Jpred

Jpred

Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction, that has existed since 1998 in different versions. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 134 000 jobs per month and has carried out over 2 million predictions in total for users in 179 countries. == JPred 2 == The static HTML pages of JPred 2 are still available for reference. == JPred 3 == The JPred v3 followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References). This release added new functionality and fixed many bugs. The highlights are: New, friendlier user interface Retrained and optimised version of Jnet (v2) - mean secondary structure prediction accuracy of >81% Batch submission of jobs Better error checking of input sequences/alignments Predictions now (optionally) returned via e-mail Users may provide their own query names for each submission JPred now makes a prediction even when there are no PSI-BLAST hits to the query PS/PDF output now incorporates all the predictions == JPred 4 == The current version of JPred (v4) has the following improvements and updates incorporated: Retrained on the latest UniRef90 and SCOPe/ASTRAL version of Jnet (v2.3.1) - mean secondary structure prediction accuracy of >82%. Upgraded the Web Server to the latest technologies (Bootstrap framework, JavaScript) and updating the web pages – improving the design and usability through implementing responsive technologies. Added RESTful API and mass-submission and results retrieval scripts - resulting in peak throughput above 20,000 predictions per day. Added prediction jobs monitoring tools. Upgraded the results reporting – both, on the web-site, and through the optional email summary reports: improved batch submission, added results summary preview through Jalview results visualization summary in SVG and adding full multiple sequence alignments into the reports. Improved help-pages, incorporating tool-tips, and adding one-page step-by-step tutorials. Sequence residues are categorised or assigned to one of the secondary structure elements, such as alpha-helix, beta-sheet and coiled-coil. Jnet uses two neural networks for its prediction. The first network is fed with a window of 17 residues over each amino acid in the alignment plus a conservation number. It uses a hidden layer of nine nodes and has three output nodes, one for each secondary structure element. The second network is fed with a window of 19 residues (the result of first network) plus the conservation number. It has a hidden layer with nine nodes and has three output nodes.

Reverse correlation technique

The reverse correlation technique is a data driven study method used primarily in psychological and neurophysiological research. This method earned its name from its origins in neurophysiology, where cross-correlations between white noise stimuli and sparsely occurring neuronal spikes could be computed quicker when only computing it for segments preceding the spikes. The term has since been adopted in psychological experiments that usually do not analyze the temporal dimension, but also present noise to human participants. In contrast to the original meaning, the term is here thought to reflect that the standard psychological practice of presenting stimuli of defined categories to the participants is "reversed": Instead, the participant's mental representations of categories are estimated from interactions of the presented noise and the behavioral responses. It is used to create composite pictures of individual and/or group mental representations of various items (e.g. faces, bodies, and the self) that depict characteristics of said items (e.g. trustworthiness and self-body image). This technique is helpful when evaluating the mental representations of those with and without mental illnesses. == Terms == This technique utilizes spike-triggered average to explain what areas of signal and noise in an image are valuable for the given research question. Signal is information used to produce objects of value that help explain and connect the world around us. Noise is commonly referred to as unwanted signal that obscures the information that the signal is trying to present. Most importantly for reverse correlation studies, noise is randomly varying information. To determine the areas of importance using reverse correlation, noise is applied to a base image and then evaluated by observers. A base image is any image void of noise that relates to the research question. A base image that has noise superimposed on top is the stimuli that is presented to and evaluated by participants. Each time a new set of stimuli is presented to a participant, this is known as a trial. After a participant has responded to hundreds to thousands of trials, a researcher is ready to create a classification image. A classification image (abbreviated as "CI" in some studies) is a single image that represents the average noise patterns in the images selected by participants. A classification image can also be computed for groups by averaging the individuals’ classification images. These classification images are what researchers use to interpret the data and draw conclusions. As a whole, the reverse correlation method is a process that results in a composite image (from an individual or group) that can be used to estimate and interpret mental representations. == Basic study layout == The reverse correlation method is typically executed as an in-lab computer experiment. This method follows four broad steps. Each of the following steps are described in greater detail below. After creating a research question and determining that the reverse correlation method is the most suitable technique to answer the question, a researcher must (1) design randomly varying stimuli. After the stimuli have been prepared, a researcher should (2) collect data from participants who will see and respond to approximately 300 -1,000 trials. Each trial will either consist of one or two images (side by side) derived from the same base image with noise superimposed on top. Participant responses will depend on the chosen study design; if a researcher presents only one image at a time, participants rate the image on a 4pt scale, but when two images are shown, the participant is asked to choose which best aligns with the given category (e.g. choose the image that looks the most aggressive). Once all of the data is collected, the researcher will (3) compute classification images for each participant and using those images compute group classification images. Finally, with the classification images available, the researcher will (4) evaluate the images and draw conclusions about their results. === Step 1: making stimuli === When designing the stimuli for a reverse correlation study, the two primary factors that one should consider are (1) the base image and (2) the noise that will be used. While not all bases are images per se, the majority are and for this reason the base is typically referred to as a base image. The base image should represent whatever the research question is addressing. For example, if you are interested in peoples’ mental representations of Chinese people, it would not make sense to use a base image of a Spanish or Caucasian person. Again, if you are interested in the mental representations of male vocal patterns, it would make the most sense to use a base vocal pattern that has been produced by a male. Having a base is important because it provides a kind of anchor for participants to work from. When there is no base image, the number of trials that are required increases dramatically, thus making it harder to collect data. While there are studies that have excluded a base image, (e.g. the S study), for more elaborate and nuanced research questions, it is important to have a base image that is a fair representation of what participants are being asked to categorize. Photographs of faces are generally the most popular base image. Although the reverse correlation method is capable of investigating a wide variety of research questions, the most common application of the method is for evaluating faces on a single trait. Reverse correlation studies that address evaluations of the face are sometimes referred to as being a face space reverse correlation model (FSRCM). Thankfully, there are existing databases for face images of varying demographics and emotion that work well as base images. The reverse correlation method can also be used to help researchers identify what areas of an image (e.g. the areas on the face) have diagnostic value. In order to identify these areas of value, researchers start by minimizing the space a participant can pull information from. By imposing a “mask” on an image (e.g. blur an image while leaving random areas un-blurred), this reduces the information individuals might see, and forces them to focus on certain areas. Then, if/when participants are able to correctly identify an image with a trait repeatedly, we can draw conclusions about what areas have diagnostic value. While faces and visual stimuli are the most popular, this is not the only stimuli that can be used in a reverse correlation study. This method was originally designed for auditory stimuli which allows researchers to investigate how perceivers interpret auditory information and create trait based attributions to different sound patterns. For example, by segmenting a vocal recording of a single word (total sound time 426 ms) into six segments (71 ms each), and varying each segment's pitch using Gaussian distributions, researchers were able to uncover what vocal patterns people associated with certain traits. Specifically, this study investigated how listeners rated sound clips of the word “really” as sounding more interrogative (i.e. like the more common reverse correlation studies this study had participants listen to two sound clips per trial, choose which fit the category the best, and then created an average of the pitch contours). Beyond face and auditory perception, research utilizing the reverse correlation method has expanded to investigate how individuals see three-dimensional objects in images with noise (but no signal). After selecting your base image, regardless of what the image is, it is helpful to apply a Gaussian blur to smooth noise in the image. While noise will be applied later, it is helpful to reduce existing noise in the photo before applying your chosen noise. There are three primary choices when it comes to noise: white noise, sine-wave noise, and Gabor noise. The latter two of these constrain the configurations that the noise can have, and because of this white noise is usually the most commonly used. Regardless of the type of noise that is chosen, it is crucial that the noise randomly varies. === Step 2: data collection === Once the stimuli for the study has been developed, the researcher must make a few decisions before actually collecting the data. The researcher must come to a conclusion on how many stimuli will be presented at a time and how many trials the participants will see. In terms of stimuli presentation, a researcher can choose from either a 2-Image Forced Choice (2IFC) or a 4-Alternative Forced Choice (4AFC). The 2IFC presents two images at once (side by side) and requires participants to choose between the two on a specified category (e.g. which image looks the most like a male). Typically the noise from the left image is the mathematical inverse of the noise from the right image. This method was developed to better answer questions that could n

Valantic

Valantic GmbH (stylised as valantic) is an IT service and consulting company headquartered in Munich, Germany. == History == Valantic GmbH was founded in 2012 under the name Dabero Service Group. Until it was renamed Valantic GmbH in 2017, the company merged with IT service providers and consulting firms. These included, among others, Realtime AG, a company for SAP systems. The companies involved in these mergers were also renamed in 2017 and have since used the Valantic brand name. Realtime AG, for example, became Valantic ERP Services AG. During the COVID-19 pandemic and the resulting economic pressures, demand increased for IT service providers, particularly those offering customised software, IT consulting, SAP services, customer experience, cybersecurity, IoT, and digital work environments. In the following years, Valantic expanded by integrating additional companies. In 2021, Valantic expanded into other European countries through the integration of the Dutch company ISM eCompany and the Portuguese consulting firm Abaco. In 2022, the consulting firm C-Clear/Atom Ideas from Belgium joined Valantic. In February 2019, DPE Deutsche Private Equity Management III GmbH (DPE) took over the majority shareholding in Valantic. The founder, Holger von Daniels, and the further management retained a 25% stake. By 2025, DPE had invested €500 million in Valantic. In the following years, Valantic expanded its international locations. In 2023, Valantic incorporated the Danish company Inspari into the group, thereby entering the Scandinavian market. Inspari is a company for Microsoft technologies such as Azure and Power Platform. In the same year, Valantic joined forces with the Aiopsgroup, an international provider of online shopping applications for private and business customers of large companies. The company is based in Bulgaria with additional locations across Eastern Europe and other places. Additionally, the SAP applications division was expanded through the merger with the Spanish company Saptools. As a result, the companies became one of the largest European end-to-end consulting and implementation house for SAP services. By the end of 2023, Valantic had locations in 18 countries. In November 2024, Valantic announced its merger with the Danish digital consultancy Venzo. Through the integration of the company, founded in 2007 and oriented towards Microsoft technologies and digital transformation projects in the areas of automation, artificial intelligence, security, infrastructure and change management, Valantic further expanded its presence in Denmark and the Nordic countries. In July 2025, Valantic announced its merger with Utiligence GmbH, a Mannheim-based consulting firm for SAP technologies. Utiligence works primarily for the energy industry and supports companies in the integration of SAP S/4HANA and the digitalisation of business processes. == Company structure == Valantic is a partnership-based organisation, with partners acting as decision-makers in matters relating to corporate strategy, employee development and acquisitions. Valantic pursues a holacratic approach, promoting an open and self-organised way of working instead of hierarchical structures. By merging with other companies, Valantic is expanding its range of services and tapping into international markets and market shares. The new companies use Valantic's core systems and support processes, but usually retain their original structure. In the 2024 financial year, the company generated revenue of €544 million and employed 3,874 on average. Valantic has over 40 locations internationally. == Services == Valantic GmbH is a consulting firm, software provider and implementation partner. The company offers services in the areas of digital strategy and analytics (business intelligence and data science), customer experience management, SAP services, smart industries (Industry 4.0, supply chain management, and production planning and control processes), and financial services automation. The automation of financial services is aimed at financial service providers and banks. Valantic has been offering services in the field of generative artificial intelligence (GenAI) since 2023. Part of these services involves enabling companies to use GenAI securely and in compliance with regulations in order to make internal work processes more efficient. Its customers include large corporations, several medium-sized companies and DAX-listed companies. == Research == Since 2018, Valantic has published an annual study on the development of the SAP landscape in German-speaking countries. The study examines topics such as the migration to SAP S/4HANA, cloud strategies, technological trends and the use of artificial intelligence in business processes. The 2025 survey of 201 SAP professionals from the DACH region showed, for example, an increase in ongoing and completed S/4HANA migration projects, as well as a further shift towards private-cloud systems. The use of artificial intelligence continued to grow, as did the use of the SAP Business Technology Platform and the Business Data Cloud. In 2025, Valantic, together with the Handelsblatt Research Institute, published the trend study Digital 2030 – The Rise of Applied AI. The study was based on a survey of around 700 executives from companies in Germany, Austria, and Switzerland on the economic effects of current digitalisation trends. According to the study, most respondents consider artificial intelligence, cybersecurity, and cloud computing to hold the greatest strategic importance for business success by 2030. Around 70% of the participating companies stated that they are already achieving measurable business benefits through the use of AI applications, for example in quality control, document management, logistics, or customer service.

Camera interface

The Camera Interface block or CAMIF is the hardware block that interfaces with different image sensor interfaces and provides a standard output that can be used for subsequent image processing. A typical Camera Interface would support at least a parallel interface although these days many camera interfaces are beginning to support the Mobile Industry Processor Interface (MIPI) Camera Serial Interface (CSI) interface. == Electrical connections == The camera interface's parallel interface consists of the following lines: 8 to 12 bits parallel data line These are parallel data lines that carry pixel data. The data transmitted on these lines change with every Pixel Clock (PCLK). Horizontal Sync (HSYNC) This is a special signal that goes from the camera sensor or ISP to the camera interface. An HSYNC indicates that one line of the frame is transmitted. Vertical Sync (VSYNC) This signal is transmitted after the entire frame is transferred. This signal is often a way to indicate that one entire frame is transmitted. Pixel Clock (PCLK) This is the pixel clock and it would change on every pixel. NOTE: The above lines are all treated as input lines to the Camera Interface hardware.

Carrenza

Carrenza was a cloud-computing company based in London, United Kingdom. The company was acquired by Six Degrees Technology Group in 2016. == Operations == Carrenza was a UK-based IT company that provides Cloud computing technologies. It offered a range of public cloud, private cloud and hybrid cloud services, including Infrastructure as a Service (IaaS), Platform as a Service (PaaS), enterprise application integration and system integration. Carrenza partnered with several enterprise IT providers and was an accredited VMware Enterprise Service Partner and HP (Hewlett-Packard) Cloud Agile Partner. The company was based on Commercial Street, in the heart of the East London Tech City district, which is host to a large number of technology companies. == History == Carrenza was formed in 2001 as a consultancy by chief executive and founder Dan Sutherland. It began trading in 2004 and launched its first enterprise cloud computing platform in 2006, becoming one of the first companies in Europe to provide this type of hosting service. In 2009, it formed a partnership with Comic Relief and its affiliated campaigns Red Nose Day Sport Relief to provide IT infrastructure services to the charity, an arrangement that has won industry recognition. In 2013 it launched its first overseas services, with a mainland Europe cloud node based in Amsterdam. == Partnerships and customers == Carrenza had formed partnerships with a range of IT providers. It was one of the first companies in Europe to become a HP Cloud Agile partner., using HP blade servers and HP 3PAR SAN technology to power its cloud computing services. The company's products also use VMware vCloud IaaS tools and it is taking part in the VMware lighthouse initiative helping develop the next generation of VMware products and services. Other technology companies that Carrenza has worked closely with include Cisco, for enterprise security and loadblancing services, and Oracle. The company was the first to deploy Oracle Database 11g stretched RAC in production. It has also won two Oracle partner awards, including a Special Recognition award for its work with Comic Relief. The company has also been recognised by the UK IT Industry, receiving awards in 2009 for Community Project of the Year and in 2010 for best small business project for its Monopoly City Streets Work. Other companies that have partnered with Carrenza for their cloud-based IT services include Age UK, Haymarket Media Group, the World Wide Fund for Nature, Royal Bank of Scotland, eBay and Cineworld. == Accreditations == Carrenza's services are accredited for their compliance with several key international IT security and quality standards. These include: ISO27001:2005, Information Security Management System for all Carrenza services. UK Government G-Cloud, Carrenza has been awarded a place on the UK government's G-Cloud iii framework as an Infrastructure as a Service provider.

XLNet

The XLNet was an autoregressive Transformer designed as an improvement over BERT, with 340M parameters and trained on 33 billion words. It was released on 19 June 2019, under the Apache 2.0 license. It achieved state-of-the-art results on a variety of natural language processing tasks, including language modeling, question answering, and natural language inference. == Architecture == The main idea of XLNet is to model language autoregressively like the GPT models, but allow for all possible permutations of a sentence. Concretely, consider the following sentence:My dog is cute.In standard autoregressive language modeling, the model would be tasked with predicting the probability of each word, conditioned on the previous words as its context: We factorize the joint probability of a sequence of words x 1 , … , x T {\displaystyle x_{1},\ldots ,x_{T}} using the chain rule: Pr ( x 1 , … , x T ) = Pr ( x 1 ) Pr ( x 2 | x 1 ) Pr ( x 3 | x 1 , x 2 ) … Pr ( x T | x 1 , … , x T − 1 ) . {\displaystyle \Pr(x_{1},\ldots ,x_{T})=\Pr(x_{1})\Pr(x_{2}|x_{1})\Pr(x_{3}|x_{1},x_{2})\ldots \Pr(x_{T}|x_{1},\ldots ,x_{T-1}).} For example, the sentence "My dog is cute" is factorized as: Pr ( My , dog , is , cute ) = Pr ( My ) Pr ( dog | My ) Pr ( is | My , dog ) Pr ( cute | My , dog , is ) . {\displaystyle \Pr({\text{My}},{\text{dog}},{\text{is}},{\text{cute}})=\Pr({\text{My}})\Pr({\text{dog}}|{\text{My}})\Pr({\text{is}}|{\text{My}},{\text{dog}})\Pr({\text{cute}}|{\text{My}},{\text{dog}},{\text{is}}).} Schematically, we can write it as → My → My dog → My dog is → My dog is cute . {\displaystyle {\texttt {}}{\texttt {}}{\texttt {}}{\texttt {}}\to {\text{My }}{\texttt {}}{\texttt {}}{\texttt {}}\to {\text{My dog }}{\texttt {}}{\texttt {}}\to {\text{My dog is }}{\texttt {}}\to {\text{My dog is cute}}.} However, for XLNet, the model is required to predict the words in a randomly generated order. Suppose we have sampled a randomly generated order 3241, then schematically, the model is required to perform the following prediction task: is dog is dog is cute → My dog is cute {\displaystyle {\texttt {}}{\texttt {}}{\texttt {}}{\texttt {}}\to {\texttt {}}{\texttt {}}{\text{is }}{\texttt {}}\to {\texttt {}}{\text{dog is }}{\texttt {}}\to {\texttt {}}{\text{dog is cute}}\to {\text{My dog is cute}}} By considering all permutations, XLNet is able to capture longer-range dependencies and better model the bidirectional context of words. === Two-Stream Self-Attention === To implement permutation language modeling, XLNet uses a two-stream self-attention mechanism. The two streams are: Content stream: This stream encodes the content of each word, as in standard causally masked self-attention. Query stream: This stream encodes the content of each word in the context of what has gone before. In more detail, it is a masked cross-attention mechanism, where the queries are from the query stream, and the key-value pairs are from the content stream. The content stream uses the causal mask M causal = [ 0 − ∞ − ∞ … − ∞ 0 0 − ∞ … − ∞ 0 0 0 … − ∞ ⋮ ⋮ ⋮ ⋱ ⋮ 0 0 0 … 0 ] {\displaystyle M_{\text{causal}}={\begin{bmatrix}0&-\infty &-\infty &\dots &-\infty \\0&0&-\infty &\dots &-\infty \\0&0&0&\dots &-\infty \\\vdots &\vdots &\vdots &\ddots &\vdots \\0&0&0&\dots &0\end{bmatrix}}} permuted by a random permutation matrix to P M causal P − 1 {\displaystyle PM_{\text{causal}}P^{-1}} . The query stream uses the cross-attention mask P ( M causal − ∞ I ) P − 1 {\displaystyle P(M_{\text{causal}}-\infty I)P^{-1}} , where the diagonal is subtracted away specifically to avoid the model "cheating" by looking at the content stream for what the current masked token is. Like the causal masking for GPT models, this two-stream masked architecture allows the model to train on all tokens in one forward pass. == Training == Two models were released: XLNet-Large, cased: 110M parameters, 24-layer, 1024-hidden, 16-heads XLNet-Base, cased: 340M parameters, 12-layer, 768-hidden, 12-heads. It was trained on a dataset that amounted to 32.89 billion tokens after tokenization with SentencePiece. The dataset was composed of BooksCorpus, and English Wikipedia, Giga5, ClueWeb 2012-B, and Common Crawl. It was trained on 512 TPU v3 chips, for 5.5 days. At the end of training, it still under-fitted the data, meaning it could have achieved lower loss with more training. It took 0.5 million steps with an Adam optimizer, linear learning rate decay, and a batch size of 8192.

Summify

Summify was a social news aggregator founded by Mircea Paşoi and Cristian Strat, two former Google and Microsoft interns from Romania. The service emailed its users a periodic summary of news articles shared from their social networks based on their relevance and importance. The platform supported Twitter, Facebook, and Google Reader accounts. == History == In 2009, Paşoi and Strat created ReadFu, a plugin that provided a contextual summary and statistics of the target page of a hyperlink. In January 2010, ReadFu was accepted into the Vancouver-based start-up incubator Bootup Labs. On March 20, 2010 the service was renamed to Summify and a private beta began. On August 11, 2010 Paşoi and Strat announced a new direction for the service. It would become a real-time social news reader that aggregates incoming news from social networks and displays articles by importance using social reactions. After some feedback that the users preferred article digests by email more than the real-time news reader version, Summify discontinued the news reader version. In March 2011, Summify completed a Seed round, with investors including Rob Glaser, Accel Partners, and Stewart Butterfield. Summify received coverage from various news and media outlets such as TechCrunch. It was also featured in various news platforms, such as Time, The Globe and Mail, Mashable, VentureBeat, Gizmodo, Lifehacker, and The Next Web. Summify released a free app on the Apple App Store on July 8, 2011. The app allowed users to read their web summaries from iOS mobile devices. Summify was acquired by Twitter on January 19, 2012. The service shut down soon after, on June 22, 2012.