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Systems Biology Analysis of Transcription Networks, Artificial Intelligence, and High-End Computing Coming to Fruition in Personalized Oncology

Posted in Artificial Intelligence in CANCER, Artificial Intelligence in Health Care - Tools & Innovations, Artificial Intelligence in Medicine - Applications in Therapeutics, Big Data, BioIT: BioInformatics, BioIT: BioInformatics, NGS, Clinical & Translational, Pharmaceutical R&D Informatics, Clinical Genomics, Cancer Informatics, Biological Networks, Biological Networks, Gene Regulation and Evolution, Cancer - General, Cancer and Current Therapeutics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Genomics, Cell Biology, Cell Biology, Signaling & Cell Circuits, Clinical & Translational, Clinical Genomics, Genomic Expression, Intelligent Information Systems, tagged activation of transcription factors, Artificial intelligence, Artificial Intelligence & Clinical Trials, Biological Networks, Columbia University Medical Center, DarwinHealth, mutational analysis, RNA-Seq, transcription control on July 14, 2020| Leave a Comment »

Systems Biology analysis of Transcription Networks, Artificial Intelligence, and High-End Computing Coming to Fruition in Personalized Oncology

Curator: Stephen J. Williams, Ph.D.

In the June 2020 issue of the journal Science, writer Roxanne Khamsi has an interesting article “Computing Cancer’s Weak Spots; An algorithm to unmask tumors’ molecular linchpins is tested in patients”[1], describing some early successes in the incorporation of cancer genome sequencing in conjunction with artificial intelligence algorithms toward a personalized clinical treatment decision for various tumor types. In 2016, oncologists Amy Tiersten collaborated with systems biologist Andrea Califano and cell biologist Jose Silva at Mount Sinai Hospital to develop a systems biology approach to determine that the drug ruxolitinib, a STAT3 inhibitor, would be effective for one of her patient’s aggressively recurring, Herceptin-resistant breast tumor. Dr. Califano, instead of defining networks of driver mutations, focused on identifying a few transcription factors that act as ‘linchpins’ or master controllers of transcriptional networks withing tumor cells, and in doing so hoping to, in essence, ‘bottleneck’ the transcriptional machinery of potential oncogenic products. As Dr. Castilano states

“targeting those master regulators and you will stop cancer in its tracks, no matter what mutation initially caused it.”

It is important to note that this approach also relies on the ability to sequence tumors by RNA-seq to determine the underlying mutations which alter which master regulators are pertinent in any one tumor. And given the wide tumor heterogeneity in tumor samples, this sequencing effort may have to involve multiple biopsies (as discussed in earlier posts on tumor heterogeneity in renal cancer).

As stated in the article, Califano co-founded a company called Darwin-Health in 2015 to guide doctors by identifying the key transcription factors in a patient’s tumor and suggesting personalized therapeutics to those identified molecular targets (OncoTarget™). He had collaborated with the Jackson Laboratory and most recently Columbia University to conduct a $15 million 3000 patient clinical trial. This was a bit of a stretch from his initial training as a physicist and, in 1986, IBM hired him for some artificial intelligence projects. He then landed in 2003 at Columbia and has been working on identifying these transcriptional nodes that govern cancer survival and tumorigenicity. Dr. Califano had figured that the number of genetic mutations which potentially could be drivers were too vast:

A 2018 study which analyzed more than 9000 tumor samples reported over 1.5 million mutations[2]

and impossible to develop therapeutics against. He reasoned that you would just have to identify the common connections between these pathways or transcriptional nodes and termed them master regulators.

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

Chen H, Li C, Peng X, et al. Cell. 2018;173(2):386-399.e12.

Abstract

The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on “chromatin-state” to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.

A diagram of how concentrating on these transcriptional linchpins or nodes may be more therapeutically advantageous as only one pharmacologic agent is needed versus multiple agents to inhibit the various upstream pathways:

From: Khamsi R: Computing cancer’s weak spots. Science 2020, 368(6496):1174-1177.

VIPER Algorithm (Virtual Inference of Protein activity by Enriched Regulon Analysis)

The algorithm that Califano and DarwinHealth developed is a systems biology approach using a tumor’s RNASeq data to determine controlling nodes of transcription. They have recently used the VIPER algorithm to look at RNA-Seq data from more than 10,000 tumor samples from TCGA and identified 407 transcription factor genes that acted as these linchpins across all tumor types. Only 20 to 25 of them were implicated in just one tumor type so these potential nodes are common in many forms of cancer.

Other institutions like the Cold Spring Harbor Laboratories have been using VIPER in their patient tumor analysis. Linchpins for other tumor types have been found. For instance, VIPER identified transcription factors IKZF1 and IKF3 as linchpins in multiple myeloma. But currently approved therapeutics are hard to come by for targets with are transcription factors, as most pharma has concentrated on inhibiting an easier target like kinases and their associated activity. In general, developing transcription factor inhibitors in more difficult an undertaking for multiple reasons.

Network-based inference of protein activity helps functionalize the genetic landscape of cancer. Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A:. Nature genetics 2016, 48(8):838-847 [3]

Abstract

Identifying the multiple dysregulated oncoproteins that contribute to tumorigenesis in a given patient is crucial for developing personalized treatment plans. However, accurate inference of aberrant protein activity in biological samples is still challenging as genetic alterations are only partially predictive and direct measurements of protein activity are generally not feasible. To address this problem we introduce and experimentally validate a new algorithm, VIPER (Virtual Inference of Protein-activity by Enriched Regulon analysis), for the accurate assessment of protein activity from gene expression data. We use VIPER to evaluate the functional relevance of genetic alterations in regulatory proteins across all TCGA samples. In addition to accurately inferring aberrant protein activity induced by established mutations, we also identify a significant fraction of tumors with aberrant activity of druggable oncoproteins—despite a lack of mutations, and vice-versa. In vitro assays confirmed that VIPER-inferred protein activity outperforms mutational analysis in predicting sensitivity to targeted inhibitors.

Figure 1

Schematic overview of the VIPER algorithm From: Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, Ding BB, Ye BH, Califano A: Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nature genetics 2016, 48(8):838-847.

(a) Molecular layers profiled by different technologies. Transcriptomics measures steady-state mRNA levels; Proteomics quantifies protein levels, including some defined post-translational isoforms; VIPER infers protein activity based on the protein’s regulon, reflecting the abundance of the active protein isoform, including post-translational modifications, proper subcellular localization and interaction with co-factors. (b) Representation of VIPER workflow. A regulatory model is generated from ARACNe-inferred context-specific interactome and Mode of Regulation computed from the correlation between regulator and target genes. Single-sample gene expression signatures are computed from genome-wide expression data, and transformed into regulatory protein activity profiles by the aREA algorithm. (c) Three possible scenarios for the aREA analysis, including increased, decreased or no change in protein activity. The gene expression signature and its absolute value (|GES|) are indicated by color scale bars, induced and repressed target genes according to the regulatory model are indicated by blue and red vertical lines. (d) Pleiotropy Correction is performed by evaluating whether the enrichment of a given regulon (R₄) is driven by genes co-regulated by a second regulator (R₄∩R₁). (e) Benchmark results for VIPER analysis based on multiple-samples gene expression signatures (msVIPER) and single-sample gene expression signatures (VIPER). Boxplots show the accuracy (relative rank for the silenced protein), and the specificity (fraction of proteins inferred as differentially active at p < 0.05) for the 6 benchmark experiments (see Table 2). Different colors indicate different implementations of the aREA algorithm, including 2-tail (2T) and 3-tail (3T), Interaction Confidence (IC) and Pleiotropy Correction (PC).

Powerful Artificial Intelligence (AI) Tools Being Developed for the COVID-19 Fight

Posted in Artificial Intelligence in Health Care - Tools & Innovations, Artificial Intelligence in Medicine - Application for Diagnosis, Artificial Intelligence in Medicine - Applications in Therapeutics, Big Data, Biomarkers: Inflammation, Cancer Researchers Fighting COVID-19, coronavirus, Coronavirus Gene Expression, COVID-19, COVID-19 effects on Human Heart, COVID-19: Pandemic Surgery Guidance, Disease Biology, Economic Impact of Coronavirus Pandemic, Health Economics and Outcomes Research, HealthCare IT, Image Processing/Computing, Imaging-based Cancer Patient Management, Immune-Mediation (independent immunopathology: lung and reticuloendothelial system), Infectious Disease & New Antibiotic Targets, Infectious Disease Immunodiagnostics, Intelligent Information Systems, number of asymptomatic infections, SAR-Cov-2 a vasculotropic (blood vessels) RNA Virus, SARS-CoV-2, SARS-COV2 Hijacking the Complement and Coagulation Systems, Seasonality & Environmental Factors in Resurgence, Serology tests for coronavirus antibodies, Treatment Protocols for COVID-19, Vaccinology, Viral diseases, Virology - Vector-borne DIsease, tagged #COVID-19, AI, Artificial intelligence, Artificial Intelligence & Clinical Trials, biotech innovation, COVID-19, DiA, IBM Watson, imaging, Pandemic, SARS-CoV-2, Technion – Israel Institute of Technology on May 13, 2020| Leave a Comment »

Powerful AI Tools Being Developed for the COVID-19 Fight

Curator: Stephen J. Williams, Ph.D.

Source: https://www.ibm.com/blogs/research/2020/04/ai-powered-technologies-accelerate-discovery-covid-19/

IBM Releases Novel AI-Powered Technologies to Help Health and Research Community Accelerate the Discovery of Medical Insights and Treatments for COVID-19

April 3, 2020 | Written by: Dario Gil

IBM Research has been actively developing new cloud and AI-powered technologies that can help researchers across a variety of scientific disciplines accelerate the process of discovery. As the COVID-19 pandemic unfolds, we continue to ask how these technologies and our scientific knowledge can help in the global battle against coronavirus.

Today, we are making available multiple novel, free resources from across IBM to help healthcare researchers, doctors and scientists around the world accelerate COVID-19 drug discovery: from gathering insights, to applying the latest virus genomic information and identifying potential targets for treatments, to creating new drug molecule candidates.

Though some of the resources are still in exploratory stages, IBM is making them available to qualifying researchers at no charge to aid the international scientific investigation of COVID-19.

Today’s announcement follows our recent leadership in launching the U.S. COVID-19 High Performance Computing Consortium, which is harnessing massive computing power in the effort to help confront the coronavirus.

Streamlining the Search for Information

Healthcare agencies and governments around the world have quickly amassed medical and other relevant data about the pandemic. And, there are already vast troves of medical research that could prove relevant to COVID-19. Yet, as with any large volume of disparate data sources, it is difficult to efficiently aggregate and analyze that data in ways that can yield scientific insights.

To help researchers access structured and unstructured data quickly, we are offering a cloud-based AI research resource that has been trained on a corpus of thousands of scientific papers contained in the COVID-19 Open Research Dataset (CORD-19), prepared by the White House and a coalition of research groups, and licensed databases from the DrugBank, Clinicaltrials.gov and GenBank. This tool uses our advanced AI and allows researchers to pose specific queries to the collections of papers and to extract critical COVID-19 knowledge quickly. Please note, access to this resource will be granted only to qualified researchers. To learn more and request access, please click here.

Aiding the Hunt for Treatments

The traditional drug discovery pipeline relies on a library of compounds that are screened, improved, and tested to determine safety and efficacy. In dealing with new pathogens such as SARS-CoV-2, there is the potential to enhance the compound libraries with additional novel compounds. To help address this need, IBM Research has recently created a new, AI-generative framework which can rapidly identify novel peptides, proteins, drug candidates and materials.

We have applied this AI technology against three COVID-19 targets to identify 3,000 new small molecules as potential COVID-19 therapeutic candidates. IBM is releasing these molecules under an open license, and researchers can study them via a new interactive molecular explorer tool to understand their characteristics and relationship to COVID-19 and identify candidates that might have desirable properties to be further pursued in drug development.

To streamline efforts to identify new treatments for COVID-19, we are also making the IBM Functional Genomics Platform available for free for the duration of the pandemic. Built to discover the molecular features in viral and bacterial genomes, this cloud-based repository and research tool includes genes, proteins and other molecular targets from sequenced viral and bacterial organisms in one place with connections pre-computed to help accelerate discovery of molecular targets required for drug design, test development and treatment.

Select IBM collaborators from government agencies, academic institutions and other organizations already use this platform for bacterial genomic study. And now, those working on COVID-19 can request the IBM Functional Genomics Platform interface to explore the genomic features of the virus. Access to the IBM Functional Genomics Platform will be prioritized for those conducting COVID-19 research. To learn more and request access, please click here.

Drug and Disease Information

Clinicians and healthcare professionals on the frontlines of care will also have free access to hundreds of pieces of evidence-based, curated COVID-19 and infectious disease content from IBM Micromedex and EBSCO DynaMed. Using these two rich decision support solutions, users will have access to drug and disease information in a single and comprehensive search. Clinicians can also provide patients with consumer-friendly patient education handouts with relevant, actionable medical information. IBM Micromedex is one of the largest online reference databases for medication information and is used by more than 4,500 hospitals and health systems worldwide. EBSCO DynaMed provides peer-reviewed clinical content, including systematic literature reviews in 28 specialties for comprehensive disease topics, health conditions and abnormal findings, to highly focused topics on evaluation, differential diagnosis and management.

The scientific community is working hard to make important new discoveries relevant to the treatment of COVID-19, and we’re hopeful that releasing these novel tools will help accelerate this global effort. This work also outlines our long-term vision for the future of accelerated discovery, where multi-disciplinary scientists and clinicians work together to rapidly and effectively create next generation therapeutics, aided by novel AI-powered technologies.

Learn more about IBM’s response to COVID-19: IBM.com/COVID19.

Source: https://www.ibm.com/blogs/research/2020/04/ai-powered-technologies-accelerate-discovery-covid-19/

DiA Imaging Analysis Receives Grant to Accelerate Global Access to its AI Ultrasound Solutions in the Fight Against COVID-19

Source: https://www.grantnews.com/news-articles/?rkey=20200512UN05506&filter=12337

Grant will allow company to accelerate access to its AI solutions and use of ultrasound in COVID-19 emergency settings

TEL AVIV, Israel, May 12, 2020 /PRNewswire-PRWeb/ — DiA Imaging Analysis, a leading provider of AI based ultrasound analysis solutions, today announced that it has received a government grant from the Israel Innovation Authority (IIA) to develop solutions for ultrasound imaging analysis of COVID-19 patients using Artificial Intelligence (AI).Using ultrasound in point of care emergency settings has gained momentum since the outbreak of COVID-19 pandemic. In these settings, which include makeshift hospital COVID-19 departments and triage “tents,” portable ultrasound offers clinicians diagnostic decision support, with the added advantage of being easier to disinfect and eliminating the need to transport patients from one room to another.However, analyzing ultrasound images is a process that it is still mostly done visually, leading to a growing market need for automated solutions and decision support.As the leading provider of AI solutions for ultrasound analysis and backed by Connecticut Innovations, DiA makes ultrasound analysis smarter and accessible to both new and expert ultrasound users with various levels of experience. The company’s flagship LVivo Cardio Toolbox for AI-based cardiac ultrasound analysis enables clinicians to automatically generate objective clinical analysis, with increased accuracy and efficiency to support decisions about patient treatment and care.

The IIA grant provides a budget of millions NIS to increase access to DiA’s solutions for users in Israel and globally, and accelerate R&D with a focus on new AI solutions for COVID-19 patient management. DiA solutions are vendor-neutral and platform agnostic, as well as powered to run in low processing, mobile environments like handheld ultrasound.Recent data highlights the importance of looking at the heart during the progression of COVID-19, with one study citing 20% of patients hospitalized with COVID-19 showing signs of heart damage and increased mortality rates in those patients. DiA’s LVivo cardiac analysis solutions automatically generate objective, quantified cardiac ultrasound results to enable point-of-care clinicians to assess cardiac function on the spot, near patients’ bedside.

According to Dr. Ami Applebaum, the Chairman of the Board of the IIA, “The purpose of IIA’s call was to bring solutions to global markets for fighting COVID-19, with an emphasis on relevancy, fast time to market and collaborations promising continuity of the Israeli economy. DiA meets these requirements with AI innovation for ultrasound.”DiA has received several FDA/CE clearances and established distribution partnerships with industry leading companies including GE Healthcare, IBM Watson and Konica Minolta, currently serving thousands of end users worldwide.”We see growing use of ultrasound in point of care settings, and an urgent need for automated, objective solutions that provide decision support in real time,” said Hila Goldman-Aslan, CEO and Co-founder of DiA Imaging Analysis, “Our AI solutions meet this need by immediately helping clinicians on the frontlines to quickly and easily assess COVID-19 patients’ hearts to help guide care delivery.”

About DiA Imaging Analysis:
DiA Imaging Analysis provides advanced AI-based ultrasound analysis technology that makes ultrasound accessible to all. DiA’s automated tools deliver fast and accurate clinical indications to support the decision-making process and offer better patient care. DiA’s AI-based technology uses advanced pattern recognition and machine-learning algorithms to automatically imitate the way the human eye detects image borders and identifies motion. Using DiA’s tools provides automated and objective AI tools, helps reduce variability among users, and increases efficiency. It allows clinicians with various levels of experience to quickly and easily analyze ultrasound images.

For additional information, please visit http://www.dia-analysis.com.

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Multiple Barriers Identified Which May Hamper Use of Artificial Intelligence in the Clinical Setting

Posted in Arrhythmia Detection with Machine Learning Algorithms, Artificial Intelligence - General, Artificial Intelligence Applications in Health Care, Artificial Intelligence in Medicine - Application for Diagnosis, Image Processing/Computing, tagged Artificial intelligence, Artificial Intelligence & Clinical Trials, Clinical trial, FDA, Machine Learning, pneumonia on July 21, 2019| Leave a Comment »

Multiple Barriers Identified Which May Hamper Use of Artificial Intelligence in the Clinical Setting

Reporter: Stephen J. Williams, PhD.

From the Journal Science:Science 21 Jun 2019: Vol. 364, Issue 6446, pp. 1119-1120

By Jennifer Couzin-Frankel

3.3.21

3.3.21 Multiple Barriers Identified Which May Hamper Use of Artificial Intelligence in the Clinical Setting, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair

In a commentary article from Jennifer Couzin-Frankel entitled “Medicine contends with how to use artificial intelligence” the barriers to the efficient and reliable adoption of artificial intelligence and machine learning in the hospital setting are discussed. In summary these barriers result from lack of reproducibility across hospitals. For instance, a major concern among radiologists is the AI software being developed to read images in order to magnify small changes, such as with cardiac images, is developed within one hospital and may not reflect the equipment or standard practices used in other hospital systems. To address this issue, lust recently, US scientists and government regulators issued guidance describing how to convert research-based AI into improved medical images and published these guidance in the Journal of the American College of Radiology. The group suggested greater collaboration among relevant parties in developing of AI practices, including software engineers, scientists, clinicians, radiologists etc.

As thousands of images are fed into AI algorithms, according to neurosurgeon Eric Oermann at Mount Sinai Hospital, the signals they recognize can have less to do with disease than with other patient characteristics, the brand of MRI machine, or even how a scanner is angled. For example Oermann and Mount Sinai developed an AI algorithm to detect spots on a lung scan indicative of pneumonia and when tested in a group of new patients the algorithm could detect pneumonia with 93% accuracy.

However when the group from Sinai tested their algorithm from tens of thousands of scans from other hospitals including NIH success rate fell to 73-80%, indicative of bias within the training set: in other words there was something unique about the way Mt. Sinai does their scans relative to other hospitals. Indeed, many of the patients Mt. Sinai sees are too sick to get out of bed and radiologists would use portable scanners, which generate different images than stand alone scanners.

The results were published in Plos Medicine as seen below:

PLoS Med. 2018 Nov 6;15(11):e1002683. doi: 10.1371/journal.pmed.1002683. eCollection 2018 Nov.

Variable generalization performance of a deep learning model to detect pneumonia in chest radiographs: A cross-sectional study.

Zech JR1, Badgeley MA2, Liu M2, Costa AB3, Titano JJ4, Oermann EK3.

Abstract

BACKGROUND:

There is interest in using convolutional neural networks (CNNs) to analyze medical imaging to provide computer-aided diagnosis (CAD). Recent work has suggested that image classification CNNs may not generalize to new data as well as previously believed. We assessed how well CNNs generalized across three hospital systems for a simulated pneumonia screening task.

METHODS AND FINDINGS:

A cross-sectional design with multiple model training cohorts was used to evaluate model generalizability to external sites using split-sample validation. A total of 158,323 chest radiographs were drawn from three institutions: National Institutes of Health Clinical Center (NIH; 112,120 from 30,805 patients), Mount Sinai Hospital (MSH; 42,396 from 12,904 patients), and Indiana University Network for Patient Care (IU; 3,807 from 3,683 patients). These patient populations had an age mean (SD) of 46.9 years (16.6), 63.2 years (16.5), and 49.6 years (17) with a female percentage of 43.5%, 44.8%, and 57.3%, respectively. We assessed individual models using the area under the receiver operating characteristic curve (AUC) for radiographic findings consistent with pneumonia and compared performance on different test sets with DeLong’s test. The prevalence of pneumonia was high enough at MSH (34.2%) relative to NIH and IU (1.2% and 1.0%) that merely sorting by hospital system achieved an AUC of 0.861 (95% CI 0.855-0.866) on the joint MSH-NIH dataset. Models trained on data from either NIH or MSH had equivalent performance on IU (P values 0.580 and 0.273, respectively) and inferior performance on data from each other relative to an internal test set (i.e., new data from within the hospital system used for training data; P values both <0.001). The highest internal performance was achieved by combining training and test data from MSH and NIH (AUC 0.931, 95% CI 0.927-0.936), but this model demonstrated significantly lower external performance at IU (AUC 0.815, 95% CI 0.745-0.885, P = 0.001). To test the effect of pooling data from sites with disparate pneumonia prevalence, we used stratified subsampling to generate MSH-NIH cohorts that only differed in disease prevalence between training data sites. When both training data sites had the same pneumonia prevalence, the model performed consistently on external IU data (P = 0.88). When a 10-fold difference in pneumonia rate was introduced between sites, internal test performance improved compared to the balanced model (10× MSH risk P < 0.001; 10× NIH P = 0.002), but this outperformance failed to generalize to IU (MSH 10× P < 0.001; NIH 10× P = 0.027). CNNs were able to directly detect hospital system of a radiograph for 99.95% NIH (22,050/22,062) and 99.98% MSH (8,386/8,388) radiographs. The primary limitation of our approach and the available public data is that we cannot fully assess what other factors might be contributing to hospital system-specific biases.

CONCLUSION:

Pneumonia-screening CNNs achieved better internal than external performance in 3 out of 5 natural comparisons. When models were trained on pooled data from sites with different pneumonia prevalence, they performed better on new pooled data from these sites but not on external data. CNNs robustly identified hospital system and department within a hospital, which can have large differences in disease burden and may confound predictions.

PMID: 30399157 PMCID: PMC6219764 DOI: 10.1371/journal.pmed.1002683

[Indexed for MEDLINE] Free PMC Article

Images from this publication.See all images (3)Free text

Surprisingly, not many researchers have begun to use data obtained from different hospitals. The FDA has issued some guidance in the matter but considers “locked” AI software or unchanging software as a medical device. However they just announced development of a framework for regulating more cutting edge software that continues to learn over time.

Still the key point is that collaboration over multiple health systems in various countries may be necessary for development of AI software which is used in multiple clinical settings. Otherwise each hospital will need to develop their own software only used on their own system and would provide a regulatory headache for the FDA.

Top 12 Artificial Intelligence Innovations Disrupting Healthcare by 2020

The launch of SCAI – Interview with Gérard Biau, director of the Sorbonne Center for Artificial Intelligence (SCAI).

Real Time Coverage @BIOConvention #BIO2019: Machine Learning and Artificial Intelligence #AI: Realizing Precision Medicine One Patient at a Time

50 Contemporary Artificial Intelligence Leading Experts and Researchers

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Real Time Coverage @BIOConvention #BIO2019: Precision Medicine Beyond Oncology June 5 Philadelphia PA

Posted in Big Data & Analytics, Data Science, Pharmaceutical R&D Informatics, REAL TIME Conference Coverage Twitter's Hashtags and Handles per Presentation/session, Scientific & Biotech Conferences: Press Coverage, Transcriptomics, tagged #pharmaIT, AI, Artificial Intelligence & Clinical Trials, Big data, Machine Learning, Neurological Disorders, Personalized and Precision Medicine & Genomic Research, Personalized medicine, precision medicine on June 5, 2019| Leave a Comment »

Real Time Coverage @BIOConvention #BIO2019: Precision Medicine Beyond Oncology June 5 Philadelphia PA

Reporter: Stephen J Williams PhD @StephenJWillia2

Speakers

Erin McCallisterSenior Editor at BioCentury

Jennifer CozzoneGlobal Personalised Healthcare Lead, Specialty Care atRoche

Aurélie DeleforgePrecision Medicine Practice Lead at Bionest Partners

Ms. elizabeth DonleyCEO at NeuroPointDX

Precision Medicine has helped transform cancer care from one-size-fits-all chemotherapy to a new era, where patients’ tumors can be analyzed and therapy selected based on their genetic makeup. Until now, however, precision medicine’s impact has been far less in other therapeutic areas, many of which are ripe for transformation. Efforts are underway to bring the successes of precision medicine to neurology, immunology, ophthalmology, and other areas. This move raises key questions of how the lessons learned in oncology can be used to advance precision medicine in other fields, what types of data and tools will be important to personalizing treatment in these areas, and what sorts of partnerships and payer initiatives will be needed to support these approaches and their ultimate commercialization and use. The panel will also provide an in depth look at precision medicine approaches aimed at better understanding and improving patient care in highly complex disease areas like neurology.

Speaker panel: The big issue now with precision medicine is there is so much data and hard to put experimental design and controls around randomly collected data.

The frontier is how to CURATE randomly collected data to make some sense of it
One speaker was at a cancer meeting and the oncologist had no idea what to make of genomic reports they were given. Then there is a lack of action or worse a misdiagnosis.
So for e.g. with Artificial Intelligence algorithms to analyze image data you can see things you can’t see with naked eye but if data quality not good the algorithms are useless – if data not curated properly data is wasted

Data needs to be organized and curated.

If relying of AI for big data analysis the big question still is: what are the rates of false negative and false positives? Have to make sure so no misdiagnosis.

Please follow LIVE on TWITTER using the following @ handles and # hashtags:

@Handles

@pharma_BI

@AVIVA1950

@BIOConvention

# Hashtags

#BIO2019 (official meeting hashtag)

#itstartswithone

#RightMixMatters

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Live Coverage: MedCity Converge 2018 Philadelphia: AI in Cancer and Keynote Address

Posted in Artificial Intelligence - Breakthroughs in Theories and Technologies, Artificial Intelligence Applications in Health Care, Big Data, BioIT: BioInformatics, Cancer - General, Cancer and Current Therapeutics, Cancer Informatics, Cancer Vaccines: Targeting Cancer Genes for Immunotherapy, Conference Coverage with Social Media, Health Care System by Country, HealthCare IT, Immuno-Oncology & Genomics, Personalized and Precision Medicine & Genomic Research, tagged Artificial intelligence, Artificial Intelligence & Clinical Trials, Cancer immunotherapy, Conference Coverage with Social Media, Meeting Report, Personalized and Precision Medicine & Genomic Research, personalized cancer therapy on July 11, 2018| Leave a Comment »

Live Coverage: MedCity Converge 2018 Philadelphia: AI in Cancer and Keynote Address

Reporter: Stephen J. Williams, PhD

3.3.4 Live Coverage: MedCity Converge 2018 Philadelphia: AI in Cancer and Keynote Address, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair

8:30 AM -9:15

Practical Applications of AI in Cancer

We are far from machine learning dictating clinical decision making, but AI has important niche applications in oncology. Hear from a panel of innovative startups and established life science players about how machine learning and AI can transform different aspects in healthcare, be it in patient recruitment, data analysis, drug discovery or care delivery.

Moderator: Ayan Bhattacharya, Advanced Analytics Specialist Leader, Deloitte Consulting LLP
Speakers:
Wout Brusselaers, CEO and Co-Founder, Deep 6 AI @woutbrusselaers ‏
Tufia Haddad, M.D., Chair of Breast Medical Oncology and Department of Oncology Chair of IT, Mayo Clinic
Carla Leibowitz, Head of Corporate Development, Arterys @carlaleibowitz
John Quackenbush, Ph.D., Professor and Director of the Center for Cancer Computational Biology, Dana-Farber Cancer Institute

Ayan: working at IBM and Thompon Rueters with structured datasets and having gone through his own cancer battle, he is now working in healthcare AI which has an unstructured dataset(s)

Carla: collecting medical images over the world, mainly tumor and calculating tumor volumetrics

Tufia: drug resistant breast cancer clinician but interested in AI and healthcareIT at Mayo

John: taking large scale datasets but a machine learning skeptic

moderator: how has imaging evolved?

Carla: ten times images but not ten times radiologists so stressed field needs help with image analysis; they have seen measuring lung tumor volumetrics as a therapeutic diagnostic has worked

moderator: how has AI affected patient recruitment?

Tufia: majority of patients are receiving great care but AI can offer profiles and determine which patients can benefit from tertiary care;

John: 1980 paper on no free lunch theorem; great enthusiasm about optimization algortihisms fell short in application; can extract great information from e.g. images

moderator: how is AI for healthcare delivery working at mayo?

Tufia: for every hour with patient two hours of data mining. for care delivery hope to use the systems to leverage the cognitive systems to do the data mining

John: problem with irreproducible research which makes a poor dataset: also these care packages are based on population data not personalized datasets; challenges to AI is moving correlation to causation

Carla: algorithisms from on healthcare network is not good enough, Google tried and it failed

John: curation very important; good annotation is needed; needed to go in and develop, with curators, a systematic way to curate medial records; need standardization and reproducibility; applications in radiometrics can be different based on different data collection machines; developed a machine learning model site where investigators can compare models on a hub; also need to communicate with patients on healthcare information and quality information

Ayan: Australia and Canada has done the most concerning AI and lifescience, healthcare space; AI in most cases is cognitive learning: really two types of companies 1) the Microsofts, Googles, and 2) the startups that may be more pure AI

Final Notes: We are at a point where collecting massive amounts of healthcare related data is simple, rapid, and shareable. However challenges exist in quality of datasets, proper curation and annotation, need for collaboration across all healthcare stakeholders including patients, and dissemination of useful and accurate information

9:15 AM–9:45 AM

Opening Keynote: Dr. Joshua Brody, Medical Oncologist, Mount Sinai Health System

The Promise and Hype of Immunotherapy

Immunotherapy is revolutionizing oncology care across various types of cancers, but it is also necessary to sort the hype from the reality. In his keynote, Dr. Brody will delve into the history of this new therapy mode and how it has transformed the treatment of lymphoma and other diseases. He will address the hype surrounding it, why so many still don’t respond to the treatment regimen and chart the way forward—one that can lead to more elegant immunotherapy combination paths and better outcomes for patients.

Speaker:
Joshua Brody, M.D., Assistant Professor, Mount Sinai School of Medicine @joshuabrodyMD

Director Lymphoma therapy at Mt. Sinai

lymphoma a cancer with high PD-L1 expression
hodgkin’s lymphoma best responder to PD1 therapy (nivolumab) but hepatic adverse effects
CAR-T (chimeric BCR and TCR); a long process which includes apheresis, selection CD3/CD28 cells; viral transfection of the chimeric; purification
complete remissions of B cell lymphomas (NCI trial) and long term remissions past 18 months
side effects like cytokine release (has been controlled); encephalopathy (he uses a hand writing test to see progression of adverse effect)

Vaccines

teaching the immune cells as PD1 inhibition exhausting T cells so a vaccine boost could be an adjuvant to PD1 or checkpoint therapy
using Flt3L primed in-situ vaccine (using a Toll like receptor agonist can recruit the dendritic cells to the tumor and then activation of T cell response); therefore vaccine does not need to be produced ex vivo; months after the vaccine the tumor still in remission
versus rituximab, which can target many healthy B cells this in-situ vaccine strategy is very specific for the tumorigenic B cells
HoWEVER they did see resistant tumor cells which did not overexpress PD-L1 but they did discover a novel checkpoint (cannot be disclosed at this point)