DREAM Challenges (Dialogue for Reverse Engineering Assessment and Methods) is a non-profit initiative for advancing biomedical and systems biology research via crowd-sourced competitions. Started in 2006, DREAM challenges collaborate with Sage Bionetworks to provide a platform for competitions run on the Synapse platform. Over 60 DREAM challenges have been conducted over the span of over 15 years. == Overview == DREAM Challenges were founded in 2006 by Gustavo Stolovizky from IBM Research and Andrea Califano from Columbia University. Current chair of the DREAM organization is Paul Boutros from University of California. Further organization spans emeritus chairs Justin Guinney and Gustavo Stolovizky, and multiple DREAM directors. Individual challenges focus on tackling a specific biomedical research question, typically narrowed down to a specific disease. A prominent disease focus has been on oncology, with multiple past challenges focused on breast cancer, acute myeloid leukemia, and prostate cancer or similar diseases. The data involved in an individual challenge reflects the disease context; while cancers typically involve data such as mutations in the human genome, gene expression and gene networks in transcriptomics, and large scale proteomics, newer challenges have shifted towards single cell sequencing technologies as well as emerging gut microbiome related research questions, thus reflecting trends in the wider research community. Motivation for DREAM Challenges is that via crowd-sourcing data to a larger audience via competitions, better models and insight is gained than if the analysis was conducted by a single entity. Past competitions have been published in such scientific venues as the flagship journals of the Nature Portfolio and PLOS publishing groups. Results of DREAM challenges are announced via web platforms, and the top performing participants are invited to present their results in the annual RECOMB/ISCB Conferences with RSG/DREAM organized by the ISCB. While DREAM Challenges have emphasized open science and data, in order to mitigate issues rising from highly sensitive data such as genomics in patient cohorts, "model to data" approaches have been adopted. In such challenges participants submit their models via containers such as Docker or Singularity. This allows retaining confidentiality of the original data as these containers are then run by the organizers on the confidential data. This differs from the more traditional open data model, where participants submit predictions directly based on the provided open data. == Challenge organization == DREAM challenge comprises a core DREAM/Sage Bionetworks organization group as well as an extended scientific expert group, who may have contributed to creation and conception of the challenge or by providing key data. Additionally, new DREAM challenges may be proposed by the wider research community. Pharmaceutical companies or other private entities may also be involved in DREAM challenges, for example in providing data. == Challenge structure == Timelines for key stages (such as introduction webinars, model submission deadlines, and final deadline for participation) are provided in advance. After the winners are announced, organizers start collaborating with the top performing participants to conduct post hoc analyses for a publication describing key findings from the competition. Challenges may be split into sub-challenges, each addressing a different subtopic within the research question. For example, regarding cancer treatment efficacy predictions, these may be separate predictions for progression-free survival, overall survival, best overall response according to RECIST, or exact time until event (progression or death). == Participation == During DREAM challenges, participants typically build models on provided data, and submit predictions or models that are then validated on held-out data by the organizers. While DREAM challenges avoid leaking validation data to participants, there are typically mid-challenge submission leaderboards available to assist participants in evaluating their performance on a sub-sampled or scrambled dataset. DREAM challenges are free for participants. During the open phase anybody can register via Synapse to participate either individually or as a team. A person may only register once and may not use any aliases. There are some exceptions, which disqualify an individual from participating, for example: Person has privileged access to the data for the particular challenge, thus providing them with an unfair advantage. Person has been caught or is under suspicion of cheating or abusing previous DREAM Challenges. Person is a minor (under age 18 or the age of majority in jurisdiction of residence). This may be alleviated via parental consent.
Averbis
Averbis has a focus on healthcare, pharma, automotive and intellectual property analytics. Averbis is involved in various research projects of the German Federal Ministry of Economics and Energy and the European Union such as DebugIT, EUCases, Mantra and SEMCARE. In addition to these projects, Averbis was also involved in the following projects: Greenpilot is a virtual library, which provides technical information in the fields of nutrition, environment and agriculture. Medpilot is a virtual library, which provides information about medicine and related sciences. In 2013, Averbis has been nominated for the German Founder Prize 2013. Averbis GmbH provides text analytics and text mining software to transform unstructured text into actionable information. It was founded in 2007 by IT experts after years of relevant scientific experience in the field of text mining and multilingual information retrieval. Averbis works in the field of terminology management, natural language processing, machine learning and semantic search. Its text mining software is embedded into the text mining framework UIMA.
BERT (language model)
Bidirectional encoder representations from transformers (BERT) is a language model introduced in October 2018 by researchers at Google. It learns to represent text as a sequence of vectors using self-supervised learning. It uses the encoder-only transformer architecture. BERT dramatically improved the state of the art for large language models. As of 2020, BERT is a ubiquitous baseline in natural language processing (NLP) experiments. BERT is trained by masked token prediction and next sentence prediction. With this training, BERT learns contextual, latent representations of tokens in their context, similar to ELMo and GPT-2. It found applications for many natural language processing tasks, such as coreference resolution and polysemy resolution. It improved on ELMo and spawned the study of "BERTology", which attempts to interpret what is learned by BERT. BERT was originally implemented in the English language at two model sizes, BERTBASE (110 million parameters) and BERTLARGE (340 million parameters). Both were trained on the Toronto BookCorpus (800M words) and English Wikipedia (2,500M words). The weights were released on GitHub. On March 11, 2020, 24 smaller models were released, the smallest being BERTTINY with just 4 million parameters. == Architecture == BERT is an "encoder-only" transformer architecture. At a high level, BERT consists of 4 modules: Tokenizer: This module converts a piece of English text into a sequence of integers ("tokens"). Embedding: This module converts the sequence of tokens into an array of real-valued vectors representing the tokens. It represents the conversion of discrete token types into a lower-dimensional Euclidean space. Encoder: a stack of Transformer blocks with self-attention, but without causal masking. Task head: This module converts the final representation vectors into one-shot encoded tokens again by producing a predicted probability distribution over the token types. It can be viewed as a simple decoder, decoding the latent representation into token types, or as an "un-embedding layer". The task head is necessary for pre-training, but it is often unnecessary for so-called "downstream tasks," such as question answering or sentiment classification. Instead, one removes the task head and replaces it with a newly initialized module suited for the task, and finetune the new module. The latent vector representation of the model is directly fed into this new module, allowing for sample-efficient transfer learning. === Embedding === This section describes the embedding used by BERTBASE. The other one, BERTLARGE, is similar, just larger. The tokenizer of BERT is WordPiece, which is a sub-word strategy like byte-pair encoding. Its vocabulary size is 30,000, and any token not appearing in its vocabulary is replaced by [UNK] ("unknown"). The first layer is the embedding layer, which contains three components: token type embeddings, position embeddings, and segment type embeddings. Token type: The token type is a standard embedding layer, translating a one-hot vector into a dense vector based on its token type. Position: The position embeddings are based on a token's position in the sequence. BERT uses absolute position embeddings, where each position in a sequence is mapped to a real-valued vector. Each dimension of the vector consists of a sinusoidal function that takes the position in the sequence as input. Segment type: Using a vocabulary of just 0 or 1, this embedding layer produces a dense vector based on whether the token belongs to the first or second text segment in that input. In other words, type-1 tokens are all tokens that appear after the [SEP] special token. All prior tokens are type-0. The three embedding vectors are added together representing the initial token representation as a function of these three pieces of information. After embedding, the vector representation is normalized using a LayerNorm operation, outputting a 768-dimensional vector for each input token. After this, the representation vectors are passed forward through 12 Transformer encoder blocks, and are decoded back to 30,000-dimensional vocabulary space using a basic affine transformation layer. === Architectural family === The encoder stack of BERT has 2 free parameters: L {\displaystyle L} , the number of layers, and H {\displaystyle H} , the hidden size. There are always H / 64 {\displaystyle H/64} self-attention heads, and the feed-forward/filter size is always 4 H {\displaystyle 4H} . By varying these two numbers, one obtains an entire family of BERT models. For BERT: the feed-forward size and filter size are synonymous. Both of them denote the number of dimensions in the middle layer of the feed-forward network. the hidden size and embedding size are synonymous. Both of them denote the number of real numbers used to represent a token. The notation for encoder stack is written as L/H. For example, BERTBASE is written as 12L/768H, BERTLARGE as 24L/1024H, and BERTTINY as 2L/128H. == Training == === Pre-training === BERT was pre-trained simultaneously on two tasks: Masked language modeling (MLM): In this task, BERT ingests a sequence of words, where one word may be randomly changed ("masked"), and BERT tries to predict the original words that had been changed. For example, in the sentence "The cat sat on the [MASK]," BERT would need to predict "mat." This helps BERT learn bidirectional context, meaning it understands the relationships between words not just from left to right or right to left but from both directions at the same time. Next sentence prediction (NSP): In this task, BERT is trained to predict whether one sentence logically follows another. For example, given two sentences, "The cat sat on the mat" and "It was a sunny day", BERT has to decide if the second sentence is a valid continuation of the first one. This helps BERT understand relationships between sentences, which is important for tasks like question answering or document classification. ==== Masked language modeling ==== In masked language modeling, 15% of tokens would be randomly selected for masked-prediction task, and the training objective was to predict the masked token given its context. In more detail, the selected token is: replaced with a [MASK] token with probability 80%, replaced with a random word token with probability 10%, not replaced with probability 10%. The reason not all selected tokens are masked is to avoid the dataset shift problem. The dataset shift problem arises when the distribution of inputs seen during training differs significantly from the distribution encountered during inference. A trained BERT model might be applied to word representation (like Word2Vec), where it would be run over sentences not containing any [MASK] tokens. It is later found that more diverse training objectives are generally better. As an illustrative example, consider the sentence "my dog is cute". It would first be divided into tokens like "my1 dog2 is3 cute4". Then a random token in the sentence would be picked. Let it be the 4th one "cute4". Next, there would be three possibilities: with probability 80%, the chosen token is masked, resulting in "my1 dog2 is3 [MASK]4"; with probability 10%, the chosen token is replaced by a uniformly sampled random token, such as "happy", resulting in "my1 dog2 is3 happy4"; with probability 10%, nothing is done, resulting in "my1 dog2 is3 cute4". After processing the input text, the model's 4th output vector is passed to its decoder layer, which outputs a probability distribution over its 30,000-dimensional vocabulary space. ==== Next sentence prediction ==== Given two sentences, the model predicts if they appear sequentially in the training corpus, outputting either [IsNext] or [NotNext]. During training, the algorithm sometimes samples two sentences from a single continuous span in the training corpus, while at other times, it samples two sentences from two discontinuous spans. The first sentence starts with a special token, [CLS] (for "classify"). The two sentences are separated by another special token, [SEP] (for "separate"). After processing the two sentences, the final vector for the [CLS] token is passed to a linear layer for binary classification into [IsNext] and [NotNext]. For example: Given "[CLS] my dog is cute [SEP] he likes playing [SEP]", the model should predict [IsNext]. Given "[CLS] my dog is cute [SEP] how do magnets work [SEP]", the model should predict [NotNext]. === Fine-tuning === BERT is meant as a general pretrained model for various applications in natural language processing. That is, after pre-training, BERT can be fine-tuned with fewer resources on smaller datasets to optimize its performance on specific tasks such as natural language inference and text classification, and sequence-to-sequence-based language generation tasks such as question answering and conversational response generation. The original BERT paper published results demonstrating that a small amount of fine
Language engineering
Language engineering involves the creation of natural language processing systems, whose cost and outputs are measurable and predictable. It is a distinct field contrasted to natural language processing and computational linguistics. A recent trend of language engineering is the use of Semantic Web technologies for the creation, archiving, processing, and retrieval of machine processable language data. Meta-Language Engineering is a proposed extension of Language Engineering first recorded in 2025, associated with the work of Delyone de Paula Canedo Filho. The term is used to designate an approach that, in addition to natural language processing, encompasses the symbolic, cognitive, and epistemological structuring of language systems.
Stereo cameras
The stereo cameras approach is a method of distilling a noisy video signal into a coherent data set that a computer can begin to process into actionable symbolic objects, or abstractions. Stereo cameras is one of many approaches used in the broader fields of computer vision and machine vision. == Calculation == In this approach, two cameras with a known physical relationship (i.e. a common field of view the cameras can see, and how far apart their focal points sit in physical space) are correlated via software. By finding mappings of common pixel values, and calculating how far apart these common areas reside in pixel space, a rough depth map can be created. This is very similar to how the human brain uses stereoscopic information from the eyes to gain depth cue information, i.e. how far apart any given object in the scene is from the viewer. The camera attributes must be known, focal length and distance apart etc., and a calibration done. Once this is completed, the systems can be used to sense the distances of objects by triangulation. Finding the same singular physical point in the two left and right images is known as the correspondence problem. Correctly locating the point gives the computer the capability to calculate the distance that the robot or camera is from the object. On the BH2 Lunar Rover the cameras use five steps: a bayer array filter, photometric consistency dense matching algorithm, a Laplace of Gaussian (LoG) edge detection algorithm, a stereo matching algorithm and finally uniqueness constraint. == Uses == This type of stereoscopic image processing technique is used in applications such as 3D reconstruction, robotic control and sensing, crowd dynamics monitoring and off-planet terrestrial rovers; for example, in mobile robot navigation, tracking, gesture recognition, targeting, 3D surface visualization, immersive and interactive gaming. Although the Xbox Kinect sensor is also able to create a depth map of an image, it uses an infrared camera for this purpose, and does not use the dual-camera technique. Other approaches to stereoscopic sensing include time of flight sensors and ultrasound.
Line Drawing System-1
LDS-1 (Line Drawing System-1) was a calligraphic (vector, rather than raster) display processor and display device created by Evans & Sutherland in 1969. This model was known as the first graphics device with a graphics processing unit. == Features == It was controlled by a variety of host computers. Straight lines were smoothly rendered in real-time animation. General principles of operation were similar to the systems used today: 4x4 transformation matrices, 1x4 vertices. Possible uses included flight simulation (in the product brochure there are screenshots of landing on a carrier), scientific imaging and GIS systems. == History == The first LDS-1 was shipped to the customer (BBN) in August 1969. Only a few of these systems were ever built. One was used by the Los Angeles Times as their first typesetting/layout computer. One went to NASA Ames Research Center for Human Factors Research. Another was bought by the Port Authority of New York to develop a tugboat pilot trainer for navigation in the harbor. The MIT Dynamic Modeling had one, and there was a program for viewing an ongoing game of Maze War.
Keka HR
Keka HR is a software company that provides cloud-based human resource management and payroll automation software. Keka HR specializes in providing business services in the field of HR technology, payroll automation, recruiting, leave, attendance and performance management. The company was founded by Vijay Yalamanchili on July 21, 2014. The company is headquartered in Hyderabad, with operations in Singapore and the United States. == History == Keka HR was established in 2014 in Hyderabad, Telangana, India. In 2015, the company entered the Indian HR market and received the HYSEA Startup Award. By 2019, Keka HR had surpassed $1 million in annual recurring revenue (ARR). During the COVID-19 pandemic in 2020, the company reported a sevenfold increase in sales. By 2021, the company had raised $1.6 million through Recur Club. In 2022, Keka HR secured $57 million in Series A funding from West Bridge Capital. The company's headquarters are located in Gachibowli, Hyderabad, with offices in Singapore and Seattle, Washington.