Innovative TechBio Ideas: AI/ML tools, startups, companies and investors
Innovative TechBio Ideas: AI/ML tools, startups, companies and investors
MetaphysicalCells: A newsletter about Science, Technology and AI Drug Discovery
Hi everyone and welcome back to MetaphysicalCells!
I want to give a big thank you 🌼 to all my subscribers and followers!
And to all those who are celebrating Easter this week, may you have a sunny, blessed and holy Easter 🐇🐣! I will be celebrating on 5 May, during the Orthodox Easter in Greece.
Today’s Quote
"Your synapses store all your knowledge and skills as roughly 100 terabytes’ worth of information, while your DNA stores merely about a gigabyte, barely enough to store a single movie download."
By Max Tegmark (Life 3.0: Being Human in the Age of Artificial Intelligence)
Fresh News 🎣
🐟 New AI Tool from bioXcelerate Set to Speed Up Drug Discovery
bioXcelerate AI is applying cutting-edge statistics, ML and software engineering in the health data science industry (PleioGraph, isGWAS, Evolutionary Alghoritms, MR-Clust and Network & Knowledge Graphs).
The health data science division of Optima Partners Limited, bioXcelerate, announced, in March 20, 2024, its new AI tool, PleioGraph, that can aid drug developers to identify genetic colocalization—the process by which genes, proteins, and cells interact with each other to cause disease.
Roche and AI Drug Discovery
According to a McKinsey Global Institute report, Generative AI—a type of AI that can produce various types of content: like text, imagery, audio and synthetic data—is transforming nearly all aspects of the pharmaceutical industry, revamping the way companies operate and potentially unlocking billions of dollars in value. In particular, they estimated that the technology could generate from $60 billion to $110 billion a year in economic value across the pharmaceutical industry value chain ⛓️:
Research and Early Discovery: 15-28 billion
scientific knowledge extraction, in silico compound screening, large molecule optimization and drug-vector design, indication selection for asset strategy and trial and portfolio optimization.
Clinical Development: 13-25 billion
trial performance copilot, smart data management, regulatory intelligence engine and major submission content writer.
Medical: 3-5 billion
customer insight generation, sharper more efficient medical writing and rapid summaries of scientific and medical literature.
Operations: 4-7 billion
augmented sourcing, generative AI virtual assistant for manufacturing, reimagined investigations in quality and no-touch planning & real time inventory optimization.
Enterprise: 8-16 billion
security, data governance and cost tracking.
Commercial: 18-30 billion
personalized content creation, medical and legal review assistance and automation, customer-enablement co-pilot, generating strategic insights and optimizing the patient experience.
Let’s see know in detail how an increase in collaboration between AI drug developers and Roche (and also Genentech, an independent subsidiary of Roche) can make a difference in the AI Drug Discovery R&D space: 🥂
Founded in 2002, the Roche Venture Fund is the corporate venture capital arm of Roche Holding based in Basel, Switzerland, that invests in early stage biotech and diagnostics companies to develop commercially successful innovative life science companies. Regarding TechBio and Drug Discovery they invest into:
⏩ Fabric Genomics is an AI-driven genomics software to accurately analyze whole genomes, exomes and gene panels. Founded in 2019—and partnered in 2013 with Artis Ventures—Fabric's analytic capabilities begin with raw data analysis and include the delivery of comprehensive insights from high throughput panels. On December 07, 2023, PlumCare RWE and Fabric Genomics partnered to deliver the Fabric AI platform with the PlumCare RWE FirstSteps newborn genome screening program in Greece.
⏩ Freenome is a biotechnology company based in South San Francisco that has pioneered the most comprehensive multiomics platform for early cancer detection with a simple blood test, combining tumor and non-tumor signals with ML to detect cancer in its earliest stages using a standard blood draw. In 2023, Freenome partnered with Geisinger for the Sanderson Study, a study that encompasses both traditional and real-world data to generate evidence of clinical validation. Freenome has raised more than $1.1 billion and on February 15, 2024 raised $254M in a new funding round led by Roche, to develop tests that can potentially detect multiple early-stage cancers.
⏩ Nimble Therapeutics is a biotechnology company inspired by Nature’s elegance and turbocharged by a paradigm-shifting peptide discovery & development engine, and has begun operating as a standalone business after spinning out from F. Hoffmann La Roche in 2019 with $10M in financing.
On January 5, 2023, Nimble Therapeutics announced that the company has expanded its collaboration and executed a license agreement with Genentech, a member of the Roche Group. In particular, Nimble and Genentech have been working together for a while to discover peptide therapies across multiple therapeutic areas, by using Nimble's iterative, data driven approach and an extensive in-house monomer library to navigate through a chemical space many orders of magnitude larger than what has previously been available. Genentech will pay out $20M to Nimble upfront.
On February, 13, 2024, Roche announced that it has entered into an agreement with PathAI—a global leader in AI powered technology for pathology—that will exclusively work with Roche Tissue Diagnostics (RTD) to develop AI-enabled digital pathology algorithms in the companion diagnostics space. The Boston Massachusetts-based PathAI, has the pathology market’s first algorithm to use additive multiple instance learning (aMIL)—the AIM-HER2 Breast Cancer—that delivers automated digital HER2 scoring. MIL models enable spatial credit assignment such that the contribution of each region in the image can be exactly computed and visualized, to provide greater transparency for how AI predictions are made. PathAI and Roche announced their first partnership in 2021 and the collaboration began with distributing PathAI’s research-use-only algorithms through the cloud version of Roche’s uPath software, with a focus on immuno-oncology for the treatment of multiple types of cancers. PathAI has raised a total of $355.2M in funding over 6 rounds.
On November 30, 2023, ShapeTX announced the expansion of its partnership with Roche—which was initially established in August 2021—marking the beginning of a new program where ShapeTX will use its proprietary AI-powered RNA editing platform to develop a potential one-time therapy for patients with high unmet needs for an undisclosed disease. Shape Therapeutics (Washington, US 2018) is a next-generation gene therapy platform that enables the development of cures in neurodegenerative disorders, oncology, metabolic and rare genetic diseases. This is done by using the ShapeTX gene therapy platform—RNAskipTM, RNAfixTM, RNAswitch payload technologies, next-generation tissue-specific AAVidTM delivery technology and SquareBio—a solution for scalable gene therapy manufacturing based on industrialisation of human stable cell lines. At the core of its technology is the ShapeTX AI analytics platform, where data drives decisions. Shape Therapeutics has raised a total of $147.5M.
On November 21, 2023, Roche’s Genentech partnered with the computing giant Nvidia in a multiyear deal that highlights the pharmaceutical industry’s growing hopes of using AI to speed up the process of designing and developing new drugs. The partnership will revolve around the use of Nvidia’s DGX Cloud and BioNemo offerings.
On October 26, 2023, Roche announced its collaborations with Ibex Medical Analytics and Amazon Web Services, enabling pathology laboratories to access Ibex's AI-powered decision support tools to support clinicians in breast and prostate cancer diagnosis through the navify Digital Pathology software platform. Ibex Medical Analytics Ltd in Israel, is offering the Galen Prostate—a Pathology AI associated/FDA approved device—and is using AI to develop clinical-grade algorithms and digital workflows that detect cancer as accurately as a human pathologist. On September 6, 2023, Ibex closed a $55M Series C financing round led by 83North. Additional participants in the round were Sienna Venture Capital and existing investors in the company, Octopus Ventures, aMoon, Planven Entrepreneur Ventures and Dell Technologies Capital. The financing brings the total funding to over $100M since Ibex’s inception in 2016.
On September 11, 2023, Herophilus announced that Genentech acquired its proprietary high-throughput human organoid-based drug discovery platform comprising the Orchard™, Orchestra™ and OrCA™ technologies. Herophilus (US, 2016) is reinventing neuro-drug discovery by combining human brain models, scaled biology and ML to systematically discover and develop novel drugs with greater therapeutic potential for complex brain diseases.
They use patient stem cell-derived brain organoids to model brain disease.
In particular, by using their advanced organoid technologies they generate brain region specific organoid models containing neural and glial cell type diversity, synaptic connectivity, tissue architecture and neural network activity. Their integrated automation, software and analytics platform supports long-term culture and assay of thousands of high quality and reproducible brain organoids, enabling them to harness the biological richness of brain organoid models. And by applying leading-edge data analytics and ML approaches they integrate large scale high-dimensional phenotypic datasets and create comprehensive systems biology descriptions of brain disease.
On July 8, 2022—less than a year after entering into a collaboration focused on using AI tools to improve the early detection of cancer—Roche and EarlySign expanded their partnership to include AI-powered lung cancer diagnosis. EarlySign's LungFlag software incorporates ML to analyze a variety of signals (basic demographic, medical, drug, and routine clinical lab data) and flag high-risk patients.
EarlySign’s proprietary ML based solutions analyze many of the “hidden” factors residing in electronic health records, including routine laboratory test results, demographics, medications and diagnostic codes to accurately identify individuals at higher risk of having or developing a specific disease or condition. Medial EarlySign has raised $50M.
In 2021, Roche partnered up with Cambridge Quantum, to employ Cambridge Quantum’s leading quantum chemistry platform EUMEN to augment the Alzheimer’s disease research efforts at Roche. Cambridge Quantum (Cambridge Cambridgeshire, UK 2014) develops tools for the commercialization of quantum computers by understanding quantum protocols and also quantum algorithms. Accordingly, Roche has prepared a task force to integrate quantum computing into its R&D via Roche’s pRED—Pharma Research and Early Development—initiative. Cambridge Quantum has raised a total of $72.8M.
In 2021, Roche and its Genentech division tapped data curation developer Flywheel—a data management platform for ML that allows you to standardize data curation and automate data preparation pipelines—to help train its ML models aimed at discovering potential new drugs. Flywheel (US, 2012) is a cloud-based company with a medical imaging AI platform that helps imaging/data scientists accelerate drug development initiatives and builds reliable, scalable medical imaging solutions that seamlessly integrate advanced AI technology from NVIDIA and other technology partners to enable robust imaging data management and analysis. On June 27, 2023, Flywheel announced it has raised $54M in Series D funding co-led by:
💠 Novalis LifeSciences LLC (a boutique investment and advisory firm) and NVentures, NVIDIA’s venture capital arm.
💠 Microsoft also participated in the round, along with insiders Invenshure, 8VC, Beringea, Hewlett Packard Enterprise, Intuitive Ventures, iSelect, Gundersen Health System, Seraph and Great North Ventures.
💠 Faegre Drinker Biddle & Reath LLP served as counsel to Flywheel in connection with the financing.
Flywheel was founded in 2015 and the company has raised $110M in total.
On December 7, 2021, Recursion announced a transformational collaboration with Roche and Genentech, in order for Recursion to work with both Roche and Genentech's R&D units to leverage technology-enabled drug discovery through the Recursion Operating System (OS). Under the terms of the agreement, Recursion will receive an upfront payment of $150M while Roche and Genentech (combined) may initiate up to 40 programs, each of which, if successfully developed and commercialized, could yield more than $300M in development, commercialization and net sales milestones for Recursion, as well as tiered royalties on net sales.
Recursion Pharmaceutical (Utah US, 2013) has at its headquarters clusters of robots that treat millions of cells per week with drugs, stain them with six dyes and then take pictures to capture and quantify as many morphological features as they can. By pushing these data through a ML pipeline, they hope to find relationships that are invisible to the human and to tease out clusters of effects that can guide their drug discovery. Recursion has raised a total of $665.4M.
Moreover, Recursion in 2023 entered into agreements to acquire Cyclica and Valence, two companies in the AI-enabled drug discovery space. Subsequently, Recursion announced a collaboration and a $50M investment from NVIDIA. Then Recursion launched Valence Labs, formerly Valence Discovery, a company with roots at Mila and mentorship from Yoshua Bengio (a Canadian computer scientist, most noted for his work on AI networks and DL), dedicated to advancing DL in drug discovery, delivering impactful research and transformative technology and embracing open-source and open-science knowledge sharing with the ML community.
On October 2, 2023, just over one and a half years into the exciting collaboration with Roche and Genentech, Recursion announced that they have reached the first milestone: after building fit-for-purpose oncology maps for their partner spanning whole-genome arrayed CRISPR knockouts and hundreds of thousands of small molecules, they have identified and validated the first hit series for this particular disease, and Roche has exercised the Small Molecule Validation Program Option.
In 2020, Roche Canada launched the Roche AI Centre of Excellence (CoE), a collaborative center to combine the expertise of three national AI institutes: the Amii, Mila and the Vector Institute. The CoE focuses on advancing AI based digital solutions that optimize and reduce the cost of healthcare delivery and improve health outcomes.
✳ Part of Amii is DrugBank, one of Canada’s fastest growing health tech companies, that provides data solutions for healthcare companies working in precision medicine, drug discovery, drug repurposing and clinical software applications. DrugBank offers products, such as structured clinical and scientific data to pharma companies such as Healx, Aria Pharmaceuticals and Molecular Health.
✳ In 2022 Yoshua Bengio—who founded in 1983 what was to become the Mila Institute (Quebec Institute for Artificial Intelligence)—was the third among the most recognised and influential researchers in the field of AI, according to Stanford University’s ranking.
✳ In 2023, “The Vector Institute has released its list of Canadian AI startups to watch in 2023”, a report highlighting 20 Canadian AI startup companies to watch over the next 12 months, in the health, drug discovery and transportation space.
In 2020, Genesis Therapeutics—a Stanford University spinout company—announced that it has entered into a multi-target collaboration agreement with Genentech to leverage Genesis’ graph ML and drug discovery expertise. Genesis Therapeutics’ (South San Francisco, California, US 2019) platform—GEMS: Genesis Exploration of Molecular Space—integrates DL and molecular simulations for property prediction, and language models for molecular generation:
Dynamic PotentialNet of GEMS predicts potency, selectivity and ADMET even for data-poor and previously undruggable targets.
In addition to these predictive models, GEMS uses chemically aware ML models that can be directed to create novel molecules and explore specific regions of chemical space for each drug program. During Hit ID, GEMS generates billions of drug-like and synthetically accessible molecules, enabling a diverse exploration of chemical space.
During Hit-to-Lead and Lead Optimization, their chemists direct GEMS to generate novel molecules from a specific starting point, to explore scaffold hops and optimize promising series.
In 2023, Genesis announced that it closed an oversubscribed $200M round of Series B financing. This funding brings the total capital raised by Genesis Therapeutics to over $280M, from top technology and biotech investors, including
⚙ Fidelity,
⚙ BlackRock and
In 2020, Reverie Labs announced a multi-target collaboration agreement with Roche and Genentech. Reverie Labs will use its unique technology platform to perform virtual screening, hit-to-lead generation and lead optimization on several kinase inhibitor discovery programs. At Reverie Labs (Boston Massachusetts, US 2017) they regularly enumerate and screen millions of compounds in their virtual libraries for hit identification, they employ simulation techniques to understand the energetics of bound ligands to their protein targets & to design superior kinase inhibitors, they predict important molecular properties (including on-target binding, toxicity & ADMET) and many more. Reverie Labs has raised a total of $32M.
On 28 February 2024, Ginkgo Bioworks announced the acquisition of key assets of Reverie Labs. Ginkgo has acquired Reverie's infrastructure and software for training large-scale AI foundation models and four of Reverie's key AI team members will join Ginkgo.
In October 2020, it was announced a collaboration between Roche and Cambridge Massachusetts based Dyno Therapeutics—to develop gene therapies using AI—valued at up to $1.8 billion. Dyno Therapeutics founded in 2018 in US, is transforming the gene therapy landscape with AI-powered AAV vectors, such as Dyno bCap 1™ capsid product, a breakthrough central nervous system (CNS)-targeted AAV gene delivery vector that provides dramatically improved CNS delivery and liver detargeting—when compared to leading natural capsids—and stronger all-around characteristics relative to other engineered CNS-IV capsids. Moreover, in 2023 Dyno launched Dyno eCap 1™ capsid product, a leading eye AAV gene delivery vector that provides significantly improved delivery to the eye compared to other externally engineered capsids, including transduction throughout multiple layers of the retina. Dyno places a big emphasis on collaboration, and already has partnerships with Roche, Astellas Pharma, Novartis, Spark Therapeutics and Sarepta Therapeutics. In 2021, Dyno Therapeutics closed a $100M series A financing led by Andreessen Horowitz (for a total of $109M over 2 rounds).
In 2019, Oxford-based Exscientia announced a partnership with Roche worth up to €60M. Exscientia agreed to use its AI drug discovery platform Centaur Chemist to discover preclinical candidates for Roche. Exscientia Ltd (Oxford UK, 2012) is the first company to automate drug design and it’s one of the six companies Winning the Race to Get AI-Designed Drugs to the Clinic. Exscientia has raised a total of $474.4M.
In 2018, Roche Diagnostics and Genialis announced a partnership to help biologists tackle any issues with next generation RNA-sequencing and analysis workflow-related issues. Genialis (Texas US, 2011) is developing next-generation patient classifiers using ML and high-throughput omics data and they offer: Genialis ResponderID—a biomarker discovery platform—and the Genialis Expressions software—that enables ML driven biomarker discovery by aggregating consistently analyzed and annotated data. The Genialis Expressions software is built on FAIR—findability, accessibility, interoperability and reusability—data management principles, in order to analyze sequencing data across numerous NGS platforms. Genialis has raised a total of $15.5M.
Also in 2018, Roche paid $1.9 billion for Flatiron's army of electronic health record curators. Flatiron Health was founded in 2012 and became an independent affiliate of the Roche Group in 2018 following its acquisition by Roche.
In 2017, Genentech announced its collaboration with GNS Healthcare, in order to use the GNS REFS™—Reverse Engineering and Forward Simulation—causal ML and simulation platform to find and validate potential new oncology drug candidates, and also collaborate to unlock knowledge from various data resources such as longitudinal electronic medical records, next generation sequencing and other omic data. GNS Healthcare (Cambridge Massachusetts, US 2000) had the first in silico multiple myeloma patient called Gemini—namely a computer model of disease progression and drug response at individual patient level. The Gemini Digital Twin will be used also during the GNS and Servier AI collaboration, to advance multiple myeloma drug discovery and clinical development. GNS Healthcare has raised a total of $77.3M.
GNS Healthcare as of January 9, 2023 is Aitia Bio. Aitia—derived from the Greek word for causality—will focus on further leveraging its Gemini Digital Twins to discover the next generation of breakthrough drugs to improve outcomes for patients.
For the second part of this newsletter: “Innovative TechBio Ideas: AI/ML tools, startups, companies and investors (2nd part)”.