The Shapiro—Senapathy algorithm (S&S) is a computational method for identifying splice sites in eukaryotic genes. The algorithm employs a Position Weight Matrix (PWM) scoring formula to predict donor and acceptor splice sites in any given gene. This methodology has been used to discover splice sites and disease-causing splice site mutations in the human genome, and has become a standard tool in clinical genomics. The S&S algorithm has been cited in thousands of clinical studies, according to Google Scholar. It has also formed the basis of widely used software, including Human Splicing Finder, SROOGLE, and Alamut, which identify splice sites and splice site mutations that cause disease. The algorithm has uncovered splicing mutations in diseases ranging from cancers to inherited disorders, and predicted the deleterious effects of these mutations including exon skipping, intron retention, and cryptic splice site activation. == The algorithm == A splice site defines the boundary between a coding exon and a non-coding intron in eukaryotic genes. The S&S algorithm employs a sliding window, corresponding to the length of the splice site motif, to scan a gene sequence and detect potential splice sites. For each sliding window, the algorithm calculates a score by comparing the nucleotide sequence to a Position Weight Matrix (PWM) derived from known splice sites. This formula generates a percentile score, indicating the likelihood that a given sequence functions as a donor or acceptor splice site. The majority of disease-causing mutations in the human genome are located in splice sites. Clinical genomics studies analyze the splice site scores generated by the S&S algorithm to predict the consequences of splice site mutations including exon skipping and intron retention. The algorithm's sensitivity to single-nucleotide changes allows it to determine mutations that may impact RNA splicing and contribute to disease. In addition to identifying real splice sites, the S&S algorithm has been used to discover cryptic splice sites — alternative splice sites activated by mutations — which may disrupt normal splicing. The algorithm detects mutations that lead to the activation of cryptic splice sites, which may be located proximal to real splice sites or deep within non-coding introns. It has thus been used to determine the causes of numerous diseases that are due to cryptic splicing. == Cancer gene discovery using S&S == The S&S algorithm has been used to identify splice-site mutations in genes associated with several cancers. For example, genes causing commonly occurring cancers including breast cancer, ovarian cancer, colorectal cancer, leukemia, head and neck cancers, prostate cancer, retinoblastoma, squamous cell carcinoma, gastrointestinal cancer, melanoma, liver cancer, Lynch syndrome, skin cancer, and neurofibromatosis have been found. In addition, splicing mutations in genes causing less commonly known cancers including gastric cancer, gangliogliomas, Li-Fraumeni syndrome, Loeys–Dietz syndrome, Osteochondromas (bone tumor), Nevoid basal cell carcinoma syndrome, and Pheochromocytomas have been identified. Specific mutations in different splice sites in various genes causing breast cancer (e.g., BRCA1, PALB2), ovarian cancer (e.g., SLC9A3R1, COL7A1, HSD17B7), colon cancer (e.g., APC, MLH1, DPYD), colorectal cancer (e.g., COL3A1, APC, HLA-A), skin cancer (e.g., COL17A1, XPA, POLH), and Fanconi anemia (e.g., FANC, FANA) have been uncovered. The mutations in the donor and acceptor splice sites in different genes causing a variety of cancers that have been identified by S&S are shown in Table 1. == Discovery of genes causing inherited disorders using S&S == Specific mutations in different splice sites in various genes that cause inherited disorders, including, for example, Type 1 diabetes (e.g., PTPN22, TCF1 (HCF-1A)), hypertension (e.g., LDL, LDLR, LPL), Marfan syndrome (e.g., FBN1, TGFBR2, FBN2), cardiac diseases (e.g., COL1A2, MYBPC3, ACTC1), eye disorders (e.g., EVC, VSX1) have been uncovered. A few example mutations in the donor and acceptor splice sites in different genes causing a variety of inherited disorders identified using S&S are shown in Table 2. == Genes causing immune system disorders == More than 100 immune system disorders affect humans, including inflammatory bowel diseases, multiple sclerosis, systemic lupus erythematosus, bloom syndrome, familial cold autoinflammatory syndrome, and dyskeratosis congenita. The Shapiro–Senapathy algorithm has been used to discover genes and mutations involved in many immune disorder diseases, including Ataxia telangiectasia, B-cell defects, epidermolysis bullosa, and X-linked agammaglobulinemia. Xeroderma pigmentosum, an autosomal recessive disorder is caused by faulty proteins formed due to new preferred splice donor site identified using S&S algorithm and resulted in defective nucleotide excision repair. Type I Bartter syndrome (BS) is caused by mutations in the gene SLC12A1. S&S algorithm helped in disclosing the presence of two novel heterozygous mutations c.724 + 4A > G in intron 5 and c.2095delG in intron 16 leading to complete exon 5 skipping. Mutations in the MYH gene, which is responsible for removing the oxidatively damaged DNA lesion are cancer-susceptible in the individuals. The IVS1+5C plays a causative role in the activation of a cryptic splice donor site and the alternative splicing in intron 1, S&S algorithm shows, guanine (G) at the position of IVS+5 is well conserved (at the frequency of 84%) among primates. This also supported the fact that the G/C SNP in the conserved splice junction of the MYH gene causes the alternative splicing of intron 1 of the β type transcript. Splice site scores were calculated according to S&S to find EBV infection in X-linked lymphoproliferative disease. Identification of Familial tumoral calcinosis (FTC) is an autosomal recessive disorder characterized by ectopic calcifications and elevated serum phosphate levels and it is because of aberrant splicing. == Application of S&S in hospitals for clinical practice and research == The Shapiro–Senapathy (S&S) algorithm has played a significant role in advancing the diagnosis and treatment of human diseases through its application in modern clinical genomics. With the widespread adoption of next-generation sequencing (NGS) technologies, the S&S algorithm is now routinely integrated into clinical practice by geneticists and diagnostic laboratories. It is implemented in various computational tools such as Human Splicing Finder (HSF), Splice Site Finder (SSF), and Alamut Visual, which assist in interpreting the functional impact of genetic variants on RNA splicing. The algorithm is particularly useful in identifying pathogenic splice site mutations in cases where the clinical presentation is unclear or where conventional diagnostic methods have failed to identify a causative gene. Its utility has been demonstrated across diverse patient cohorts, including individuals from different ethnic backgrounds with various cancers and inherited genetic disorders. The following are selected examples illustrating its application in clinical research. === Cancers === === Inherited disorders === == S&S - Algorithm for identifying splice sites, exons and split genes == The Shapiro–Senapathy algorithm (SSA) was developed to identify splice sites in uncharacterized genomic sequences, with early applications in the Human Genome Project. The method introduced a Position Weight Matrix (PWM)-based approach to analyze splicing sequences across eukaryotic organisms, marking the first computational framework to systematically define splice sites using probabilistic scoring. Key innovations of the algorithm included: Exon Detection – Exons were defined as sequences bounded by acceptor and donor splice sites with S&S scores above a threshold, requiring an open reading frame (ORF) for validation. Gene Prediction – The method enabled the identification of complete genes by assembling predicted exons, forming a basis for later gene-finding tools. Mutation Analysis – The algorithm distinguishes deleterious splice-site mutations (which disrupt protein function by lowering S&S scores) from neutral variations. This capability allowed researchers to study disease-linked cryptic splice sites in humans, animals, and plants. SSA's PWM-based framework influenced subsequent computational methods, including machine learning and neural network approaches, for splice-site prediction and alternative splicing research. It remains a foundational tool in genomics and disease studies. == Discovering the mechanisms of aberrant splicing in diseases == The Shapiro–Senapathy algorithm has been used to determine the various aberrant splicing mechanisms in genes due to deleterious mutations in the splice sites, which cause numerous diseases. Deleterious splice site mutations impair the normal splicing of the gene transcripts, and thereby make the encoded protei
Haskins Laboratories
Haskins Laboratories, Inc. is an independent research laboratory, founded in 1935 and located in New Haven, Connecticut since 1970. Many current Haskins researchers are affiliated with Yale University's Child Study Center and/or the University of Connecticut. Haskins is a multidisciplinary and international community of researchers who conduct basic research on spoken and written language and global literacy. A guiding perspective of their research has been to view speech and language as emerging from biological processes, including those of adaptation, response to stimuli, and conspecific interaction. Haskins Laboratories has a long history of technological and theoretical innovation, from creating systems of rules for speech synthesis and development of an early working prototype of a reading machine for the blind to developing the landmark concept of phonemic awareness as the critical preparation for learning to read an alphabetic writing system. == Research tools and facilities == Haskins Laboratories is equipped, in-house, with a comprehensive suite of tools and capabilities to advance its mission of research into language and literacy. As of 2014, these included: Anechoic chamber Electroencephalography BioSemi 264 electrode, 24 bit Active Two System EGI 128 electrode, Geodesic EEG System 300 Electromagnetic articulography (EMMA) Carstens AG501 NDI WAVE Eye tracking: HL is equipped with 3 SR Research eye-trackers. 2 Model Eyelink 1000 systems. 1 Model Eyelink 1000plus system. Magnetic resonance imaging: Haskins has access to MRI scanners through agreements with the University of Connecticut and the Yale School of Medicine. On-site, HL has a Linux computer cluster dedicated to analysis of MRI data. Motion capture: HL is equipped with a Vicon motion capture system with one Basler high-speed digital camera, six Vicon MX T-20 cameras and a Vicon MX Giganet for synching camera data and connecting cameras to the data capture computer. Near infrared spectroscopy: HL has a TechEn CW6 8x8 system (four emitters; eight detectors). Ultrasound sonogram == History == Many researchers have contributed to scientific breakthroughs at Haskins Laboratories since its founding. All of them are indebted to the pioneering work and leadership of Caryl Parker Haskins, Franklin S. Cooper, Alvin Liberman, Seymour Hutner and Luigi Provasoli. The history presented here focuses on the research program of the division of Haskins Laboratories that, since the 1940s, has been most well known for its work in the areas of speech, language, and reading. === 1930s === Caryl Haskins and Franklin S. Cooper established Haskins Laboratories in 1935. It was originally affiliated with Harvard University, MIT, and Union College in Schenectady, NY. Caryl Haskins conducted research in microbiology, radiation physics, and other fields in Cambridge, MA and Schenectady. In 1939 Haskins Laboratories moved its center to New York City. Seymour Hutner joined the staff to set up a research program in microbiology, genetics, and nutrition. The descendant of the division led by Hutner program eventually became a department of Pace University in New York. The two identically named organizations are no longer formally affiliated. === 1940s === The U. S. Office of Scientific Research and Development, under Vannevar Bush asked Haskins Laboratories to evaluate and develop technologies for assisting blinded World War II veterans. Experimental psychologist Alvin Liberman joined Haskins Laboratories to assist in developing a "sound alphabet" to represent the letters in a text for use in a reading machine for the blind. Luigi Provasoli joined Haskins Laboratories to set up a research program in marine biology. The program in marine biology moved to Yale University in 1970 and disbanded with Provasoli's retirement in 1978. === 1950s === Franklin S. Cooper invented the pattern playback, a machine that converts pictures of the acoustic patterns of speech back into sound. With this device, Alvin Liberman, Cooper, and Pierre Delattre (and later joined by Katherine Safford Harris, Leigh Lisker, Arthur Abramson, and others), discovered the acoustic cues for the perception of phonetic segments (consonants and vowels). Liberman and colleagues proposed a motor theory of speech perception to resolve the acoustic complexity: they hypothesized that we perceive speech by tapping into a biological specialization, a speech module, that contains knowledge of the acoustic consequences of articulation. Liberman, aided by Frances Ingemann and others, organized the results of the work on speech cues into a groundbreaking set of rules for speech synthesis by the Pattern Playback. === 1960s === Franklin S. Cooper and Katherine Safford Harris, working with Peter MacNeilage, were the first researchers in the U.S. to use electromyographic techniques, pioneered at the University of Tokyo, to study the neuromuscular organization of speech. Leigh Lisker and Arthur Abramson looked for simplification at the level of articulatory action in the voicing of certain contrasting consonants. They showed that many acoustic properties of voicing contrasts arise from variations in voice onset time, the relative phasing of the onset of vocal cord vibration and the end of a consonant. Their work has been widely replicated and elaborated, here and abroad, over the following decades. Donald Shankweiler and Michael Studdert-Kennedy used a dichotic listening technique (presenting different nonsense syllables simultaneously to opposite ears) to demonstrate the dissociation of phonetic (speech) and auditory (nonspeech) perception by finding that phonetic structure devoid of meaning is an integral part of language, typically processed in the left cerebral hemisphere. Liberman, Cooper, Shankweiler, and Studdert-Kennedy summarized and interpreted fifteen years of research in "Perception of the Speech Code", still among the most cited papers in the speech literature. It set the agenda for many years of research at Haskins and elsewhere by describing speech as a code in which speakers overlap (or coarticulate) segments to form syllables. Researchers at Haskins connected their first computer to a speech synthesizer designed by Haskins Laboratories' engineers. Ignatius Mattingly, with British collaborators, John N. Holmes and J.N. Shearme, adapted the Pattern playback rules to write the first computer program for synthesizing continuous speech from a phonetically spelled input. A further step toward a reading machine for the blind combined Mattingly's program with an automatic look-up procedure for converting alphabetic text into strings of phonetic symbols. === 1970s === In 1970, Haskins Laboratories moved to New Haven, Connecticut, and entered into affiliation agreements with Yale University and the University of Connecticut; Haskins remains fully independent of both Yale and UConn, administratively and financially. The lab's original location in New Haven, at 270 Crown Street (from 1970 to 2005), was leased from Yale University. Isabelle Liberman, Donald Shankweiler, and Alvin Liberman teamed up with Ignatius Mattingly to study the relationship between speech perception and reading, a topic implicit in Haskins Laboratories' research program since its inception. They developed the concept of phonemic awareness, the knowledge that would-be readers must be aware of the phonemic structure of their language in order to be able to read. Leonard Katz related the work to contemporary cognitive theory and provided expertise in experimental design and data analysis. Under the broad rubric of the "alphabetic principle", this is the core of the lab's present program of reading pedagogy. Patrick Nye joined Haskins Laboratories to lead a team working on the reading machine for the blind. The project culminated when the addition of an optical character recognizer allowed investigators to assemble the first automatic text-to-speech reading machine. By the end of the decade this technology had advanced to the point where commercial concerns assumed the task of designing and manufacturing reading machines for the blind. In 1973, Franklin S. Cooper was selected to form a panel of six experts charged with investigating the famous 18-minute gap in the White House office tapes of President Richard Nixon related to the Watergate scandal. Building on earlier work, Philip Rubin developed the sinewave synthesis program, which was then used by Robert Remez, Rubin, and colleagues to show that listeners can perceive continuous speech without traditional speech cues from a pattern of sinewaves that track the changing resonances of the vocal tract. This paved the way for a view of speech as a dynamic pattern of trajectories through articulatory-acoustic space. Philip Rubin and colleagues developed Paul Mermelstein's anatomically simplified vocal tract model, originally worked on at Bell Laboratories, into the first articulatory synthesizer that can be controlled in a phy
Convolutional layer
In artificial neural networks, a convolutional layer is a type of network layer that applies a convolution operation to the input. Convolutional layers are some of the primary building blocks of convolutional neural networks (CNNs), a class of neural network most commonly applied to images, video, audio, and other data that have the property of uniform translational symmetry. The convolution operation in a convolutional layer involves sliding a small window (called a kernel or filter) across the input data and computing the dot product between the values in the kernel and the input at each position. This process creates a feature map that represents detected features in the input. == Concepts == === Kernel === Kernels, also known as filters, are small matrices of weights that are learned during the training process. Each kernel is responsible for detecting a specific feature in the input data. The size of the kernel is a hyperparameter that affects the network's behavior. === Convolution === For a 2D input x {\displaystyle x} and a 2D kernel w {\displaystyle w} , the 2D convolution operation can be expressed as: y [ i , j ] = ∑ m = 0 k h − 1 ∑ n = 0 k w − 1 x [ i + m , j + n ] ⋅ w [ m , n ] {\displaystyle y[i,j]=\sum _{m=0}^{k_{h}-1}\sum _{n=0}^{k_{w}-1}x[i+m,j+n]\cdot w[m,n]} where k h {\displaystyle k_{h}} and k w {\displaystyle k_{w}} are the height and width of the kernel, respectively. This generalizes immediately to nD convolutions. Commonly used convolutions are 1D (for audio and text), 2D (for images), and 3D (for spatial objects, and videos). === Stride === Stride determines how the kernel moves across the input data. A stride of 1 means the kernel shifts by one pixel at a time, while a larger stride (e.g., 2 or 3) results in less overlap between convolutions and produces smaller output feature maps. === Padding === Padding involves adding extra pixels around the edges of the input data. It serves two main purposes: Preserving spatial dimensions: Without padding, each convolution reduces the size of the feature map. Handling border pixels: Padding ensures that border pixels are given equal importance in the convolution process. Common padding strategies include: No padding/valid padding. This strategy typically causes the output to shrink. Same padding: Any method that ensures the output size same as input size is a same padding strategy. Full padding: Any method that ensures each input entry is convolved over for the same number of times is a full padding strategy. Common padding algorithms include: Zero padding: Add zero entries to the borders of input. Mirror/reflect/symmetric padding: Reflect the input array on the border. Circular padding: Cycle the input array back to the opposite border, like a torus. The exact numbers used in convolutions is complicated, for which we refer to (Dumoulin and Visin, 2018) for details. == Variants == === Standard === The basic form of convolution as described above, where each kernel is applied to the entire input volume. === Depthwise separable === Depthwise separable convolution separates the standard convolution into two steps: depthwise convolution and pointwise convolution. The depthwise separable convolution decomposes a single standard convolution into two convolutions: a depthwise convolution that filters each input channel independently and a pointwise convolution ( 1 × 1 {\displaystyle 1\times 1} convolution) that combines the outputs of the depthwise convolution. This factorization significantly reduces computational cost. It was first developed by Laurent Sifre during an internship at Google Brain in 2013 as an architectural variation on AlexNet to improve convergence speed and model size. === Dilated === Dilated convolution, or atrous convolution, introduces gaps between kernel elements, allowing the network to capture a larger receptive field without increasing the kernel size. === Transposed === Transposed convolution, also known as deconvolution, fractionally strided convolution, and upsampling convolution, is a convolution where the output tensor is larger than its input tensor. It's often used in encoder-decoder architectures for upsampling. It's used in image generation, semantic segmentation, and super-resolution tasks. == History == The concept of convolution in neural networks was inspired by the visual cortex in biological brains. Early work by Hubel and Wiesel in the 1960s on the cat's visual system laid the groundwork for artificial convolution networks. An early convolution neural network was developed by Kunihiko Fukushima in 1969. It had mostly hand-designed kernels inspired by convolutions in mammalian vision. In 1979 he improved it to the Neocognitron, which learns all convolutional kernels by unsupervised learning (in his terminology, "self-organized by 'learning without a teacher'"). During the 1988 to 1998 period, a series of CNN were introduced by Yann LeCun et al., ending with LeNet-5 in 1998. It was an early influential CNN architecture for handwritten digit recognition, trained on the MNIST dataset, and was used in ATM. (Olshausen & Field, 1996) discovered that simple cells in the mammalian primary visual cortex implement localized, oriented, bandpass receptive fields, which could be recreated by fitting sparse linear codes for natural scenes. This was later found to also occur in the lowest-level kernels of trained CNNs. The field saw a resurgence in the 2010s with the development of deeper architectures and the availability of large datasets and powerful GPUs. AlexNet, developed by Alex Krizhevsky et al. in 2012, was a catalytic event in modern deep learning. In that year’s ImageNet competition, the AlexNet model achieved a 16% top-five error rate, significantly outperforming the next best entry, which had a 26% error rate. The network used eight trainable layers, approximately 650,000 neurons, and around 60 million parameters, highlighting the impact of deeper architectures and GPU acceleration on image recognition performance. From the 2013 ImageNet competition, most entries adopted deep convolutional neural networks, building on the success of AlexNet. Over the following years, performance steadily improved, with the top-five error rate falling from 16% in 2012 and 12% in 2013 to below 3% by 2017, as networks grew increasingly deep.
Pill reminder
A pill reminder is any device that reminds users to take medications. Traditional pill reminders are pill containers with electric timers attached, which can be preset for certain times of the day to set off an alarm. More sophisticated pill reminders can also detect when they have been opened, and therefore when the user is away during the time they were supposed to take their medication, they will be reminded of it when they return. This reminder can be in the form of a light, which also helps for deaf or hearing-impaired users. == Mobile app == A newer type of pill reminder is a mobile app that reminds the owner to take the medication. Some of these applications might effectively support adherence to taking medications.
Inverse consistency
In image registration, inverse consistency measures the consistency of mappings between images produced by a registration algorithm. The inverse consistency error, introduced by Christiansen and Johnson in 2001, quantifies the distance between the composition of the mappings from each image to the other, produced by the registration procedure, and the identity function, and is used as a regularisation constraint in the loss function of many registration algorithms to enforce consistent mappings. Inverse consistency is necessary for good image registration but it is not sufficient, since a mapping can be perfectly consistent but not register the images at all. == Definition == Image registration is the process of establishing a common coordinate system between two images, and given two images I 1 : Ω 1 → R I 2 : Ω 2 → R {\displaystyle {\begin{aligned}I_{1}:\Omega _{1}\to \mathbb {R} \\I_{2}:\Omega _{2}\to \mathbb {R} \end{aligned}}} registering a source image I 1 {\displaystyle I_{1}} to a target image I 2 {\displaystyle I_{2}} consists of determining a transformation f 1 : Ω 2 → Ω 1 {\displaystyle f_{1}:\Omega _{2}\to \Omega _{1}} that maps points from the target space to the source space. An ideal registration algorithm should not be sensitive to which image in the pair is used as source or target, and the registration operator should be antisymmetric such that the mappings f 1 : Ω 2 → Ω 1 f 2 : Ω 1 → Ω 2 {\displaystyle {\begin{aligned}f_{1}:\Omega _{2}\to \Omega _{1}\\f_{2}:\Omega _{1}\to \Omega _{2}\end{aligned}}} produced when registering I 1 {\displaystyle I_{1}} to I 2 {\displaystyle I_{2}} and I 2 {\displaystyle I_{2}} to I 1 {\displaystyle I_{1}} respectively should be the inverse of each other, i.e. f 2 = f 1 − 1 {\displaystyle f_{2}=f_{1}^{-1}} and f 1 = f 2 − 1 {\displaystyle f_{1}=f_{2}^{-1}} or, equivalently, f 2 ∘ f 1 = id Ω 2 {\displaystyle f_{2}\circ f_{1}=\operatorname {id} _{\Omega _{2}}} and f 1 ∘ f 2 = id Ω 1 {\displaystyle f_{1}\circ f_{2}=\operatorname {id} _{\Omega _{1}}} , where ∘ {\displaystyle \circ } denotes the function composition operator. Real algorithms are not perfect, and when swapping the role of source and target image in a registration problem the so obtained transformations are not the inverse of each other. Inverse consistency can be enforced by adding to the loss function of the registration a symmetric regularisation term that penalises inconsistent transformations ∫ Ω 2 ‖ f 2 ( f 1 ( x ) ) − x ‖ 2 d x + ∫ Ω 1 ‖ f 1 ( f 2 ( x ) ) − x ‖ 2 d x . {\displaystyle \int _{\Omega _{2}}\left\Vert f_{2}(f_{1}(x))-x\right\Vert ^{2}\mathrm {d} x+\int _{\Omega _{1}}\left\Vert f_{1}(f_{2}(x))-x\right\Vert ^{2}\mathrm {d} x.} Inverse consistency can be used as a quality metric to evaluate image registration results. The inverse consistency error ( I C E {\displaystyle ICE} ) measures the distance between the composition of the two transforms and the identity function, and it can be formulated in terms of both average ( I C E a {\displaystyle ICE_{a}} ) or maximum ( I C E m {\displaystyle ICE_{m}} ) over a region of interest Ω {\displaystyle \Omega } of the image: I C E a = 1 ∫ Ω d x ∫ Ω ‖ f 2 ( f 1 ( x ) ) − x ‖ d x I C E m = max x ∈ Ω ‖ f 2 ( f 1 ( x ) ) − x ‖ . {\displaystyle {\begin{aligned}ICE_{a}&={\frac {1}{\int _{\Omega }\mathrm {d} x}}\int _{\Omega }\left\Vert f_{2}(f_{1}(x))-x\right\Vert \mathrm {d} x\\ICE_{m}&=\max _{x\in \Omega }\left\Vert f_{2}(f_{1}(x))-x\right\Vert .\end{aligned}}} While inverse consistency is a necessary property of good registration algorithms, inverse consistency error alone is not a sufficient metric to evaluate the quality of image registration results, since a perfectly consistent mapping, with no other constraint, may be not even close to correctly register a pair of images.
Content Disarm and Reconstruction
Content Disarm and Reconstruction (CDR) is a computer security technology for removing potentially malicious code from files. Unlike malware analysis, CDR technology does not determine or detect malware's functionality but removes all file components that are not approved within the system's definitions and policies. It is used to prevent cyber security threats from entering a corporate network perimeter. Channels that CDR can be used to protect include email and website traffic. Advanced solutions can also provide similar protection on computer endpoints, or cloud email and file sharing services. There are three levels of CDR; 1) flattening and converting the original file to a PDF, 2) stripping active content while keeping the original file type, and 3) eliminating all file-borne risk while maintaining file type, integrity and active content. Beyond these three levels, there are also more advanced forms of CDR that is able to perform "soft conversion" and "hard conversion", based on the user's preference in balancing usability and security. == Applications == CDR works by processing all incoming files of an enterprise network, deconstructing them, and removing the elements that do not match the file type's standards or set policies. CDR technology then rebuilds the files into clean versions that can be sent on to end users as intended. Because CDR removes all potentially malicious code, it can be effective against zero-day vulnerabilities that rely on being an unknown threat that other security technologies would need to patch against to maintain protection. CDR can be used to prevent cyber threats from variety of sources: Email Data Diodes Web Browsers Endpoints File Servers FTP Cloud email or webmail programs SMB/CIFS Removable media scanning (CDR Kiosk) CDR can be applied to a variety of file formats including: Images Office documents PDF Audio/video file formats Archives HTML == Open source implementations == DocBleach ExeFilter
Legal information retrieval
Legal information retrieval is the science of information retrieval applied to legal text, including legislation, case law, and scholarly works. Accurate legal information retrieval is important to provide access to the law to laymen and legal professionals. Its importance has increased because of the vast and quickly increasing amount of legal documents available through electronic means. Legal information retrieval is a part of the growing field of legal informatics. In a legal setting, it is frequently important to retrieve all information related to a specific query. However, commonly used boolean search methods (exact matches of specified terms) on full text legal documents have been shown to have an average recall rate as low as 20 percent, meaning that only 1 in 5 relevant documents are actually retrieved. In that case, researchers believed that they had retrieved over 75% of relevant documents. This may result in failing to retrieve important or precedential cases. In some jurisdictions this may be especially problematic, as legal professionals are ethically obligated to be reasonably informed as to relevant legal documents. Legal Information Retrieval attempts to increase the effectiveness of legal searches by increasing the number of relevant documents (providing a high recall rate) and reducing the number of irrelevant documents (a high precision rate). This is a difficult task, as the legal field is prone to jargon, polysemes (words that have different meanings when used in a legal context), and constant change. Techniques used to achieve these goals generally fall into three categories: boolean retrieval, manual classification of legal text, and natural language processing of legal text. == Problems == Application of standard information retrieval techniques to legal text can be more difficult than application in other subjects. One key problem is that the law rarely has an inherent taxonomy. Instead, the law is generally filled with open-ended terms, which may change over time. This can be especially true in common law countries, where each decided case can subtly change the meaning of a certain word or phrase. Legal information systems must also be programmed to deal with law-specific words and phrases. Though this is less problematic in the context of words which exist solely in law, legal texts also frequently use polysemes, words may have different meanings when used in a legal or common-speech manner, potentially both within the same document. The legal meanings may be dependent on the area of law in which it is applied. For example, in the context of European Union legislation, the term "worker" has four different meanings: Any worker as defined in Article 3(a) of Directive 89/391/EEC who habitually uses display screen equipment as a significant part of his normal work. Any person employed by an employer, including trainees and apprentices but excluding domestic servants; Any person carrying out an occupation on board a vessel, including trainees and apprentices, but excluding port pilots and shore personnel carrying out work on board a vessel at the quayside; Any person who, in the Member State concerned, is protected as an employee under national employment law and in accordance with national practice; It also has the common meaning: A person who works at a specific occupation. Though the terms may be similar, correct information retrieval must differentiate between the intended use and irrelevant uses in order to return the correct results. Even if a system overcomes the language problems inherent in law, it must still determine the relevancy of each result. In the context of judicial decisions, this requires determining the precedential value of the case. Case decisions from senior or superior courts may be more relevant than those from lower courts, even where the lower court's decision contains more discussion of the relevant facts. The opposite may be true, however, if the senior court has only a minor discussion of the topic (for example, if it is a secondary consideration in the case). An information retrieval system must also be aware of the authority of the jurisdiction. A case from a binding authority is most likely of more value than one from a non-binding authority. Additionally, the intentions of the user may determine which cases they find valuable. For instance, where a legal professional is attempting to argue a specific interpretation of law, he might find a minor court's decision which supports his position more valuable than a senior courts position which does not. He may also value similar positions from different areas of law, different jurisdictions, or dissenting opinions. Overcoming these problems can be made more difficult because of the large number of cases available. The number of legal cases available via electronic means is constantly increasing (in 2003, US appellate courts handed down approximately 500 new cases per day), meaning that an accurate legal information retrieval system must incorporate methods of both sorting past data and managing new data. == Techniques == === Boolean searches === Boolean searches, where a user may specify terms such as use of specific words or judgments by a specific court, are the most common type of search available via legal information retrieval systems. They are widely implemented but overcome few of the problems discussed above. The recall and precision rates of these searches vary depending on the implementation and searches analyzed. One study found a basic boolean search's recall rate to be roughly 20%, and its precision rate to be roughly 79%. Another study implemented a generic search (that is, not designed for legal uses) and found a recall rate of 56% and a precision rate of 72% among legal professionals. Both numbers increased when searches were run by non-legal professionals, to a 68% recall rate and 77% precision rate. This is likely explained because of the use of complex legal terms by the legal professionals. === Manual classification === In order to overcome the limits of basic boolean searches, information systems have attempted to classify case laws and statutes into more computer friendly structures. Usually, this results in the creation of an ontology to classify the texts, based on the way a legal professional might think about them. These attempt to link texts on the basis of their type, their value, and/or their topic areas. Most major legal search providers now implement some sort of classification search, such as Westlaw's “Natural Language” or LexisNexis' Headnote searches. Additionally, both of these services allow browsing of their classifications, via Westlaw's West Key Numbers or Lexis' Headnotes. Though these two search algorithms are proprietary and secret, it is known that they employ manual classification of text (though this may be computer-assisted). These systems can help overcome the majority of problems inherent in legal information retrieval systems, in that manual classification has the greatest chances of identifying landmark cases and understanding the issues that arise in the text. In one study, ontological searching resulted in a precision rate of 82% and a recall rate of 97% among legal professionals. The legal texts included, however, were carefully controlled to just a few areas of law in a specific jurisdiction. The major drawback to this approach is the requirement of using highly skilled legal professionals and large amounts of time to classify texts. As the amount of text available continues to increase, some have stated their belief that manual classification is unsustainable. === Natural language processing === In order to reduce the reliance on legal professionals and the amount of time needed, efforts have been made to create a system to automatically classify legal text and queries. Adequate translation of both would allow accurate information retrieval without the high cost of human classification. These automatic systems generally employ Natural Language Processing (NLP) techniques that are adapted to the legal domain, and also require the creation of a legal ontology. Though multiple systems have been postulated, few have reported results. One system, “SMILE,” which attempted to automatically extract classifications from case texts, resulted in an f-measure (which is a calculation of both recall rate and precision) of under 0.3 (compared to perfect f-measure of 1.0). This is probably much lower than an acceptable rate for general usage. Despite the limited results, many theorists predict that the evolution of such systems will eventually replace manual classification systems. === Citation-Based ranking === In the mid-90s the Room 5 case law retrieval project used citation mining for summaries and ranked its search results based on citation type and count. This slightly pre-dated the PageRank algorithm at Stanford which was also a citation-based ranking. Ranking of results was based