Gary Bryce Fogel (born 1968) is an American biologist and computer scientist. He is the Chief Executive Officer of Natural Selection, Inc. He is most known for his applications of computational intelligence and machine learning to bioinformatics, computational biology, and industrial optimization. == Education and Research == Fogel was born and raised in La Jolla, California, graduating from La Jolla High School. He received a B.A. in biology with a minor in earth sciences from the University of California, Santa Cruz in 1991 and a Ph.D. in biology from the University of California, Los Angeles in 1998. Fogel has published over 150 peer-reviewed publications in conferences and journals, 2 edited books, and 11 patents. As CEO of Natural Selection, Inc., his research focuses on the application of computational intelligence, machine learning, and predictive analytics in areas not limited to: Viral evolution, cellular differentiation, drug discovery, RNA structure, cis-regulatory elements, cancer, and evolutionary game theory as well as the development of evolutionary algorithms and other approaches. == Service == Between 2008–2018 Gary Fogel was editor-in-chief of the Elsevier journal BioSystems. He has served previously as an associate editor for IEEE Transactions on Artificial Intelligence, IEEE Computational Intelligence Magazine (2005–2010), IEEE Transactions on Evolutionary Computation (2001–2013), IEEE Transactions on Emerging Topics in Computational Intelligence (2016–2018), IEEE/ACM Transactions on Computational Biology and Bioinformatics (2004–2008), International Journal of Bioinformatics Research and Applications (2004–2007), International Journal of Data Mining and Bioinformatics (2005–2007), as a consulting editor for the Journal of Computational Intelligence in Bioinformatics (2006–2007), and as an editorial board member of Ecological Informatics (2005–2009) and BMC Big Data Analytics (2015–2020). Within the IEEE Computational Intelligence Society, Fogel founded the Bioinformatics and Bioengineering Technical Committee and established the IEEE Computational Intelligence in Bioinformatics and Computational Biology conference series, chairing the first two meetings in 2004 and 2005 in San Diego. He co-founded the IEEE Conference on Artificial Intelligence in 2023. Fogel served on the IEEE Computational Intelligence Society Administrative Committee (2004–2009, 2014–2022) and served as IEEE CIS Vice President of Conferences (2010–2013, 2019). == Teaching == Gary Fogel also serves as adjunct faculty at San Diego State University in the department of aerospace engineering as well as in the Computational Science Research Center. He has authored four books and numerous articles on the history of early aviation focusing on motorless flight. He is an associate fellow of the American Institute of Aeronautics and Astronautics and serves on the AIAA History Committee. == Awards == 2023 – Outstanding Contribution to Aerospace Education Award, AIAA San Diego Section 2022 – Elected Fellow of the Asia-Pacific Artificial Intelligence Association 2019 – Top 100 AI Leaders in Drug Discovery and Advanced Healthcare by Deep Knowledge Analytics 2019 – Outstanding Contribution to Aerospace Education Award, AIAA San Diego Section 2016 – Meritorious Service Award, IEEE Computational Intelligence Society 2016 – Outstanding Contribution to the Community Award, AIAA San Diego Section 2015 – Outstanding Enhancement of the Image of the Aerospace Profession Award, AIAA San Diego Section 2012 – Medal for Significant Achievement, San Diego Chapter of Sigma Xi 2012 – Fellow of the Institute of Electrical and Electronics Engineers for contributions to computational intelligence and its application to biology, chemistry, and medicine. == Aeromodeling == Gary Fogel has established national and world records for model aircraft. He helped establish the National Model Aviation Heritage program for the Academy of Model Aeronautics. He is a leader member, contest director, and fellow of the Academy of Model Aeronautics, and was inducted into the Academy of Model Aeronautics Hall of Fame in 2025.
Huawei Mobile Services
Huawei Mobile Services (HMS) is a collection of proprietary services and high level application programming interfaces (APIs) developed by Huawei Technologies Co., Ltd. Its hub known as HMS Core serves as a toolkit for app development on Huawei devices. HMS is typically installed on Huawei devices on top of running HarmonyOS 4.x and earlier operating system on its earlier devices running the Android operating system with EMUI including devices already distributed with Google Mobile Services. Alongside, HMS Core Wear Engine for Android phones with lightweight based LiteOS wearable middleware app framework integration connectivity like notifications, status etc. HMS consists of seven key services and the HMS Core. The key services are Huawei ID, Huawei Cloud, AppGallery, Themes, Huawei Video, Browser, and Assistant. The web browser is based on Chromium. Huawei Quick Apps is the alternative to Google Instant Apps. By January 2020, over 50,000 apps had been integrated with HMS Core. Its rival, Google Mobile Services has 3 million apps on Google's Play Store. The AppGallery claimed 180 billion downloads in 2019. In March 2020, HMS was used by 650 million monthly active users across 170 countries. A Chinese phone manufacturer, LeTV, hosted a smartphone business communication meeting in Beijing on September 27, 2021, to demonstrate its phone, the LeTV S1. This was the first smartphone from a third-party manufacturer to include Huawei Mobile Services (HMS). == HMS on Android and HarmonyOS == Huawei Mobile Services on Android goes all the way back to August 2016 as Huawei ID services for phones, basic functionalities for Huawei P9 series. However, in May 2019 proved to be a significant change to HMS when Google was prohibited from working with Huawei on any new devices extending ecosystem for AppGallery store front launched in April 2018, year prior. This also included bundling Google's Apps, including Gmail, Maps and YouTube. Any new Huawei devices launched after 16 May 2019 were unable to receive updates from Google services and would be considered 'uncertified' meaning Huawei's only solution at the time was to turn HMS into a genuine competitor to Google and incentivize app developers to utilize the platform. Huawei officially launched Huawei Mobile Services in China on December 24, 2019, as a beta. Huawei expanded Huawei Mobile Services in Europe in February 2020 and other markets in Asia, Latin America, Middle East & Africa, Canada, Mexico followed outside banned US market. HMS is available on the Honor 9X Pro, View 30 Pro, Huawei Mate XS. HMS is also available, alongside GMS, on many other Huawei models launched before the ban. Huawei promised developers it would take, “less than 10 minutes", to port their app over to HMS - to illustrate the ease of portability between Google's Play Store and the HMS AppGallery. On January 15, 2020, HMS Core 4.0 (Huawei Mobile Services Core 4.0) was officially launched. Huawei announced that at this time, there were already 1.3 million developers and 55,000 applications on board. The next day, Huawei held a developer day event in London and invested £20 million to encourage developers in the United Kingdom and Ireland to use HMS. On July 15, 2021, Huawei expanded HMS with classic HarmonyOS dual-framework that provided Java support and eventually with JavaScript and ArkTS (eTS) language support with HMS Core 6.0 for app development with primarily Android apps, alongside limited HAP imperative developed based apps that shares AOSP file system libraries in all types of devices from smartphones, tablets, smart screens, smartwatches, and car machines. Including various third-party development frameworks, such as React Native, Cordova, etc. At HDC 2023, Huawei unveiled HarmonyOS 5, marking a total break from the hybrid Android derived platform. This shift replaced the legacy Android and classic HarmonyOS-based HMS SDK with a full native API developer kit SDK built solely on OpenHarmony. The architecture moved from middleware services to vertical integration path. In this new model, HMS Core libraries are no longer external add-ons but are bundled directly into the system and DevEco Studio as native HarmonyOS Kits. == HMS Core == HMS Core is a hub for Huawei Mobile Services and serves as a toolkit for app development on Huawei devices. The core comprises Development, Growth and Monetizing and was created as a replacement for Google Mobile Services (GMS) Core. HMS core services were available in more than 55,000 apps in June 2020; HMS Core 5.0 debuted in September 2020. HMS Core 6.0 was launched in June 2021 with extended support for Huawei Cloud services. In June 2021, the number of registered developers within the HMS ecosystem was 4 million, and the number of apps integrated with the HMS Core had reached 134,000. As of July 2022, registered developers within HMS ecosystem had grown to 5 million, and the number of apps integrated with the HMS Core reached 203,000. The number of apps had grown to 220,000 by 30 September 2022. == AppGallery == The AppGallery has a key rival, Google's Play Store on Android. The AppGallery is available in 170 countries, across 78 languages. == Reception == The reception of HMS is mixed, with the majority of discussion based around the key Google/Android apps which are not yet present on the AppGallery and whether or not this presents a significant problem to users. The open development of HMS Core has been regarded by some as benefiting the Android project as a whole, "If Huawei continues to invest in a holistically open approach ... the result could be that we could all end up a bit less beholden to Google".
Novell File Reporter
Novell File Reporter (NFR) is software that allows network administrators to identify files stored on the network and generates reports regarding the size of individual files, file type, when files were last accessed, and where duplicates exist. Additionally, the File Reporter tracks storage volume capacity and usage. It is a component of the Novell File Management Suite. == How it works == Novell File Reporter examines and reports on terabytes of data via a central reporting engine (NFR Engine) and distributed agents (NFR Agents). The NFR Engine schedules the scans of file instances conducted by NFR Agents, processes and compiles the scans for reporting purposes, and provides report information to the user interface. In addition to the standard reports it can generate, the NFR Engine can also produce "trigger reports" in response to specific events (a server volume crossing a capacity threshold, for example). Accordingly, the NFR Engine monitors the data gathered by the NFR Agents in order to identify these "triggers." The NFR Engine when working in either eDirectory or Active Directory connects to the directory via a Directory Services Interface (DSI) and thus can monitor and check file permissions.
AVT Statistical filtering algorithm
AVT Statistical filtering algorithm is an approach to improving quality of raw data collected from various sources. It is most effective in cases when there is inband noise present. In those cases AVT is better at filtering data then, band-pass filter or any digital filtering based on variation of. Conventional filtering is useful when signal/data has different frequency than noise and signal/data is separated/filtered by frequency discrimination of noise. Frequency discrimination filtering is done using Low Pass, High Pass and Band Pass filtering which refers to relative frequency filtering criteria target for such configuration. Those filters are created using passive and active components and sometimes are implemented using software algorithms based on Fast Fourier transform (FFT). AVT filtering is implemented in software and its inner working is based on statistical analysis of raw data. When signal frequency/(useful data distribution frequency) coincides with noise frequency/(noisy data distribution frequency) we have inband noise. In this situations frequency discrimination filtering does not work since the noise and useful signal are indistinguishable and where AVT excels. To achieve filtering in such conditions there are several methods/algorithms available which are briefly described below. == Averaging algorithm == Collect n samples of data Calculate average value of collected data Present/record result as actual data == Median algorithm == Collect n samples of data Sort the data in ascending or descending order. Note that order does not matter Select the data that happen to be in n/2 position and present/record it as final result representing data sample == AVT algorithm == AVT algorithm stands for Antonyan Vardan Transform and its implementation explained below. Collect n samples of data Calculate the standard deviation and average value Drop any data that is greater or less than average ± one standard deviation Calculate average value of remaining data Present/record result as actual value representing data sample This algorithm is based on amplitude discrimination and can easily reject any noise that is not like actual signal, otherwise statistically different than 1 standard deviation of the signal. Note that this type of filtering can be used in situations where the actual environmental noise is not known in advance. Notice that it is preferable to use the median in above steps than average. Originally the AVT algorithm used average value to compare it with results of median on the data window. == Filtering algorithms comparison == Using a system that has signal value of 1 and has noise added at 0.1% and 1% levels will simplify quantification of algorithm performance. The R script is used to create pseudo random noise added to signal and analyze the results of filtering using several algorithms. Please refer to "Reduce Inband Noise with the AVT Algorithm" article for details. This graphs show that AVT algorithm provides best results compared with Median and Averaging algorithms while using data sample size of 32, 64 and 128 values. Note that this graph was created by analyzing random data array of 10000 values. Sample of this data is graphically represented below. From this graph it is apparent that AVT outperforms other filtering algorithms by providing 5% to 10% more accurate data when analyzing same datasets. Considering random nature of noise used in this numerical experiment that borderlines worst case situation where actual signal level is below ambient noise the precision improvements of processing data with AVT algorithm are significant. == AVT algorithm variations == === Cascaded AVT === In some situations better results can be obtained by cascading several stages of AVT filtering. This will produce singular constant value which can be used for equipment that has known stable characteristics like thermometers, thermistors and other slow acting sensors. === Reverse AVT === Collect n samples of data Calculate the standard deviation and average value Drop any data that is within one standard deviation ± average band Calculate average value of remaining data Present/record result as actual data This is useful for detecting minute signals that are close to background noise level. == Possible applications and uses == Use to filter data that is near or below noise level Used in planet detection to filter out raw data from the Kepler space telescope Filter out noise from sound sources where all other filtering methods (Low-pass filter, High-pass filter, Band-pass filter, Digital filter) fail. Pre-process scientific data for data analysis (Smoothness) before plotting see (Plot (graphics)) Used in SETI (Search for extraterrestrial intelligence) for detecting/distinguishing extraterrestrial signals from cosmic background Use AVT as image filtering algorithm to detect altered images. This image of Jupiter generated from this program, detecting alterations in original picture that was modified to be visually appealing by applying filters. Another version of this comparison is the Reverse AVT filter applied to the same original Jupiter Image, where we only see that altered portion as Noise that was eliminated by AVT algorithm. Use AVT as image filtering algorithm to estimate data density from images. Picture of Pillars of Creation Nebula shows data density in filtered images from Hubble and Webb. Note that image on the left has big patches of missing data marked with simpler color patterns.
Ontology merging
Ontology merging defines the act of bringing together two conceptually divergent ontologies or the instance data associated to two ontologies. This is similar to work in database merging (schema matching). This merging process can be performed in a number of ways, manually, semi automatically, or automatically. Manual ontology merging although ideal is extremely labour-intensive and current research attempts to find semi or entirely automated techniques to merge ontologies. These techniques are statistically driven often taking into account similarity of concepts and raw similarity of instances through textual string metrics and semantic knowledge. These techniques are similar to those used in information integration employing string metrics from open source similarity libraries.
Concurrent MetateM
Concurrent MetateM is a multi-agent language in which each agent is programmed using a set of (augmented) temporal logic specifications of the behaviour it should exhibit. These specifications are executed directly to generate the behaviour of the agent. As a result, there is no risk of invalidating the logic as with systems where logical specification must first be translated to a lower-level implementation. The root of the MetateM concept is Gabbay's separation theorem; any arbitrary temporal logic formula can be rewritten in a logically equivalent past → future form. Execution proceeds by a process of continually matching rules against a history, and firing those rules when antecedents are satisfied. Any instantiated future-time consequents become commitments which must subsequently be satisfied, iteratively generating a model for the formula made up of the program rules. == Temporal Connectives == The Temporal Connectives of Concurrent MetateM can divided into two categories, as follows: Strict past time connectives: '●' (weak last), '◎' (strong last), '◆' (was), '■' (heretofore), 'S' (since), and 'Z' (zince, or weak since). Present and future time connectives: '◯' (next), '◇' (sometime), '□' (always), 'U' (until), and 'W' (unless). The connectives {◎,●,◆,■,◯,◇,□} are unary; the remainder are binary. === Strict past time connectives === ==== Weak last ==== ●ρ is satisfied now if ρ was true in the previous time. If ●ρ is interpreted at the beginning of time, it is satisfied despite there being no actual previous time. Hence "weak" last. ==== Strong last ==== ◎ρ is satisfied now if ρ was true in the previous time. If ◎ρ is interpreted at the beginning of time, it is not satisfied because there is no actual previous time. Hence "strong" last. ==== Was ==== ◆ρ is satisfied now if ρ was true in any previous moment in time. ==== Heretofore ==== ■ρ is satisfied now if ρ was true in every previous moment in time. ==== Since ==== ρSψ is satisfied now if ψ is true at any previous moment and ρ is true at every moment after that moment. ==== Zince, or weak since ==== ρZψ is satisfied now if (ψ is true at any previous moment and ρ is true at every moment after that moment) OR ψ has not happened in the past. === Present and future time connectives === ==== Next ==== ◯ρ is satisfied now if ρ is true in the next moment in time. ==== Sometime ==== ◇ρ is satisfied now if ρ is true now or in any future moment in time. ==== Always ==== □ρ is satisfied now if ρ is true now and in every future moment in time. ==== Until ==== ρUψ is satisfied now if ψ is true at any future moment and ρ is true at every moment prior. ==== Unless ==== ρWψ is satisfied now if (ψ is true at any future moment and ρ is true at every moment prior) OR ψ does not happen in the future.
Shapiro–Senapathy algorithm
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