The Cancer Imaging Archive (TCIA) is an open-access database of medical images for cancer research. The site is funded by the National Cancer Institute's (NCI) Cancer Imaging Program, and the contract is operated by the University of Arkansas for Medical Sciences. Data within the archive is organized into collections which typically share a common cancer type and/or anatomical site. The majority of the data consists of CT, MRI, and nuclear medicine (e.g. PET) images stored in DICOM format, but many other types of supporting data are also provided or linked to, in order to enhance research utility. All data are de-identified in order to comply with the Health Insurance Portability and Accountability Act and National Institutes of Health data sharing policies. TCIA resources are intended to support: Development of computer aided diagnosis methods (quantitative imaging) Evaluation of unbiased science reproducibility by acceptable standard statistical methods Research on correlation of clinical diagnostic medical images with digital microscopic histological images Exploratory biomarker research for which imaging is a key element Collaboration between cross-disciplinary investigators where imaging is crucial to research on tumor heterogeneity, between patients and within the tumor; tissue temporal response tracking - objective measurements of tumor progression; imaging genomics and Big Data linkages and analysis (clinical, histo-pathology, genomics) TCIA is recognized as a recommended repository for the Scientific Data, PLOS One, and F1000Research journals. It is also listed in the Registry of Research Data Repositories. == History == Prior to the creation of TCIA, the NCI funded development of the National Biomedical Imaging Archive. NBIA is an open-source Web application which was designed to allow the storage and query of DICOM images. TCIA was subsequently initiated in December 2010 to expand data sharing activities by funding a service component which would help address the technical and policy challenges associated with medical imaging research. TCIA leverages open-source tools such as NBIA and Clinical Trials Processor in order to provide its services. == Organization of the archive == The site content is organized into five categories: About Us - Provides a general overview of the site the organizations responsible for operating it. Share Your Data - Provides an overview of how to apply to upload data to the archive. Access the Archive - Provides information about the available data, methods for accessing that data and system usage metrics. Research Activities - Provides information about major research initiatives being conducted using TCIA data as well as information about publication guidelines. Help - Provides information about how to get support using the archive as well as documentation and data usage policies. == Methods for accessing data == Most collections on the Cancer Imaging Archive can be accessed without an account, but a few are restricted to specific users and therefore require an account to access them. TCIA has several ways to browse, filter, and download data. They include: Downloading the entire contents of a collection in bulk Leveraging the NBIA application to filter or search within or across collections Utilizing the RESTful Application programming interface to filter or search within or across collections === Browsing, bulk downloading and access to supporting data === The home page includes a list of all available collections. Basic information about the data such as the cancer type, cancer location, modalities, and number of subjects are also provided. Clicking on a collection name presents a page which describes the data including its original research purpose, how the data were generated, and how it might be useful to other TCIA users. For example, doi:10.7937/K9/TCIA.2015.L4FRET6Z describes the NSCLC-Radiomics-Genomics Collection. In the lower section of the page there are links to search or download the images and any available supporting data in the Data Access tab. Additional tabs provide information about data versions and how to cite the data if used in publications. Many collections contain additional data types such as genomics, patient demographics, treatment details, and expert analyses of the images. This data is usually only found by browsing the collection pages as opposed to searching in NBIA or using the API. === Filtering or searching with NBIA === On each Collection page and also in the main menu of the site there are links to "Search TCIA". This will load the NBIA application which allows simple, advanced and free text searches. Search results follow the conventional DICOM hierarchy of patient -> study -> series. TCIA provides comprehensive documentation on the various features of the NBIA software. === RESTful API === A number of search and download commands are also available through the API. New iterations on the API are released as new versions, so that existing applications developed against older versions of the API continue to function. == Research activities == A list of known publications based on TCIA data is maintained as a convenience to researchers who might want to investigate how it has been used previously. In addition to peer-reviewed publications there are also several major research initiatives described in the Research Activities section of the site. === The CIP TCGA Radiology Initiative for Radiogenomics Research === A large number of collections contain subjects which were analyzed as part of the NIH/NHGRI database known as The Cancer Genome Atlas (TCGA). This offers researchers the ability to correlate clinical images using shared unique identifiers each study that has in TCGA extensive genomic analysis, digital pathology slides and bulk download of individual demographic data and clinical data. A multi-institutional network of investigators volunteering their time is using the data to develop methods to determine prognosis or predict the response to therapy. TCGA collections are designated by nomenclature shared by the TCGA Data Portal (e.g.: TCGA-BRCA, TCGA-GBM, etc). They are subject to a special publication policy which is unique from the other public data on TCIA. === Challenge competitions === TCIA also provides specific data sets used for "Challenge" competitions such as international digital image-focused professional societies like MICCAI, SPIE, or ISBI. A directory of previous and upcoming challenges is maintained on the site. === Digital object identifiers === To facilitate data sharing, many publications encourage authors to include data citations to the data that the authors used in creating the results described in their scholarly papers. In addition, new journals are now available for describing data collections outright (e.g., Nature Scientific Data). TCIA assigns digital object identifiers (DOIs) to all collections when they are submitted, and also has the ability to create persistent identifiers linked to subsets of data held within TCIA that authors may use for data citations in their scholarly papers.
Hierarchical navigable small world
Hierarchical navigable small world (HNSW) is an algorithm for approximate nearest neighbor search. It is used to find items that are similar to a query item in a large collection, without comparing the query with every item one by one. The algorithm is commonly used for searching vector data. In these systems, an item such as a document, image, song, or user profile is represented by a list of numbers called a vector. Items with similar vectors are treated as similar according to the model that produced the vectors. HNSW provides a way to search these vectors quickly, especially in large datasets. HNSW stores vectors in a graph. Each vector is a node, and links connect it to some nearby vectors. The graph has several layers: upper layers contain fewer nodes and act like a rough map, while the bottom layer contains all nodes and gives a more detailed view. A search starts in an upper layer, follows links toward nodes that are closer to the query, and then repeats the process in lower layers until it finds a set of likely nearest neighbors. == Background == The nearest neighbor search problem asks which items in a dataset are closest to a query item. A direct search can compare the query with every item in the dataset, but this becomes slow when the dataset is large. Exact search methods based on spatial trees, such as the k-d tree and R-tree, can also become less effective for high-dimensional data, a problem often associated with the curse of dimensionality. Approximate nearest neighbor methods trade some exactness for speed or lower resource use. Instead of always guaranteeing the exact closest item, they try to return close items quickly. Other approximate methods include locality-sensitive hashing and product quantization. HNSW builds on research into small-world networks and navigable graphs. In a small-world graph, most nodes can be reached from other nodes through a short chain of links. In a navigable graph, a search procedure can use local information to move toward a target. Jon Kleinberg's work on navigation in small-world networks is an important example of this research area. Later work studied ways to add links that make graphs easier to navigate greedily. The HNSW algorithm extends earlier navigable small world methods for similarity search by adding a hierarchy of graph layers. This hierarchy helps the algorithm find a good region of the graph before doing a more detailed search in the bottom layer. == Algorithm == HNSW is based on a proximity graph. In this graph, nearby vectors are connected by edges. The algorithm uses these edges to move through the dataset, rather than scanning every vector. The graph is hierarchical. Every vector appears in the bottom layer. Some vectors are also placed in higher layers, with fewer vectors appearing as the layers go upward. The upper layers allow long-range movement across the dataset, while the lower layers allow a more detailed search near promising candidates. A typical search proceeds as follows: The search begins from an entry point in the highest layer. At each step, the algorithm looks at neighboring nodes and moves to a neighbor that is closer to the query. When it cannot find a closer neighbor in that layer, it moves down to the next layer. In the bottom layer, it explores a wider set of candidate nodes and returns the nearest candidates found. This search strategy is often described as greedy navigation. The algorithm repeatedly chooses locally better nodes, using the graph structure to approach the query point. == Construction and parameters == The HNSW graph is built incrementally. When a new vector is inserted, the algorithm assigns it a maximum layer, searches for nearby existing nodes, and connects the new node to selected neighbors in each layer where it appears. Implementations usually expose parameters that control the trade-off between speed, accuracy, memory use, and construction time. A higher number of graph connections can improve recall but requires more memory. A larger search candidate list can improve accuracy but makes queries slower. A larger construction candidate list can improve the quality of the graph but makes index building slower. Because HNSW is approximate, its results are not always identical to a full exact search. Its practical performance depends on the dataset, distance measure, implementation, and parameter settings. Benchmarking studies have found HNSW-based libraries to be strong performers among approximate nearest neighbor methods, although worst-case performance can differ from performance on common benchmark datasets. == Use in vector search systems == HNSW is used as an index in systems that store and search high-dimensional vectors. These systems include vector databases, search engines, and database extensions. Typical uses include semantic search, recommender systems, image similarity search, and retrieval-augmented generation. Several software projects implement or support HNSW. Libraries include hnswlib, which is associated with the original HNSW authors, and FAISS. Database and search systems that document HNSW support include Apache Lucene, Chroma, ClickHouse, DuckDB, MariaDB, Milvus, pgvector, Qdrant, and Redis.
KXEN Inc.
KXEN was an American software company which existed from 1998 to 2013 when it was acquired by SAP AG. == History == KXEN was founded in June 1998 by Roger Haddad and Michel Bera. It was based in San Francisco, California with offices in Paris and London. On September 10, 2013, SAP AG announced plans to acquire KXEN. On October 1, 2013, a letter to KXEN customers announced the acquisition closed. KXEN primarily marketed predictive analytics software. == Predictive analytics == InfiniteInsight is a predictive modeling suite developed by KXEN that assists analytic professionals, and business executives to extract information from data. Among other functions, InfiniteInsight is used for variable importance, classification, regression, segmentation, time series, product recommendation, as described and expressed by the Java Data Mining interface, and for social network analysis. InfiniteInsight allows prediction of a behavior or a value, the forecast of a time series or the understanding of a group of individuals with similar behavior. Advanced functions include behavioral modeling, exporting the model code into different target environments or building predictive models on top of SAS or SPSS data files. Competitors are SAS Enterprise Miner, IBM SPSS Modeler, and Statistica. Open source predictive tools like the R package or Weka are also competitors, since they provide similar features free of charge.
Quickprop
Quickprop is an iterative method for determining the minimum of the loss function of an artificial neural network, following an algorithm inspired by the Newton's method. Sometimes, the algorithm is classified to the group of the second order learning methods. It follows a quadratic approximation of the previous gradient step and the current gradient, which is expected to be close to the minimum of the loss function, under the assumption that the loss function is locally approximately square, trying to describe it by means of an upwardly open parabola. The minimum is sought in the vertex of the parabola. The procedure requires only local information of the artificial neuron to which it is applied. The k {\displaystyle k} -th approximation step is given by: Δ ( k ) w i j = Δ ( k − 1 ) w i j ( ∇ i j E ( k ) ∇ i j E ( k − 1 ) − ∇ i j E ( k ) ) {\displaystyle \Delta ^{(k)}\,w_{ij}=\Delta ^{(k-1)}\,w_{ij}\left({\frac {\nabla _{ij}\,E^{(k)}}{\nabla _{ij}\,E^{(k-1)}-\nabla _{ij}\,E^{(k)}}}\right)} Where w i j {\displaystyle w_{ij}} is the weight of input i {\displaystyle i} of neuron j {\displaystyle j} , and E {\displaystyle E} is the loss function. The Quickprop algorithm is an implementation of the error backpropagation algorithm, but the network can behave chaotically during the learning phase due to large step sizes.
LIBSVM
LIBSVM and LIBLINEAR are two popular open source machine learning libraries, both developed at the National Taiwan University and both written in C++ though with a C API. LIBSVM implements the sequential minimal optimization (SMO) algorithm for kernelized support vector machines (SVMs), supporting classification and regression. LIBLINEAR implements linear SVMs and logistic regression models trained using a coordinate descent algorithm. The SVM learning code from both libraries is often reused in other open source machine learning toolkits, including GATE, KNIME, Orange and scikit-learn. Bindings and ports exist for programming languages such as Java, MATLAB, R, Julia, and Python. It is available in e1071 library in R and scikit-learn in Python. Both libraries are free software released under the 3-clause BSD license.
Question answering
Question answering (QA) is a computer science discipline within the fields of information retrieval and natural language processing (NLP) that is concerned with building systems that automatically answer questions that are posed by humans in a natural language. A question-answering implementation, usually a computer program, may construct its answers by querying a structured database of knowledge or information, usually a knowledge base. More commonly, question-answering systems can pull answers from an unstructured collection of natural language documents. Some examples of natural language document collections used for question answering systems include reference texts, compiled newswire reports, Wikipedia pages and other World Wide Web pages. == History == Two early question answering systems were BASEBALL and LUNAR. BASEBALL answered questions about Major League Baseball over a period of one year. LUNAR answered questions about the geological analysis of rocks returned by the Apollo Moon missions. Both question answering systems were very effective in their chosen domains. LUNAR was demonstrated at a lunar science convention in 1971 and it was able to answer 90% of the questions in its domain that were posed by people untrained on the system. Further restricted-domain question answering systems were developed in the following years. The common feature of all these systems is that they had a core database or knowledge system that was hand-written by experts of the chosen domain. The language abilities of BASEBALL and LUNAR used techniques similar to ELIZA and DOCTOR, the first chatterbot programs. SHRDLU was a successful question-answering program developed by Terry Winograd in the late 1960s and early 1970s. It simulated the operation of a robot in a toy world (the "blocks world"), and it offered the possibility of asking the robot questions about the state of the world. The strength of this system was the choice of a very specific domain and a very simple world with rules of physics that were easy to encode in a computer program. In the 1970s, knowledge bases were developed that targeted narrower domains of knowledge. The question answering systems developed to interface with these expert systems produced more repeatable and valid responses to questions within an area of knowledge. These expert systems closely resembled modern question answering systems except in their internal architecture. Expert systems rely heavily on expert-constructed and organized knowledge bases, whereas many modern question answering systems rely on statistical processing of a large, unstructured, natural language text corpus. The 1970s and 1980s saw the development of comprehensive theories in computational linguistics, which led to the development of ambitious projects in text comprehension and question answering. One example was the Unix Consultant (UC), developed by Robert Wilensky at U.C. Berkeley in the late 1980s. The system answered questions pertaining to the Unix operating system. It had a comprehensive, hand-crafted knowledge base of its domain, and it aimed at phrasing the answer to accommodate various types of users. Another project was LILOG, a text-understanding system that operated on the domain of tourism information in a German city. The systems developed in the UC and LILOG projects never went past the stage of simple demonstrations, but they helped the development of theories on computational linguistics and reasoning. Specialized natural-language question answering systems have been developed, such as EAGLi for health and life scientists. Question answering systems have been extended in recent years to encompass additional domains of knowledge For example, systems have been developed to automatically answer temporal and geospatial questions, questions of definition and terminology, biographical questions, multilingual questions, and questions about the content of audio, images, and video. Current question answering research topics include: interactivity—clarification of questions or answers answer reuse or caching semantic parsing answer presentation knowledge representation and semantic entailment social media analysis with question answering systems sentiment analysis utilization of thematic roles Image captioning for visual question answering Embodied question answering In 2011, Watson, a question answering computer system developed by IBM, competed in two exhibition matches of Jeopardy! against Brad Rutter and Ken Jennings, winning by a significant margin. Facebook Research made their DrQA system available under an open source license. This system uses Wikipedia as knowledge source. The open source framework Haystack by deepset combines open-domain question answering with generative question answering and supports the domain adaptation of the underlying language models for industry use cases. Large Language Models (LLMs)[36] like GPT-4[37], Gemini[38] are examples of successful QA systems that are enabling more sophisticated understanding and generation of text. When coupled with Multimodal[39] QA Systems, which can process and understand information from various modalities like text, images, and audio, LLMs significantly improve the capabilities of QA systems. == Types == Question-answering research attempts to develop ways of answering a wide range of question types, including fact, list, definition, how, why, hypothetical, semantically constrained, and cross-lingual questions. Answering questions related to an article in order to evaluate reading comprehension is one of the simpler form of question answering, since a given article is relatively short compared to the domains of other types of question-answering problems. An example of such a question is "What did Albert Einstein win the Nobel Prize for?" after an article about this subject is given to the system. Closed-book question answering is when a system has memorized some facts during training and can answer questions without explicitly being given a context. This is similar to humans taking closed-book exams. Closed-domain question answering deals with questions under a specific domain (for example, medicine or automotive maintenance) and can exploit domain-specific knowledge frequently formalized in ontologies. Alternatively, "closed-domain" might refer to a situation where only a limited type of questions are accepted, such as questions asking for descriptive rather than procedural information. Question answering systems in the context of machine reading applications have also been constructed in the medical domain, for instance related to Alzheimer's disease. Open-domain question answering deals with questions about nearly anything and can only rely on general ontologies and world knowledge. Systems designed for open-domain question answering usually have much more data available from which to extract the answer. An example of an open-domain question is "What did Albert Einstein win the Nobel Prize for?" while no article about this subject is given to the system. Another way to categorize question-answering systems is by the technical approach used. There are a number of different types of QA systems, including: rule-based systems, statistical systems, and hybrid systems. Rule-based systems use a set of rules to determine the correct answer to a question. Statistical systems use statistical methods to find the most likely answer to a question. Hybrid systems use a combination of rule-based and statistical methods. == Architecture == As of 2001, question-answering systems typically included a question classifier module that determined the type of question and the type of answer. Different types of question-answering systems employ different architectures. For example, modern open-domain question answering systems may use a retriever-reader architecture. The retriever is aimed at retrieving relevant documents related to a given question, while the reader is used to infer the answer from the retrieved documents. Systems such as GPT-3, T5, and BART use an end-to-end architecture in which a transformer-based architecture stores large-scale textual data in the underlying parameters. Such models can answer questions without accessing any external knowledge sources. == Methods == Question answering is dependent on a good search corpus; without documents containing the answer, there is little any question answering system can do. Larger collections generally mean better question answering performance, unless the question domain is orthogonal to the collection. Data redundancy in massive collections, such as the web, means that nuggets of information are likely to be phrased in many different ways in differing contexts and documents, leading to two benefits: If the right information appears in many forms, the question answering system needs to perform fewer complex NLP techniques to understand the text. Correct answers can be filtered from false positives because the syst
Operational taxonomic unit
An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. == Molecular OTU by clustering of marker gene sequences == In the approach represented by DNA barcoding, a particular locus is chosen to be used as the marker gene for classification. This locus should be universally present in the scope selected, variable enough to be different among close-related species, and be flanked by conservative sequences that allow for easy amplification and detection. There are databases containing sequences for such marker genes from many different species, allowing for comparison. (Sometimes only using one locus does not provide sufficient resolution, so multiple marker genes are used. This is the case for plants, where rbcL+matK is common.) Sequences obtained this way can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold set by the researcher. The exact threshold depends on the taxa in question and the mutational rates of the selected locus in the taxon. 97–99% are commonly used, but "it is now recognized to be somewhat arbitrary as sequence variation within and among species varies across taxa". 100% similarity (fully identical) is also common, also known as single variants. It remains debatable how well this commonly used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, research by Schmidt et al. (2014) demonstrated that 16S-derived microbial OTUs were generally ecologically consistent across habitats and several clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. === OTU clustering approaches === There are three main approaches to clustering OTUs: De novo, for which the clustering is based on similarities between sequencing reads. Closed-reference, for which the clustering is performed against a reference database of sequences. Open-reference, where clustering is first performed against a reference database of sequences, then any remaining sequences that could not be mapped to the reference are clustered de novo. Using a reference provides taxonomic context for the OTUs found. Alternatively, taxonomic context can be found after the construction of clusters by comparing representative sequences from clusters against a reference database. There are also specialized classifiers for this purpose which are much faster than naive comparison using BLAST. === OTU clustering algorithms === Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP == Molecular OTU by other methods == In addition to similarity-based grouping, marker gene sequences can be sorted into OTUs using molecular phylogeny, k-mer composition, or hybrid methods combining these methods with similarity. There are also Bayesian tree-less methods and machine learning approaches. Using phylogeny often involves manually assigning terminal clades or single nodes to an OTU, so this is usually only done for refinement. Genome skimming can be used to obtain high-copy DNA without the need to choose marker genes or to design PCR primers for the chosen genes. It can provide fairly good coverage of organelle DNA and repetitive elements such as ribosomal DNA, both of which can be used like marker genes in OTU analysis. Whole-genome sequencing is more expensive and involves the production and processing of more data. By considering the entire genome, many (sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is also possible to use entire genomes for OTU assignment. For example, genomes from different bacterial species almost always have an average nucleotide identity lower than 95%, a fact that can be used to define new OTUs (and likely new species).