concept of topology, it is only concerned with what connections exist between the components.
Natural language processingNatural language processing (NLP) is an interdisciplinary subfield of linguistics and computer science. It is primarily concerned with processing natural language datasets, such as text corpora or speech corpora, using either rule-based or probabilistic (i.e. statistical and, most recently, neural network-based) machine learning approaches. The goal is a computer capable of "understanding" the contents of documents, including the contextual nuances of the language within them.
CASPCritical Assessment of Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994. CASP provides research groups with an opportunity to objectively test their structure prediction methods and delivers an independent assessment of the state of the art in protein structure modeling to the research community and software users.
Part-of-speech taggingIn corpus linguistics, part-of-speech tagging (POS tagging or PoS tagging or POST), also called grammatical tagging is the process of marking up a word in a text (corpus) as corresponding to a particular part of speech, based on both its definition and its context. A simplified form of this is commonly taught to school-age children, in the identification of words as nouns, verbs, adjectives, adverbs, etc. Once performed by hand, POS tagging is now done in the context of computational linguistics, using algorithms which associate discrete terms, as well as hidden parts of speech, by a set of descriptive tags.
Word embeddingIn natural language processing (NLP), a word embedding is a representation of a word. The embedding is used in text analysis. Typically, the representation is a real-valued vector that encodes the meaning of the word in such a way that words that are closer in the vector space are expected to be similar in meaning. Word embeddings can be obtained using language modeling and feature learning techniques, where words or phrases from the vocabulary are mapped to vectors of real numbers.
Conditional random fieldConditional random fields (CRFs) are a class of statistical modeling methods often applied in pattern recognition and machine learning and used for structured prediction. Whereas a classifier predicts a label for a single sample without considering "neighbouring" samples, a CRF can take context into account. To do so, the predictions are modelled as a graphical model, which represents the presence of dependencies between the predictions. What kind of graph is used depends on the application.
