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Archive for the ‘Artificial Intelligence – Breakthroughs in Theories and Technologies’ Category

DeepSeek-V3 and Reasoning Model R1: Four Views (a) Explanations (b) The Chinese Perspective (c) DeepSeek Impact on Demand for Inference Chips & Training Chips, and (d) LPBI Group: Expert Content for ML Models in Healthcare, Pharmaceutical, Medical and Life Sciences

Curator: Aviva Lev-Ari, PhD, RN

With the announcement of DeepSeek on January 27, 2025, it became compelling to cover several aspects of this hot Artificial Intelligence Technology.

This curation has four Parts: 

Part A: Explanations 

Part B: The Chinese Perspective

Part C: DeepSeek potential Impact on Demand for Inference Chips & Training Chips, and

Part D: LPBI Group: Expert Content for ML Models in Healthcare, Pharmaceutical, Medical and Life Sciences

 

Part A: Explanations by Morgan Brown

@morganb

Jan 27   Read on X

🧵 Finally had a chance to dig into DeepSeek’s r1…

Let me break down why DeepSeek’s  AI innovations are blowing people’s minds (and possibly threatening Nvidia’s $2T market cap) in simple terms… 

0/ first off, shout out to @doodlestein who wrote the must-read on this here:

The Short Case for Nvidia StockAll the reasons why Nvidia will have a very hard time living up to the currently lofty expectations of the market.https://youtubetranscriptoptimizer.com/blog/05_the_short_case_for_nvda

1/ First, some context: Right now, training top AI models is INSANELY expensive. OpenAI, Anthropic, etc. spend $100M+ just on compute. They need massive data centers with thousands of $40K GPUs. It’s like needing a whole power plant to run a factory. 

2/ DeepSeek just showed up and said “LOL what if we did this for $5M instead?” And they didn’t just talk – they actually DID it. Their models match or beat GPT-4 and Claude on many tasks. The AI world is (as my teenagers say) shook. 

3/ How? They rethought everything from the ground up. Traditional AI is like writing every number with 32 decimal places. DeepSeek was like “what if we just used 8? It’s still accurate enough!” Boom – 75% less memory needed. 

4/ Then there’s their “multi-token” system. Normal AI reads like a first-grader: “The… cat… sat…” DeepSeek reads in whole phrases at once. 2x faster, 90% as accurate. When you’re processing billions of words, this MATTERS. 

5/ But here’s the really clever bit: They built an “expert system.” Instead of one massive AI trying to know everything (like having one person be a doctor, lawyer, AND engineer), they have specialized experts that only wake up when needed.

[color added by curator, See Part D, below]

6/ Traditional models? All 1.8 trillion parameters active ALL THE TIME. DeepSeek? 671B total but only 37B active at once. It’s like having a huge team but only calling in the experts you actually need for each task. 

7/ The results are mind-blowing:
– Training cost: $100M → $5M
– GPUs needed: 100,000 → 2,000
– API costs: 95% cheaper
– Can run on gaming GPUs instead of data center hardware 

8/ “But wait,” you might say, “there must be a catch!” That’s the wild part – it’s all open source. Anyone can check their work. The code is public. The technical papers explain everything. It’s not magic, just incredibly clever engineering. 

9/ Why does this matter? Because it breaks the model of “only huge tech companies can play in AI.” You don’t need a billion-dollar data center anymore. A few good GPUs might do it. 

10/ For Nvidia, this is scary. Their entire business model is built on selling super expensive GPUs with 90% margins. If everyone can suddenly do AI with regular gaming GPUs… well, you see the problem. 

11/ And here’s the kicker: DeepSeek did this with a team of <200 people. Meanwhile, Meta has teams where the compensation alone exceeds DeepSeek’s entire training budget… and their models aren’t as good. 

12/ This is a classic disruption story: Incumbents optimize existing processes, while disruptors rethink the fundamental approach. DeepSeek asked “what if we just did this smarter instead of throwing more hardware at it?” 

13/ The implications are huge:
– AI development becomes more accessible
– Competition increases dramatically
– The “moats” of big tech companies look more like puddles
– Hardware requirements (and costs) plummet 

14/ Of course, giants like OpenAI and Anthropic won’t stand still. They’re probably already implementing these innovations. But the efficiency genie is out of the bottle – there’s no going back to the “just throw more GPUs at it” approach. 

15/ Final thought: This feels like one of those moments we’ll look back on as an inflection point. Like when PCs made mainframes less relevant, or when cloud computing changed everything.

 AI is about to become a lot more accessible, and a lot less expensive. The question isn’t if this will disrupt the current players, but how fast.

/end 

P.S. And yes, all this is available open source. You can literally try their models right now. We’re living in wild times! 🚀 

Momma, I’m going viral! No substack or gofundme to share but a few things to add/clarify:

1/ The DeepSeek app is not the same thing as the model. Apps are owned and operated by a Chinese corporation, the model itself is open source.

2/ Jevon’s paradox is the counter argument. Thanks papa @satyanadella. Could be a mix shift in chip type, compute type, etc. but we’re constrained by power and compute right now, not demand constrained.

3/ The techniques used are not ground breaking. It’s the combination of them w/the relative model performance that is so exciting. These are common eng techniques that combined really fly in the face of more compute is the only answer for model performance. Compute is no longer a moat.

4/ Thanks to all for pointing out my NVIDIA market cap numbers miss and other nuances – will do better next time, coach. 🫡 

SOURCE

https://threadreaderapp.com/thread/1883686162709295541.html#google_vignette

 

Part B: The Chinese Perspective

© 2025 Jordan Schneider

DeepSeek: The View from China

China’s takes are better than yours

 

SOURCE

From: ChinaTalk <chinatalk@substack.com> on behalf of ChinaTalk <chinatalk@substack.com>
Reply-To: ChinaTalk <reply+2ktto4&8t4ds&&6fa8442469b96573268378f7538ff49c28c45589f5811b2a55b30e89ee8ff94d@mg1.substack.com>
Date: Tuesday, January 28, 2025 at 9:54 AM
To: Aviva Lev-Ari <avivalev-ari@alum.berkeley.edu>
Subject: DeepSeek: The View from China

And

https://www.chinatalk.media/p/deepseek-the-view-from-china

https://open.substack.com/pub/chinatalk/p/deepseek-the-view-from-china?r=8t4ds&utm_campaign=post&utm_medium=email

The Mystical DeepSeek. ‘The most important thing about DeepSeek is pushing intelligence’

  1. Founder and CEO Liang Wenfeng is the core person of DeepSeek. He is not the same type of person as Sam Altman. He is very knowledgeable about technology.
  2. DeepSeek has a good reputation because it was the first to release the reproducible MoE, o1, etc. It succeeded in acting early, but whether or not it did the absolute best remains to be seen. Moving forward, the biggest challenges are that resources are limited and can only be invested in the most high-potential areas. DeepSeek’s research and culture are still strong, and if given 100,000 or 200,000 chips, they might be able to do better.
  3. From its preview to its official release, DeepSeek’s model’s long-context capabilities have improved rapidly. DeepSeek’s long-context 20K can be achieved with very conventional methods.
  4. The CEO of Scale.ai said that DeepSeek has 50,000 chips, but that is definitely not reality. According to public information, DeepSeek had 10,000 old A100 chips and possibly 3,000 H800 cards before the ban. DeepSeek pays great attention to compliance and has not purchased any non-compliant GPUs, so it should have few chips. The way the United States uses GPUs is too extravagant.
  5. DeepSeek focused all its efforts on a single goal and subsequently gave up many things, such as multimodality. DeepSeek is not just serving people, but seeking intelligence itself, which may have been a key factor in its success.
  6. In some ways, quant trading can be said to be the business model of DeepSeek. Huanfang (another quantitative investment company founded by Liang Wenfeng) is the product of the last round of machine learning. DeepSeek’s highest priority is to push intelligence. Money and commercialization are not high priorities. China needs several leading AI labs to explore things that can beat OpenAI. Intelligence takes a long time to develop, and has begun to differentiate again this year, so new innovations are bound to result.
  7. From a technical perspective, DeepSeek has been instrumental as a training ground for talent.
  8. The business model of AI labs in the United States is not good either. AI does not have a good business model today and will require viable solutions in the future. Liang Wenfeng is ambitious; DeepSeek does not care about the model and is just heading towards AGI.
  9. Many of the insights from DeepSeek’s paper involve saving hardware costs. On a couple of big dimensions of scaling, DeepSeek’s techniques are able to reduce costs.
  10. In the short-term, everyone will be driven to think about how to make AI more efficient. In the long-run, questions about computing power will remain. Demand for compute remains strong and no company has enough.
  11. Discussing DeepSeek’s organization:
    1. When investing, we always choose the most advanced talent. But we see from DeepSeek’s model (the team is mostly smart young people who graduated from domestic universities) that a group that coheres well may also gradually advance their skills together. It has yet to be seen whether poaching one person might break DeepSeek’s advantage, but for now this seems unlikely.
    2. While there’s a lot of money in the market, DeepSeek’s core advantage is its culture. The research culture of DeepSeek and ByteDance are similar, and both are critical for determining the availability of funding and long-term viability. Only with an important business model can there be a sustainable culture. Both DeepSeek and ByteDance have very good business models.
  12. Why did DeepSeek catch up so fast?
    1. Reasoning models require high-quality data and training. For LLMs or multimodal AI, it’s difficult to catch up with a closed source model from scratch. The architecture of pure reasoning models hasn’t changed much, so it’s easier to catch up in reasoning.
    2. One reason R1 caught up quickly was that the task was not particularly difficult. Reinforcement learning only made the model choices more accurate. R1 did not break through the efficiency of Consensus 32, spending 32 times the efficiency, which is equivalent to moving from deep processing to parallelization, which is not pushing the boundaries of intelligence, just making it easier.

Pioneers vs. Chasers: ‘AI Progress Resembles a Step Function – Chasers Require 1/10th the Compute’

Points 13 – 17

[Points 18-48 was a long technical discussion we’ve machine-translated below]

Why didn’t the other companies take the DeepSeek approach: ‘Models from the big labs need to maintain a low profile’

Points 49, 50

The Divergence and Bets of 2025 Technology: ‘Can We Find Architectures Beyond Transformer?’

Points 51 – 56

Have developers moved from closed-source models to DeepSeek? ‘Not yet’

Points 57 – 62

OpenAI Stargate’s $500B Narrative and Changes in Computing Power Demand

  1. The emergence of DeepSeek has led people to question the latest $500B narrative from Nvidia and OpenAI. There’s no verdict yet on compute — and OpenAI’s $500B narrative is their attempt to throw themselves a lifeline.
  2. Regarding the doubts about OpenAI’s $500B infrastructure investment: because OpenAI is a commercial company, it could be risky if debt is involved.
  3. $500B is an extreme number — likely to be executed over 4 or 5 years. SoftBank and OpenAI are the leading players (the former providing capital, the latter technology) — but SoftBank’s current funds can’t support $500B; rather SoftBank is using its assets as collateral. OpenAI, meanwhile, isn’t very cash-rich either, and other AI companies are more technical participants than they are funding providers. So it will be a struggle to fully realize the $500B vision.
  4. OpenAI’s $500B computing power makes sense: during the exploration phase, the cost of trial and error is high, with both human and investment costs being substantial. But although the path isn’t clear and getting from o1 to R1 won’t be easy, at least we can see what the finish line looks like: we can track the intermediate markers, and from day one, aim for others’ proven end states; this gives us a better bearing on our progress. Being at the frontier exploring the next generation is most resource-intensive. The followers don’t bear exploration costs — they’re always just following. If Google/Anthropic succeed in their exploration areas, they might become the frontier company.
  5. In the future, Anthropic might replace all their inference with TPU or AWS chips.
  6. Domestic Chinese companies were previously constrained by computing power, but now it’s proven that the potential technical space is vast. For more efficient models, we might not need especially large cards — we can provide relatively customized chips that can be adapted for compatibility with AMD and ASIC. From an investment perspective, Nvidia’s moat is very high, but ASIC will have yet greater opportunities.
  7. The DeepSeek situation isn’t really about compute — it’s about America realizing China’s capabilities and efficiency.DeepSeek isn’t Nvidia’s vulnerability; Nvidia will grow as long as AI grows. Nvidia’s strength is its ecosystem, which has been built up over a long time. Indeed, when technology develops rapidly, the ecosystem is crucial. The real crisis comes, though, when technology matures like electricity: it becomes commoditized; then, everyone will focus on products, and many ASIC chips will emerge for specific scenario optimization.

 

Impact on the Secondary Market: ‘Short-term sentiment is under pressure, but the long-term narrative continues’

Points 70 – 74

Open-Source vs Closed Source: ‘If capabilities are similar, closed source will struggle.’

Points 75 – 78

The Impact of DeepSeek’s Breakthrough: ‘Vision Trumps Technology’

  1. DeepSeek’s breakthrough made the outside world realize China’s AI strength. Previously, outsiders thought China’s AI progress lagged America by two years, but DeepSeek shows the gap is actually 3 to 9 months, and in some areas, even shorter.
  2. When it comes to technologies and sectors that America has historically blocked China from accessing, if China can break through nonetheless, those sectors ultimately become highly competitive. AI might follow this pattern — and DeepSeek’s success may well prove this.
  3. DeepSeek didn’t suddenly explode. R1’s impressive results reverberated throughout America’s entire AI establishment.
  4. DeepSeek stands on the shoulders of giants — but exploring the frontier still requires much more time and human capital cost. R1 doesn’t mean that future training costs will decrease.
  5. AI explorers definitely need more computing power; China, as a follower, can leverage its engineering advantages. How Chinese large-model teams use less computing power to produce results, thereby having some definite resilience — or even doing better — might end up being how the US-China AI landscape plays out in the future.
  6. China is still replicating technical solutions; reasoning was proposed by OpenAI in o1, so the next gap between various AI labs will be about who can propose the next reasoning. Infinite-length reasoning might be one vision.
  7. The core difference between different AI labs’ models lies not in technology, but in what each lab’s next vision is.
  8. After all, vision matters more than technology.

Technical Discussion

There was a deep technical discussion in the article that we’ve machine-translated below.

Technical Detail 1: Supervised Fine-Tuning (SFT). ‘No need for SFT on the reasoning level’

Points 18 – 27

Technical Detail 2: Data. ‘DeepSeek values data annotation’

Points 28 – 30

Technical Detail 3: Distillation. ‘The limit of distillation is that model diversity drops

Points 31 – 43

Technical Detail 4: Process Reward. ‘The upper limit of process reward is human, but the upper limit of outcome supervision is the model itself.’

Points 44 – 48

 

SOURCE of the Chinese Perspective

https://www.chinatalk.media/p/deepseek-the-view-from-china?utm_source=substack&publication_id=4220&post_id=155916148&utm_medium=email&utm_content=share&utm_campaign=email-share&triggerShare=true&isFreemail=true&r=8t4ds&triedRedirect=true

 

Part C: DeepSeek Impact on Demand for “Inference Chips” and “Training Chips”

 

Watch Full Interviews with Ark’s Cathie Wood

 

  • Ark’s Wood on DeepSeek, AI, Crypto, Trump | Cathie Wood Full Interview

https://youtu.be/EKELCEW8lNo?si=Zri9QqcMHsESgO8N

 

  • Cathie Wood Talks DeepSeek Lessons, Musk, Driverless Cars & UK

https://youtu.be/aThejSuMX-I?si=e9uM7TpoQ1Neb-cT

 

“Inference Chips” and “Training Chips”: Technology explained

 

AI Chips Explained: Training vs. Inference Processors Unveiled

https://www.friendsofthemetaverse.com/blog/ai-chips-explained-training-vs-inference-processors-unveiled

 

Inference chips and training chips are both types of AI chips that serve different purposes. Training chips are used to develop AI models, while inference chips are used to deploy those models in real-world applications. 

An “inference chip” is designed to efficiently execute a trained AI model on new data to make predictions in real-time, prioritizing low latency and power consumption, while a “training chip” is optimized for the computationally intensive process of initially training a machine learning model, requiring high processing power and memory bandwidth, often at the cost of power efficiency; essentially, inference chips are for “applying” the learned model, while training chips are for “learning” the model itself. 

 

SOURCE

https://www.google.com/search?q=training+chips+vs+inference+chips&oq=Training+Chips+vs+Inference+chips&gs_lcrp=EgZjaHJvbWUqBggAEEUYOzIGCAAQRRg7Mg0IARAAGIYDGIAEGIoFMg0IAhAAGIYDGIAEGIoFMg0IAxAAGIYDGIAEGIoFMgoIBBAAGIAEGKIEMgoIBRAAGIAEGKIEMgoIBhAAGIAEGKIEMgoIBxAAGIAEGKIE0gEKMTc2OTVqMGoxNagCCLACAQ&sourceid=chrome&ie=UTF-8

 

Training vs. Inference (But, Really: Training Then Inference)

To recap: the AI training stage is when you feed data into your learning algorithm to produce a model, and the AI inference stage is when your  algorithm uses that training to make inferences from data. Here’s a chart for quick reference: 

Table

Inference

Feed training data into a learning algorithm

Apply the model to the inference data

Produces a model comprising code and data

Produces output data

One time-ish (Requirement to retain training data in case of re-training.)

Often continuous

Inference

Apply the model to the inference data

Produces output data

Often continuous

The difference may seem inconsequential at first glance, but defining these two stages helps to show implications for AI adoption particularly with businesses. That is, given that it’s much less resource intensive (and therefore, less expensive), it’s likely to be much easier for businesses to integrate already-trained AI algorithms with their existing systems. 

And, as always, we’re big believers in demystifying terminology for discussion purposes. Let us know what you think in the comments, and feel free to let us know what you’re interested in learning about next.

SOURCE

AI 101: Training vs. Inference

November 9, 2023 by Stephanie Doyle

https://www.backblaze.com/blog/ai-101-training-vs-inference/

 

r/AMD_Stock

“AI is really two markets, training and inference. Inference is going to be 100 times bigger than training. Nvidia is really good at training but very miscast at inference.” – Chamath Palihapitiya

Let’s discuss.

Below I layout AMD investor relevant time stamps:

7:35 – Meta AI business strategy

10:00 – Open source impact on LLM marketplace

12:10 – Telecom analogy (capex discussion)

16:35 – Closed source model economic viability

19:50 – Meta overspend on training (Nvidia)

SOURCE

https://www.reddit.com/r/AMD_Stock/comments/1cf765y/ai_is_really_two_markets_training_and_inference/

 

Part D: LPBI Group: Expert Content for ML Models in Healthcare, Pharmaceutical, Medical and Life Sciences

 

LPBI Group’s Journal http://pharmaceuticalintelligence.com had a fully developed ontology for the Healthcare, Pharmaceutical, Medical and Life Sciences domains of knowledge.

The ontology comprises of +750 categories of research. Each category consists of multiple scientific articles that were curated by domain knowledge experts in the fields of Healthcare, Pharmaceutical, Medical and Life Sciences.

  • Each article is a token, a Non Fungible Token (NFT) = a mutually exclusive scientifically written piece that makes a Prior Art artifact from the intellectual property law perspective and copyright law.
  • Each category of research is “An expert system knowledge base”
  • Examples: The last column in this table represents the number of articles in this category of research
  • Each curation is written by an expert in this domain, and
  • Each one of the 469 articles in Example #1, in this category of research had been assigned THIS category by an EXPERT in this domain. 
  • The universe of 469 articles represents an “Expert System Knowledge Base” in the domain of biological networks, gene regulation and evolution
  • Example #1 comprises of 469 NFTs
  • Example #2 comprises of 1,022 NFTs
  • Example #3 comprises of 681 NFTs
  • An ML model can be trained on the content of a Master file that included the content of all the 469 article files mentioned in Example #1 – that process is performed on Training Chips
  • The outcomes of the model involve the phase of Inference. That process is performed on Inference Chips.

 

Example #1: 469 articles in Biological Networks, Gene Regulation and Evolution

Expert, Author, Writer (EAW): Dr. Larry Bernstein
Degree: BS, MS, MD
Specialty: Clinical Pathology
e-Mail: larry.bernstein@gmail

N = 469

Biological Networks, Gene Regulation and Evolution

 

Points (a) to (f) are applicable as well to Example #2, and #3, below. Or for any other category of research from the universe of +750 categories that consists of +50 articles

 

Example #2: 1,022 articles in CANCER BIOLOGY & Innovations in Cancer Therapy

Contributor EAW: Prabodh kumar Kandala, PhD Specialty: Preclinical Oncology, Prabodh.kandala@gmail.com

Contributor EAW: Ritu Saxena, PhD
ritu.uab@gmail.com

Contributor EAW: Dr. Larry Bernstein
Degree: BS, MS, MD
Specialty: Clinical Pathology
e-Mail: larry.bernstein@gmail.com

Contributor EAW: Stephen J. Williams
Degree: Ph.D. Pharmacology
Specialty: cancer pharmacology, ovarian specialty
e-Mail: sjwilliamspa@comcast.net
Phone: 215-487-0259

Contributor EAW: Tilda Barliya
Degree: PhD
Specialty: Cancer biology, cell biology, nanotechnology and drug delivery
e-Mail: tildabarliya@gmail.com
Phone: +972-50-8622289

N = 1,022

CANCER BIOLOGY & Innovations in Cancer Therapy

 

Example #3: 681 articles in Frontiers in Cardiology and Cardiovascular Disorders

EAW: Aviva Lev-Ari, PhD, RN

EAW: Justin D. Pearlman
Degree: MD ME PhD MA FACC
Specialty: Internal Medicine, Cardiology, Cardiovascular Radiology, Image Processing, Computer Science, Electronic Records
jdpmdphd@gmail.com
Phone:617-894-6888

N = 681

Frontiers in Cardiology and Cardiovascular Disorders

 

Respectively, the categories of research are

  • “Expert systems domain knowledge bases”
  • They are ready for ML model development in each of the domains that a category comprises more than 50 articles.
  • Total number of categories of research in the Journal’s Ontology N = 757 on 1/28/2025

Read Full Post »

Coverage Afternoon Session on Precision Oncology: Advancing Precision Medicine Annual Conference, Philadelphia PA November 1 2024

Reporter: Stephen J. Williams, Ph.D.

Unlocking the Next Quantum Leap in Precision Medicine – A Town Hall Discussion (CME Eligible)

Co-Chairs

Amanda Paulovich, Professor, Aven Foundation Endowed Chair
Fred Hutchinson Cancer Center

Susan Monarezm Deputy Director ARPA-H

Henry Rodriguez, NCI/NIH

Eric Schadt, Pathos

Ezra Cohen, Tempus

Jennifer Leib, Innovation Policy Solutions

Nick Seddon, Optum Genomics

Giselle Sholler, Penn State Hershey Children’s Hospital

Janet Woodcock, formerly FDA

Amanda Paulovich: Frustrated by the variability in cancer therapy results.  Decided to help improve cancer diagnostics

  •  We have plateaued on relying on single gene single protein companion diagnostics
  • She considers that regulatory, economic, and cultural factors are hindering the innovation and resulting in the science way ahead of the clinical aspect of diagnostics
  • Diagnostic research is not as well funded as drug discovery
  • Biomarkers, the foundation for the new personalized medicine, should be at forefront Read the Tipping Point by Malcolm Gladwell
  • FDA is constrained by statutory mandates 

 

Eric Schadt

Pathos

 

  • Multiple companies trying to chase different components of precision medicine strategy including all the one involved in AI
  • He is helping companies creating those mindmaps, knowledge graphs, and create more predictive systems
  • Population screening into population groups will be using high dimensional genomic data to determine risk in various population groups however 60% of genomic data has no reported ancestry
  • He founded Sema4 but many of these companies are losing $$ on these genomic diagnostics
  • So the market is not monetizing properly
  • Barriers to progress: arbitrary evidence thresholds for payers, big variation across health care system, regulatory framework

 

Beat Childhood Cancer Consortium Giselle

 

  • Consortium of university doctors in pediatrics
  • They had a molecular tumor board to look at the omics data
  • Showed example of choroid plexus tumor success with multi precision meds vs std chemo
  • Challenges: understanding differences in genomics test (WES, NGS, transcriptome etc.
  • Precision medicine needs to be incorporated in med education.. Fellowships.. Residency
  • She spends hours with the insurance companies providing more and more evidence to justify reimbursements
  • She says getting that evidence is a challenged;  biomedical information needs to be better CURATED

 

Dr. Ezra Cohen, Tempest

 

  • HPV head and neck cancer, good prognosis, can use cituximab and radiation
  • $2 billion investment at Templest of AI driven algorithm to integrate all omics; used LLM models too

Dr. Janet Woodcock

 

  • Our theoretical problem with precision and personalized medicine is that we are trained to think of the average patient
  • ISPAT II trial a baysian trial; COVID was a platform trial
  • She said there should there be NIH sponsored trials on adaptive biomarker platform trials

This event will be covered by the LPBI Group on Twitter.  Follow on

@Pharma_BI

@StephenJWillia2

@Aviva1950

@AdvancingPM

using the following meeting hashtags

#AdvancingPM #precisionmedicine

Read Full Post »

Nobel Prize in Physics 2024 to J.J. Hopfield and to G.E. Hinton

Reporter: Aviva Lev- Ari, PhD, RN 

 

UPDATED on 10/19/2024

Why the Nobel Prize in Physics Went to AI Research 

Nobel committee recognizes scientists for foundation research in neural networks

 

The Nobel Prize Committee for Physics caught the academic community off-guard by handing the 2024 award to John J. Hopfield and Geoffrey E. Hinton for their foundational work in neural networks.

The pair won the prize for their seminal papers, both published in the 1980s, that described rudimentary neural networks. Though much simpler than the networks used for modern generative AI like ChatGPT or Stable Diffusion, their ideas laid the foundations on which later research built.

Even Hopfield and Hinton didn’t believe they’d win, with the latter telling The Associated Press he was “flabbergasted.” After all, AI isn’t what comes to mind when most people think of physics. However, the committee took a broader view, in part because the researchers based their neural networks on “fundamental concepts and methods from physics.”

“Initially, I was surprised, given it’s the Nobel Prize in Physics, and their work was in AI and machine learning,” says Padhraic Smyth, a distinguished professor at the University of California, Irvine. “But thinking about it a bit more, it was clearer to me why [the Nobel Prize Committee] did this.” He added that physicists in statistical mechanics have “long thought” about systems that display emergent behavior.

Hopfield first explored these ideas in a 1982 paper on neural networks. He described a type of neural network, later called a Hopfield network, formed by a single layer of interconnected neurons. The paper, which was originally categorized under biophysics, said a neural network could retain “memories” from “any reasonably sized subpart.”

Hinton expanded on that work to conceptualize the Boltzmann machine, a more complex neural network described in a 1985 paper Hinton co-authored with David H. Ackley and Terrence J. Sejnowski. They introduced the concept of “hidden units,” additional layers of neurons which exist between the input and output layers of a neural network but don’t directly interact with either. This makes it possible to handle tasks that require a more generalized understanding, like classifying images.

So, what’s the connection to physics?

Hopfield’s paper references the concept of a “spin glass,” a material in which disordered magnetic particles lead to complex interactions. Hinton and his co-authors drew on statistical mechanics, a field of physics that uses statistics to describe the behavior of particles in a system. They even named their network in honor of Ludwig Boltzmann, the physicist whose work formed the foundation of statistical mechanics.

And the connection between neural networks and physics isn’t a one-way street. Machine learning was crucial to the discovery of the Higgs boson, where it sorted the data generated by billions of proton collisions. This year’s Nobel Prize for Chemistry further underscored machine learning’s importance in research, as the award went to a trio of scientists who built an AI model to predict the structures of proteins.

While Hopfield and Hinton authored influential papers, their contributions to machine learning were cemented by their continued work, and both won multiple awards before the Nobel Prize. Among others, Hopfield won the Boltzmann Medal in 2022; Hinton received the IEEE Frank Rosenblatt Award in 2014, the IEEE James Clerk Maxwell Medal in 2016, and the Turing Award in 2018 (that last one alongside Yann LeCun and Yoshua Bengio).

Smyth saw Hopfield’s efforts first-hand as a student at the California Institute of Technology. “Hopfield was able to bring together mathematicians, engineers, computer scientists, and physicists. He got them in the same room, got them excited about modeling the brain, doing pattern recognition and machine learning, unified by mathematical theories he brought in from physics.”

In 2012, Hinton co-founded a company called DNNResearch with two of his students; Ilya Sutskever, who later co-founded OpenAI, and Alex Krizhevsky. Together, the trio collaborated on AlexNet, a hugely influential neural network for computer vision. Hinton also taught at the University of Toronto, where he continued to champion machine learning.

Navdeep Jaitly, now a deep learning researcher at Apple, said Hinton inspired new generations of engineers and researchers. In Jaitly’s case, the influence was direct; Jaitly studied under Hinton at the University of Toronto.

“I came in with experience in statistical modeling,” says Jaitly, “but Hinton still managed to entirely change how I think about problem solving. In terms of his contributions to machine learning, his methods are central to almost everything we do.”

SOURCE

https://spectrum.ieee.org/nobel-prize-in-physics

 

UPDATED on 10/13/2024

Website: https://www.bbc.co.uk/newsnight

https://youtu.be/MGJpR591oaM?si=6DhusxGt_B8dUpT_

 

10/8/2024

John J. Hopfield
Princeton University, NJ, USA

Born 1933 in Chicago, IL, USA. PhD 1958 from Cornell University, Ithaca, NY, USA. Professor at Princeton University, NJ, USA.

Geoffrey E. Hinton
University of Toronto, Canada

Born 1947 in London, UK. PhD 1978 from The University of Edinburgh, UK. Professor at University of Toronto, Canada.

was announced on 10/8/2024 in Stockholm, Sweden.

“for foundational discoveries and inventions that enable machine learning with artificial neural networks”

They trained artificial neural networks using physics

This year’s two Nobel Laureates in Physics have used tools from physics to develop methods that are the foundation of today’s powerful machine learning. John Hopfield created an associative memory that can store and reconstruct images and other types of patterns in data. Geoffrey Hinton invented a method that can autonomously find properties in data, and so perform tasks such as identifying specific elements in pictures.

John Hopfield invented a network that uses a method for saving and recreating patterns. We can imagine the nodes as pixels. The Hopfield network utilises physics that describes a material’s characteristics due to its atomic spin – a property that makes each atom a tiny magnet. The network as a whole is described in a manner equivalent to the energy in the spin system found in physics, and is trained by finding values for the connections between the nodes so that the saved images have low energy. When the Hopfield network is fed a distorted or incomplete image, it methodically works through the nodes and updates their values so the network’s energy falls. The network thus works stepwise to find the saved image that is most like the imperfect one it was fed with.

Geoffrey Hinton used the Hopfield network as the foundation for a new network that uses a different method: the Boltzmann machine. This can learn to recognise characteristic elements in a given type of data. Hinton used tools from statistical physics, the science of systems built from many similar components. The machine is trained by feeding it examples that are very likely to arise when the machine is run. The Boltzmann machine can be used to classify images or create new examples of the type of pattern on which it was trained. Hinton has built upon this work, helping initiate the current explosive development of machine learning.

Reference

Popular science background: They used physics to find patterns in information (pdf)


Scientific background: “For foundational discoveries and inventions that enable machine learning with artificial neural networks” (pdf)

 

SOURCE

https://www.nobelprize.org/prizes/physics/2024/press-release/

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Israeli vendor AISAP gained FDA clearance for its new AI-enabled, point-of-care ultrasound (POCUS) software platform, AISAP Cardio

Reporter: Aviva Lev-Ari, PhD, RN

FDA clears AI-powered POCUS platform for structural heart disease, heart failure

Read Full Post »

Drug Development Process been Revolutionized by Artificial Intelligence (AI) Technologies

Curators: Stephen J. Williams, PhD and Aviva Lev-Ari, PhD, RN

 

The Voice of Stephen J. Williams, PhD

LPBI Group, CSO

PENDING

The Voice of Aviva Lev-Ari, PhD, RN

1.0 LPBI Group and 2.0 LPBI Group, Founder

With the advent of AI in the last 5-7 years in our fields: Pharmaceutical, Life Sciences and Medicine, LPBI Group had launched several initiatives to advance the frontier of knowledge by using our own contents repositories of +8 giga bytes for experimenting with Machine Learning (ML) technologies for Medical Text Analysis.

These AI Technologies include

  • Natural Language Processing (NLP): Statistical ML and Deep Learning ML
  • ChatGPT and GPT-4
  • Generative AI
A quote by Brad Power, Co-founder and CEO, Cancer Patient Lab made in January 2024
LPBI Group is in the admirable position of sitting on a treasure trove of medical literature that would be useful input in the current environment of customized ChatGPTs looking for reliable medical content.

In the Drug Development (DD) field, AI technologies are been employed  chiefly, for these tasks:

(a) Generation of molecular information libraries

(b) Explorations and combinatorial experiments on protein structures, and

(c) measurements of biochemical interactions

The A.I. learns from patterns in the data to suggest possible useful drug candidates, as if matching chemical keys to the right protein locks.

Because A.I. for drug development is powered by precise scientific data, toxic “hallucinations” are far less likely than with more broadly trained chatbots. And any potential drug must undergo extensive testing in labs and in clinical trials before it is approved for patients.

“Generative A.I. is transforming the field, but the drug-development process is messy and very human,” said David Baker, a biochemist and director of the Institute for Protein Design at the University of Washington.

As of December 2023,

  • 24 AI-discovered molecules had completed Phase I trials, with 21 of them being successful. This success rate of 80–90% is higher than the historical industry average of 40–65%. 
  • In Phase II trials, the success rate is around 40%, which is similar to the historical average. 

SOURCE

AI Overview

https://www.google.com/search?q=A.I.-developed+drugs+are+in+clinical+trials&oq=A.I.-developed+drugs+are+in+clinical+trials&gs_lcrp=EgZjaHJvbWUyBggAEEUYOTIHCAEQIRigATIHCAIQIRigATIHCAMQIRigAdIBCTIxNzZqMGoxNagCCLACAQ&sourceid=chrome&ie=UTF-8

 

Examples of drugs developed by AI technologies:

NCI definition of AI Drugs:

AI drug

A drug that blocks the activity of an enzyme called aromatase, which the body uses to make estrogen in the ovaries and other tissues. Blocking aromatase lowers the amount of estrogen made by the body, which may stop the growth of cancer cells that need estrogen to grow. AI drugs are used to treat some types of breast cancer or to keep it from coming back. They may also be used to help prevent breast cancer in some women who are at a high risk of developing it. Examples of AI drugs are anastrozole, letrozole, and exemestane. AI drugs are a type of hormone therapy. Also called aromatase inhibitor.
 

SOURCE

https://www.cancer.gov/publications/dictionaries/cancer-terms/def/ai-drug

 

More examples of AI Drugs, Drugs developed with AI technologies

#1: 

INS018_055
Developed by Insilico Medicine, a Hong Kong-based biotech startup, to treat idiopathic pulmonary fibrosis (IPF). IPF is a chronic lung disease that causes scarring and can be fatal if left untreated. In January 2023, Insilico Medicine announced positive results from a Phase I safety trial of INS018_055. In February 2023, the FDA granted breakthrough status to a small molecule inhibitor identified by Insilico Medicine’s AI platforms for the drug. As of November 2023, INS018_055 was in mid-stage trials in the US and China, with some results expected in early 2025.
 
The first fully A.I. -generated drug enters clinical trials in human patients. Insilico Medicine, a Hong Kong-based biotech startup with more than $400 million in funding, created the drug as a treatment for idiopathic pulmonary fibrosis, a chronic lung disease.Jun 29, 2023
 
  • Schrödinger’s AI-driven platform
    Uses predictive modeling to optimize the molecular structure of drugs. AI is expected to integrate more advanced simulation techniques, such as quantum computing, to more accurately predict molecular behavior.

Drug discovery software developer Schrodinger Inc. (NASDAQ: SDGR) stock has been trying to recover after plummeting over 80% off its all-time high of $117 in January 2021. Schrodinger’s artificial intelligence (AI) powered software technology platform utilizes physics-based modeling and sophisticated machine learning algorithms to help clients identify the suitable molecules to treat the desired ailments. Its programs can help predict the behavior of molecules and potential outcomes.

This entails finding suitable molecules that effectively target specific cells and proteins, transcend through cell walls, are absorbed and dissolved well without interfering with other drugs or producing bad reactions to other drugs, and are scalable.

Big Name Pharma Customers of Schrödinger, Inc.

Its technology platform allows for the faster and cheaper discovery of novel molecules with a higher success rate than traditional methods. Its clients include the top 20 pharmaceutical companies in the world, including Pfizer Inc. (NYSE: PFE)Merck & Co. Inc. (NYSE: MRK), Takeda, AstraZeneca PLC (NYSE: AZN), and GlaxoSmithKline plc  (NYSE: GSK). It closed new agreements with Eli Lilly & Co. (NYSE: LLY) and Otsuka Pharmaceuticals out of Tokyo, Japan.

SOURCE

Schrodinger is an AI-Powered Drug Discovery Developer to Watch

https://www.nasdaq.com/articles/schrodinger-is-an-ai-powered-drug-discovery-developer-to-watch

 

Schrodinger’s Pipelines include:

  • SGR-1505 (MALT1)

Hematologic Malignancies

DISCOVERYPRECLINICALPHASE 1
 
  • SGR-2921 (CDC7)

AML/MDS

DISCOVERYPRECLINICALPHASE 1
 
  • SGR-3515 (Wee1/Myt1)

Solid Tumors

DISCOVERYPRECLINICALPHASE 1
 
  • SOS1

Oncology

DISCOVERYPRECLINICALPHASE 1
 
  • PRMT5-MTA

Oncology

DISCOVERYPRECLINICALPHASE 1
 
  • EGFRC797S

Oncology

DISCOVERYPRECLINICALPHASE 1
 
  • NLRP3

Immunology

DISCOVERYPRECLINICALPHASE 1
 
  • LRRK2

Neurology

DISCOVERYPRECLINICALPHASE 1
 
  • Undisclosed Programs

Multiple Areas

SOURCE

https://www.schrodinger.com/pipeline/#Proprietary-Pipeline

 

In high-tech labs, workers are generating data to train A.I. algorithms to design better medicine, faster. But the transformation is just getting underway.

Terray Therapeutics campus in Monrovia, Calif., June 17, 2024

https://www.nytimes.com/2024/06/17/business/ai-drugs-development-terray.html?smid=nytcore-ios-share&referringSource=articleShare

 

Five AI drug discovery companies you should know about

  1. Atomwise 
  2. Cradle 
  3. Exscientia 
  4. Iktos 
  5. Insilico Medicine 

According to Grand View Research, the global AI in drug discovery market size was valued at $1.1 billion in 2022, and is expected to expand at a compound annual growth rate (CAGR) of 29.6% from 2023 to 2030. The report states that the growing demand for the discovery and development of novel drug therapies and increasing manufacturing capacities of the life science industry are driving the demand for AI-empowered solutions in the drug discovery processes. 

As this report suggests, AI for drug discovery is clearly a growing field within the biopharma industry. Inevitably, as it grows even larger, we will see more companies come to the forefront of the field, hoping to change the face of drug discovery – and also the biopharma industry as a whole – so that the entire drug development process can become faster, more consistent, more accurate, and more scalable.

SOURCE

https://www.labiotech.eu/best-biotech/ai-drug-discovery-companies/#:~:text=to%20%2433%20million.-,Exscientia,manner%20using%20its%20AI%20technology.

 

At LPBI Group, Of Note is our Journal PharmaceuticalIntelligence.com

it represents our commitment to AI technologies in the following research categories and How many articles have been written in each of these topics: 

  • A total of x articles have been categorized 511 times among the following Artificial Intelligence research categories

Artificial Intelligence – General

113

An executive’s guide to AI

9

Artificial Intelligence – Breakthroughs in Theories and Technologies

94

Artificial Intelligence Applications in Health Care

81

Artificial Intelligence in CANCER

29

Artificial Intelligence in Health Care – Tools & Innovations

55

Artificial Intelligence in Medicine – Application for Diagnosis

44

Artificial intelligence applications for cardiology

21

AI-assisted Cardiac MRI

9

Artificial Intelligence in Psychiatry

5

Artificial Intelligence in Medicine – Applications in Therapeutics

50

 

LPBI Group’s involvement in Conceptual Drug Development covers the following two areas:

DrugDiscovery @LPBI Group, 2016 – 2018

Synthetic Biology in Drug Discovery, 2021 – Present

 

Applications of Artificial Intelligence to Medicine

Artificial Intelligence: Genomics & Cancer, 2021 – Present

Medicine with GPT-4 & ChatGPT, 2023 – Present

 

LPBI Group commitment to Medical Text Analysis using Machine Learning

2021-2025 Medical Text Analysis (NLP), 2020 – Present

ChatGPT + Wolfram PlugIn, 2023 – Present

 

LPBI Group Team members published two books on Drug Delivery Technologies

We had covered drug delivery technologies in two of our books. See all the Books: 

https://www.amazon.com/s?k=Aviva+Lev-Ari&i=digital-text&rh=n%3A133140011&ref=nb_sb_noss

 

  • Series E, Volume Four 

Medical 3D BioPrinting – The Revolution in Medicine, Technologies for Patient-centered Medicine: From R&D in Biologics to New Medical Devices. 

https://www.amazon.com/dp/B078QVDV2W

and

  • Series C, Volume Two 

Cancer Therapies: Metabolic, Genomics, Interventional, Immunotherapy and Nanotechnology in Therapy Delivery (Series C Book 2).

http://www.amazon.com/dp/B071VQ6YYK

 

The Table of Contents of these two book can be found in our

Spanish-language Edition, as well

  • Serie E, Volumen 4

Bioimpresión médica en 3D: la revolución de la medicina: Tecnologías para una medicina centrada en el paciente: de la I+D en agentes biológicos a los nuevos … en el paciente nº 4) (Spanish Edition) 2023

(Spanish Edition) Kindle Edition

https://www.amazon.com/dp/B0BRNVDB1P $56

 

  • Serie C, Volumen 2

Tratamientos contra el cáncer: Metabólicos, genómicos, intervencionistas, inmunoterapia y nanotecnología para la administración de tratamientos (Serie … y la oncología nº 2) 2022

(Spanish Edition) Kindle Edition

http://www.amazon.com/dp/B0BQTM44SM $75

Read Full Post »

Live Notes from JP Morgan Healthcare Conference Virtual Endpoints Preview: January 8-9 2024

Reporter: Stephen J. Williams, Ph.D.

Endpoints at #JPM24 | Primed to unlock biopharma’s next dealmaking wave
Endpoints at JP Morgan Healthcare Conference
January 8-9 | San Francisco, CA80 Mission St, San Francisco, CA

An oasis has emerged in the biopharma money desert as backers look to replenish capital — still, uncertainty remains on whether it’s a mirage or the much needed dealmaking bump the industry needs. Yet spirits run high as JPM24 marks the triumphant return of inking strategic alliances and peering into the industry crystal ball — while keeping an eye out for some major M&A.

We’re back live from San Francisco for JPM Monday and Tuesday — our calendar of can’t-miss panels and fireside chats will feature prominent biopharma leaders to watch. The Endpoints Hub provides the ultimate coworking space with everything you need — 1:1 and group meeting spots plus guest pass capabilities and more. Join us in-person at the Endpoints Hub or watch online to stay plugged into all the action.

8 JAN
Welcome remarks
8:05 AM – 8:25 AM PST
Pfizer vet Mikael Dolsten has some thoughts on Big Pharma R&D

Endpoints News founding editor John Carroll will sit down with longtime Pfizer CSO Mikael Dolsten to talk about Pfizer’s pipeline, what he’s learned on the job about preclinical research and development and what’s ahead for the pharma giant in drug development and deals.

Mikael Dolsten

Chief Scientific Officer, President, Pfizer Research & Development

Pfizer

Pfizer Mikael Dolsten: Pfizer produced a series of AI generated molecules with new properties. Sees rapid adoption of AI in the area of drug discovery and molecular design.

 
 
8:25 AM – 9:05 AM PST
What pharma wants: The industry’s dealmakers look ahead at 2024

The drug industry’s appetite for new assets hasn’t slowed down. Top business development execs will give their outlook on the year, what they’re looking for and how they see the market.

Glenn Hunzinger

Pharmaceutical & Life Sciences Consulting Solutions Leader

PwC US

Rachna Khosla

SVP, Head of Business Development

Amgen

James Sabry

Global Head of Pharma Partnering

Roche

Devang Bhuva

SVP, Corporate Development

Gilead Sciences, Inc.

Endpoints News

Dealmaking panel

Glenn Hunzinger: if you do not have a GLP1 will have a tough time getting a good market price for your company; capital markets are not where they want to be; sees a tough deal making climate like last year.  The problem with many biotech companies are they are coming earlier to the venture capital because of greater funding needs and so it is imperative that they articulate the potential of their company in scientific detail

Rachna Khosla:  Make sure your investors are not just CAPITAL PARTNERS but use their expertise and involve them in development issues you may have, especially ones that a young firm will face.  The problem is most investments assume what the future looks like (for example how antibody drug conjugates, once a field left for dead, has been rejuvenated because of advances in chemistry). 

James Sabry: noted that cardiac and metabolic drugs are now at the focus of many investors, especially with the new anti-obesity drugs on market

Devang Bhuva: Most deals we see start as collaborations or partnerships.  You want to involve an alliance management team early in the deal making process.  This process could take years.

 
9:05 AM – 9:20 AM PST
The IPO: How Apogee Therapeutics went public in the most challenging market in years

Not many biotechs went public in 2023. And of those that did, not many have had a great time of it. Apogee is the exception and our panel will offer a behind-the-scenes look at their decision to enter the market and what life is like as a young public company.

Michael Henderson

CEO

Apogee Therapeutics

Kyle LaHucik

MODERATOR

Senior Reporter

Endpoints News

Michael Henderson:  Not many biotech IPOs deals happened in 2023.  Michael feels it is because too many biotechs focused on building platforms, which was a hard sell in 2023.  He felt not many biotechs had clear milestones and investors wanted a clear primary validated target.  He said many biotech startups are in a funding crunch and most need at least $440M on their balance sheet to get to 2026.

9:50 AM – 10:10 AM PST
Top predictions for biotech in 2024

Catalent CEO Alessandro Maselli will be back at the big JPM healthcare confab to talk with Endpoints News founder John Carroll about their top predictions of what’s coming up for the biotech industry in 2024. The stakes couldn’t be higher as the industry grapples with headwinds and new opportunities in a gale of market forces. Two top observers share their thoughts on the year ahead.

Alessandro Maselli

President & CEO

Catalent

10:15 AM – 10:35 AM PST
Innovation at a crossroads: Keys to unlocking the value of science and technology

The industry has long discussed the promise of technology and the acceleration it provides in scientific advancement and across the industry value chain. However, the promise of its impact has yet to fully be realized. This discussion will outline the keys to unleashing this promise and the implications and actions to be taken by the biopharmaceutical companies across the industry.

Ray Pressburger

North America Life Sciences Industry Lead & Global Life Sciences Strategy Lead

Accenture

SPONSORED BY

10:35 AM – 11:05 AM PST
Activism and Investing: In conversation with Elliott Investment Management’s Marc Steinberg

Elliott has been behind many of 2023’s highest-profile healthcare investments, including multiple activist engagements and taking Syneos Health private. What has made large healthcare companies such interesting investment opportunities for firms like Elliott? What’s Elliott’s investing strategy in healthcare? And what should companies expect when an activist calls?

Marc Steinberg

Senior Portfolio Manager

Elliott Investment Management

Andrew Dunn

MODERATOR

Biopharma Correspondent

Endpoints News

11:05 AM – 11:35 AM PST
Creating ROI from AI

AI is predicted to transform the way drugs are made, from discovery to clinical trials to market. But beyond the initial hype and early adoption, where has AI made meaningful contributions to R&D? How does it help drug developers advance science? Endpoints publisher Arsalan Arif is convening a panel of leading experts to discuss the state of AI in the pharmaceutical landscape and the outlook for 2024. How does AI impact the drug pipeline, from the early steps of discovery to reducing trial failure rate?

Thomas Clozel

Co-Founder & CEO

Owkin

Venkat Sethuraman

SVP, Global Biometrics & Data Sciences

Bristol Myers Squibb

Frank O. Nestle

Global Head of Research & Chief Scientific Officer

Sanofi

Matthias Evers

Chief Business Officer

Evotec

Arsalan Arif

MODERATOR

Founder & Publisher

Endpoints News

SPONSORED BY

11:35 AM – 12:00 PM PST
Biopharma’s dealmaker: Behind the scenes with Centerview Partners co-president Eric Tokat

Almost every major biopharma deal in 2023 had Centerview’s name attached to it. And much of the time, Eric Tokat was the banker making those deals happen. Hear his outlook for 2024, how transactions are getting done and what’s placed his firm at the center of so much action.

E. Eric Tokat

Co-President, Investment Banking

Centerview Partners

CenterView Partners Eric Tokat feels dealmaking will improve in 2024, given the recent flurry of dealmaking at end of last year and right before main JPM Healthcare Conference.  He says Centerview wants to help the biotechs they invest in on their strategic path.  This may translate into buyers more actively involved (more than startups want) and buyers now are in the drivers seat as far as the timeline of deals and development.

Is the megamerger dead for this year?  He says it is very hard to see two major mergers happening but there will be many smaller and mid size biotech deals happening, but these deals will be more speculative in nature..  The focus for large pharma is top line growth.  Most of the buyers have an infrastructure and value is more of buying and dropping it in their business so there is now a huge emphasis on due diligence on whether synergies exist or not

 
12:00 PM – 12:30 PM PST
Founder, legend, leader: In conversation with Nobel laureate Carolyn Bertozzi

Carolyn Bertozzi’s discoveries around bioorthogonal chemistry won the Nobel Prize in Chemistry in 2022 and are at the heart of new therapies being tested in patients. Join us as we discuss what inspires her and where she sees the next big advances.

Carolyn Bertozzi

Prof. of Chemistry, Stanford University and Baker Family Director of Sarafan ChEM-H

Stanford University

Nicole DeFeudis

MODERATOR

Editor

Endpoints News

Bioorthogonal chemistry: class of high yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions toward endogenous functions.  This is also a type of ‘click chemistry’ in biological system where only specifically alter the biomolecule of interest.

Orthogonal: two chemicals not interacting with each other

Dr. Bertozzi noted she has started a new Antibody-Drug-Conjugate (ADC) company which involves designing with biorthogonal chemistry to make new functional molecules with varying properties

She noted hardly any biologists knew anything about glycobiology when she first started.  However now she feels pharma and academia are working very well with each other

Bioorthogonal and Click Chemistry
Curated by Prof. Carolyn R. Bertozzi, 2022 winner of the Nobel Prize in Chemistry

Source: https://pubs.acs.org/page/vi/bioorthogonal-click-chemistry

The 2022 Nobel Prize in Chemistry has been awarded jointly to ACS Central Science Editor-in-Chief, Carolyn R. Bertozzi of Stanford University, Morten Meldal of the University of Copenhagen, and K. Barry Sharpless of Scripps Research, for the development of click chemistry and bioorthogonal chemistry.

To celebrate this remarkable achievement, 2022 Nobel Prize winner Professor Carolyn R. Bertozzi has curated this Bioorthogonal and Click Chemistry Virtual Issue, highlighting papers published across ACS journals that have built upon the foundational work in this exciting area of chemistry.

From Mechanism to Mouse: A Tale of Two Bioorthogonal Reactions

Ellen M. Sletten and Carolyn R. Bertozzi* Acc. Chem. Res. 2011, 44, 9, 666-676 August 15, 2011

Abstract

Bioorthogonal reactions are chemical reactions that neither interact with nor interfere with a biological system. The participating functional groups must be inert to biological moieties, must selectively reactive with each other under biocompatible conditions, and, for in vivo applications, must be nontoxic to cells and organisms. Additionally, it is helpful if one reactive group is small and therefore minimally perturbing of a biomolecule into which it has been introduced either chemically or biosynthetically. Examples from the past decade suggest that a promising strategy for bioorthogonal reaction development begins with an analysis of functional group and reactivity space outside those defined by nature. Issues such as stability of reactants and products (particularly in water), kinetics, and unwanted side reactivity with biofunctionalities must be addressed, ideally guided by detailed mechanistic studies. Finally, the reaction must be tested in a variety of environments, escalating from aqueous media to biomolecule solutions to cultured cells and, for the most optimized transformations, to live organisms.

9 JAN

9:40 AM – 10:10 AM PST

Biotech downturn survival school

Our panelists have seen the worst, and made it through to the other side. Join us for downturn survival school as our panelists talk about what sets apart the ones who make it through tough times.

These panalists think it will be specialist capital year to shine while the general capital is still sitting on the sidelines

JJ Kang

CEO

Appia Bio

“2023 was a tough year while 2020 was a boon year to start a company.  We will continue to see these cycles; many of these new CEOs have never seen a biotech downturn yet and may not know how to preserve capital for the downturn”.

“Doing a partnership with Kite Pharmaceuticals early in our startp allowed us to get work done without risking a lot of capital, even if it means equity and asset dilution.  That makes sense. However even if you are small insist on being an equal partner.”

“There are many investors we talk to who do not want to invest in cell therapy.  Too risky now”

Carl Gordon

Managing Partner

OrbiMed Advisors

There are many macroeconomic factors affecting investment and capital today which will carry on through 2024.   Not raising money when you do not need money is a bad philosophy.  Always bbe raising captial.  This is especially true when you have to rely on hedge funds.  Parnerships howeve are sometimes the only way for small biotechs to leverage their strengths.

Joshua Boger

Executive Chair

Alkeus Pharmaceuticals, Inc.

Boger: Expect volatility for 2024.  This environment feels very different than past downturns.

Even in downturns there is still lots of capital; remember access to human capital is better in a downturn and is easier to access;  however it has become harder to get drug approvals

The panelists agree that access to capital and funding will be as tricky in 2024 than 2023.  They did

suggest that a new funding avenue, private credit, may be a source of capital.  This is discussed below:

When thinking about a private alternative investment asset class, the first thing that springs to mind is private equity. But there’s one more asset class with the word private in its name that has recently gained much attention. We’re talking about private credit

Indeed, this once little-known investment strategy is now growing rapidly in popularity, offering private investors worldwide an exciting opportunity to diversify their portfolio with, in theory, less risky investments that yield significant returns. 

  • Private credit investments refer to investors lending money to companies who then repay the loan at a given interest rate within the predetermined period.
  • The private credit market has grown significantly over the past years, rising from $875 million in 2020 to $1.4 trillion at the beginning of 2023. 

Please WATCH VIDEO BY GOLDMAN SACHS ON PRIVATE CREDIT

 

 

 

 

10:50 AM – 11:20 AM PST

The New Molecule: How breakthrough technologies are actually changing pharma R&D

Join us for a look at how AI, machine learning and generative technologies are actually being applied inside drugmakers’ labs. We’ll explore how new technologies are being used, their implications, how they intersect with regulatory and IP issues and how this fast-changing field is likely to evolve.

Kailash Swarna

Managing Director & Global Life Sciences Clinical Development Lead

Accenture

Artificial Intelligence is making impact in a grand way on biology in three aspects:

  1. Speeding up target validation: now we can get through 300 molecules a day
  2. Predicition like AlphaFold is doing; molecular simulations
  3. Document submission especially with regulatory and IND submissions

Pamela Carroll

COO

Isomorphic Labs formerly of AlphaFold

We were first with Novartis at last year JPM and was one year old but parnering with them in that initial year was very important for sealing the deal.

They are looking now at neurologic diseases like ALS.  She wondered whether ALS is actually multiple diseases and we need to stratify patients like we do in oncology trials.  Their main competion is the whole tech world like Amazon, Google and other Machine Learning companies so being a tech player in the biotech world means you are not just competing with other biotechs but large tech companies as well.

Jorge Conde

General Partner

Andreessen Horowitz

Need is still great for drug discovery; early adopters show AI tools can be used in big pharma. There are lots of applications of AI in managing care; a lot of back office applications including patient triaging.  He does not see big AI mergers with pharma companies –  this will be mainly partnerships not M&A deals

Alicyn Campbell

Chief Scientific Officer

Evinova, a Healthtech Subsidiary of the AstraZeneca Group

There is a need to turn AI for real world example.  For example AI tools were used in clinical trials to determine patient cohorts with pneumonitis.  At Evinova they are determining how AI can hel[p show clinical benefit with respect to efficacy and safety

Joshua Boger at #JPM24 (Brian Benton Photography)

  January 12, 2024 09:06 AM ESTUpdated 10:00 AM PeopleStartups

Vertex founder Joshua Boger on surviving downturns, ‘painful’ partnerships, and the importance of culture: #JPM24

Andrew Dunn

Biopharma Correspondent

Source: https://endpts.com/jpm24-vertex-founder-joshua-boger-on-surviving-downturns-painful-partnerships-and-the-importance-of-culture/

While the JP Morgan Healthcare Conference was full of voices of measured optimism, rooting for the market to bounce back in 2024, one longtime biotech leader warned against setting any firm expectations.

Instead of predicting when the downturn may end, Vertex Pharmaceuticals founder Joshua Boger said he advises biotech leaders to expect — and plan for — volatility. Speaking Tuesday on an Endpoints News panel alongside OrbiMed’s Carl Gordon and Appia Bio CEO JJ Kang, Boger shared lessons learned on surviving downturns, striking pharma deals, and the importance of keeping a company’s culture based on his two decades of founding and leading Vertex as CEO from 1989 to 2009. The 72-year-old is now serving as executive chairman of Alkeus Pharmaceuticals, a startup developing a rare disease drug.

“I never experienced a straight line up,” Boger said. “Everything had its cycles, and it was how you respond to the cycle, not by predicting when the end is going to be, but just by responding to the present situation.”

At Boger’s first appearance at the JP Morgan conference in 1991, he said the conference’s theme was the end of biotech financing. Just a few months later, Regeneron successfully went public, rapidly changing the outlook for the whole field.

“We had no idea we were ever going to take public money,” he said. “When Regeneron did their IPO, we went, ‘Whoa, there’s something happening here,’ and we pivoted quickly.”

Vertex went public later that year. Throughout his 20-year tenure, Boger said no pharma company ever made an acquisition offer for Vertex, which now commands a market value of $110 billion and recently won the first FDA approval for a CRISPR gene editing therapy.

“We had an uber corporate policy to always make ourselves more expensive than anyone would stomach,” Boger said.

However, Vertex did strike a range of partnerships with Big Pharmas, which Boger described as a painful but necessary part of running a biotech startup.

“It’s impossible for a partnership not to slow you down,” he said. “You can and should try as hard as you can not to do that, but just count on it. They’ll slow you down.”

Boger said startups should insist on being equal partners in pharma deals, at least making sure they have a seat at a partner’s development meetings.

“Realize they’re going to be painful, it’s going to be horrible, and you need to do it,” Boger said.

While Vertex suffered through layoffs, stock price plunges, and trial failures, Boger credited a focus on culture as key to its long-term success.

“It’s the most important ingredient for a successful company,” he said. “Technology is acquirable. Culture is not acquirable. There are 10 companies that will fail because of culture for every one that succeeds, and the successful companies in retrospect will almost always have special cultural aspects that kept them through those downtimes.”

JPM24 opens with ADCs the hottest ticket in San Francisco

By Annalee ArmstrongJan 8, 2024 6:30am

Source: https://www.fiercebiotech.com/biotech/jpm24-opens-adcs-hottest-ticket-san-francisco

The overall deal flow in biopharma tapered off in 2023 but the big companies sure know what they want (what they really, really want), according to a new report from J.P. Morgan.

And that’s antibody-drug conjugates, which drove a fourth-quarter spike in licensing deal proceeds and provided a glimmer of hope to an industry battered by outside forces and grim financing prospects.

J.P. Morgan’s annual 2023 Biopharma Licensing and Venture Report arrived on the eve of the firm’s famous conference, which is set to welcome thousands of attendees in San Francisco today—East Coast weather permitting.

2023 was tough, but clinical biotechs still had a lot of opportunities to wheel and deal, according to J.P. Morgan. While licensing deals, venture investments, M&A and IPOs were down overall in the fourth quarter, deal values stayed fairly high thanks to a flurry of late-stage tie ups.

Follow the Fierce team’s coverage of the 2024 J.P. Morgan Healthcare Conference here

Biopharma licensing partnerships accounted for $63 billion in total value during the fourth quarter from 108 deals. Just one deal—Merck’s ADC partnership with Daiichi Sankyo—accounted for $22 billion of that. Another huge one was another ADC bet, with Bristol Myers Squibb signing on to work with SystImmune for a total value of $8.4 billion. If you exclude the Merck deal, the total value of these partnerships is still higher than the previous quarter, which ended with $32.1 billion.

The total number of licensing deals compares to 149 in the same quarter a year earlier, 195 for Q4 2021 and 223 for Q4 2022.

As for venture investments, the year closed out with $17 billion total across 250 rounds, thanks to $3.5 billion earned through 79 rounds in the last quarter. Aiolos Bio snagged the title of largest venture round of the quarter with $245 million, which also proved to be the largest series A, too.

There was just one IPO in all of the fourth quarter—Cargo Therapeutics making the plunge for $300 million—and 13 overall for the year. It’s a far cry from the heyday of 2021 and experts are still unsure what 2024 will hold. J.P. Morgan reported $2.5 billion raised from 12 completed biopharma IPOs for the year on Nasdaq and NYSE. Nine out of the 12 companies had clinical programs when they took the leap to the public markets. As of December 13, five of the companies were trading above their IPO price.

As for M&A, December saw a rush of Big Pharmas snapping up companies around Christmas. J.P. Morgan tallied the fourth quarter at $37.6 billion and $128.8 billion across 112 total acquisitions for all of 2023.

AbbVie was the top buyer of the quarter with the two largest acquisitions thanks to the $10 billion outlay for ImmunoGen and $8.7 billion buy of Cerevel Therapeutics.

All of this adds up to 270 total deals in the fourth quarter total, which is lower than the third quarter which exceeded 300.

J.P. Morgan sees some big potential for smaller biopharmas looking for licensing partners, as Big Pharmas have been handing out larger upfront payments for the deals they really want.

Cancer was once again the most in-demand therapeutic areas, reaching a new height of $86.1 billion in 2023. Followed by $21.1 billion for neurological disorders.

For More Articles on Real Time Conference Coverage in this Open Access Scientific Journal see:

Part One: The Process of Real Time Coverage using Social Media

Part Two: List of BioTech Conferences 2013 to Present

https://worldmedicalinnovation.org/

https://pharmaceuticalintelligence.com/2022/05/01/2022-world-medical-innovation-forum-gene-cell-therapy-may-2-4-2022-boston-in-person/

 

https://event.technologyreview.com/emtech-digital-2022/agenda-overview

 

Read Full Post »

The Use of ChatGPT in the World of BioInformatics and Cancer Research and Development of BioGPT by MIT

Curator: Stephen J. Williams, Ph.D.

Chatbots are being used in multiple interdisciplanary areas in research and medicine and so it was a natural progression to incorporate artificial intelligence (AI), natural language processing (NLP), and chatbot technology like ChatGPT into bioinformatic analysis.

“In domains like informatics, management and marketing, media and communication science, languages and philosophy, psychology and sociology, engineering, design, and human-computer interaction, the fast expanding body of chatbot study is clearly interdisciplinary.

The field of bioinformatics is a natural fit for incorporting this technology.  The curated information below shows some use examples of this technology in bioinformatics related to cancer research.

The text in this reference source was actually generated by ChatGPT (https://chat.openai.com/chat)

Source: https://omicstutorials.com/using-chatgpt-in-bioinformatics-and-biomedical-research/

How ChatGPT can be used in bioinformatics research?
ChatGPT is a variant of the GPT (Generative Pre-trained Transformer) language model that was designed to generate human-like text in a conversational setting. It is not directly related to bioinformatics, which is the field of study that deals with the storage, retrieval, and analysis of biological data, particularly in the context of genetics and genomics. However, ChatGPT could potentially be used in a bioinformatics context as a tool for generating natural language descriptions of genetic or genomic data, or for generating responses to queries about such data.

For example, a researcher could use ChatGPT to generate descriptions of genetic variants or gene expression patterns based on input data. This could be useful for generating summaries of results for reports or papers, or for generating explanations of complex concepts for non-expert audiences. ChatGPT could also be used to generate responses to queries about genetic or genomic data, such as “What is the function of gene X?” or “What are the potential consequences of variant Y?”

It’s worth noting that ChatGPT is just one of many tools and techniques that can be used in bioinformatics, and it is unlikely to be the most suitable or effective option in every situation. There are many specialized tools and resources available for working with biological data, and it is often necessary to use a combination of these tools to fully analyze and understand the data.

Generating descriptions of genetic or genomic data: ChatGPT could be used to generate natural language descriptions of genetic or genomic data based on input data. For example, suppose a researcher has a dataset containing information about gene expression levels in different tissues. The researcher could use ChatGPT to generate a description of the data, such as:
“Gene X is highly expressed in the liver and kidney, with moderate expression in the brain and heart. Gene Y, on the other hand, shows low expression in all tissues except for the lung, where it is highly expressed.”

 

Thereby ChatGPT, at its simplest level, could be used to ask general questions like “What is the function of gene product X?” and a ChatGPT could give a reasonable response without the scientist having to browse through even highly curated databases lie GeneCards or UniProt or GenBank.  Or even “What are potential interactors of Gene X, validated by yeast two hybrid?” without even going to the curated InterActome databases or using expensive software like Genie.

Summarizing results: ChatGPT could be used to generate summaries of results from genetic or genomic studies. For example, a researcher might use ChatGPT to generate a summary of a study that found a association between a particular genetic variant and a particular disease. The summary might look something like this:
“Our study found that individuals with the variant form of gene X are more likely to develop disease Y. Further analysis revealed that this variant is associated with changes in gene expression that may contribute to the development of the disease.”

It’s worth noting that ChatGPT is just one tool that could potentially be used in these types of applications, and it is likely to be most effective when used in combination with other bioinformatics tools and resources. For example, a researcher might use ChatGPT to generate a summary of results, but would also need to use other tools to analyze the data and confirm the findings.

ChatGPT is a variant of the GPT (Generative Pre-training Transformer) language model that is designed for open-domain conversation. It is not specifically designed for generating descriptions of genetic variants or gene expression patterns, but it can potentially be used for this purpose if you provide it with a sufficient amount of relevant training data and fine-tune it appropriately.

To use ChatGPT to generate descriptions of genetic variants or gene expression patterns, you would first need to obtain a large dataset of examples of descriptions of genetic variants or gene expression patterns. You could use this dataset to fine-tune the ChatGPT model on the task of generating descriptions of genetic variants or gene expression patterns.

Here’s an example of how you might use ChatGPT to generate a description of a genetic variant:

First, you would need to pre-process your dataset of descriptions of genetic variants to prepare it for use with ChatGPT. This might involve splitting the descriptions into individual sentences or phrases, and encoding them using a suitable natural language processing (NLP) library or tool.

Next, you would need to fine-tune the ChatGPT model on the task of generating descriptions of genetic variants. This could involve using a tool like Hugging Face’s Transformers library to load the ChatGPT model and your pre-processed dataset, and then training the model on the task of generating descriptions of genetic variants using an appropriate optimization algorithm.

Once the model has been fine-tuned, you can use it to generate descriptions of genetic variants by providing it with a prompt or seed text and asking it to generate a response. For example, you might provide the model with the prompt “Generate a description of a genetic variant associated with increased risk of breast cancer,” and ask it to generate a response. The model should then generate a description of a genetic variant that is associated with increased risk of breast cancer.

It’s worth noting that generating high-quality descriptions of genetic variants or gene expression patterns is a challenging task, and it may be difficult to achieve good results using a language model like ChatGPT without a large amount of relevant training data and careful fine-tuning.

 

To train a language model like chatGPT to extract information about specific genes or diseases from research papers, you would need to follow these steps:

Gather a large dataset of research papers that contain information about the specific genes or diseases you are interested in. This dataset should be diverse and representative of the types of papers you want the model to be able to extract information from.

Preprocess the text data in the research papers by tokenizing the text and creating a vocabulary. You may also want to consider lemmatizing or stemming the text to reduce the dimensionality of the dataset.

Train the language model on the preprocessed text data. You may want to fine-tune a pre-trained model such as chatGPT on your specific dataset, or you can train a new model from scratch.

ChatGPT could also be useful for sequence analysis

A few examples of sequence analysis a ChatGPT could be useful include:

  1. Protein structure
  2. Identifying functional regions of a protein
  3. Predicting protein-protein interactions
  4. Identifying protein homologs
  5. Generating Protein alignments

All this could be done without having access to UNIX servers or proprietary software or knowing GCG coding

ChatGPT in biomedical research
There are several potential ways that ChatGPT or other natural language processing (NLP) models could be applied in biomedical research:

Text summarization: ChatGPT or other NLP models could be used to summarize large amounts of text, such as research papers or clinical notes, in order to extract key information and insights more quickly.

Data extraction: ChatGPT or other NLP models could be used to extract structured data from unstructured text sources, such as research papers or clinical notes. For example, the model could be trained to extract information about specific genes or diseases from research papers, and then used to create a database of this information for further analysis.

Literature review: ChatGPT or other NLP models could be used to assist with literature review tasks, such as identifying relevant papers, extracting key information from papers, or summarizing the main findings of a group of papers.

Predictive modeling: ChatGPT or other NLP models could be used to build predictive models based on large amounts of text data, such as electronic health records or research papers. For example, the model could be trained to predict the likelihood of a patient developing a particular disease based on their medical history and other factors.

It’s worth noting that while NLP models like ChatGPT have the potential to be useful tools in biomedical research, they are only as good as the data they are trained on, and it is important to carefully evaluate the quality and reliability of any results generated by these models.

 

ChatGPT in text mining of biomedical data
ChatGPT could potentially be used for text mining in the biomedical field in a number of ways. Here are a few examples:

Extracting information from scientific papers: ChatGPT could be trained on a large dataset of scientific papers in the biomedical field, and then used to extract specific pieces of information from these papers, such as the names of compounds, their structures, and their potential uses.

Generating summaries of scientific papers: ChatGPT could be used to generate concise summaries of scientific papers in the biomedical field, highlighting the main findings and implications of the research.

Identifying trends and patterns in scientific literature: ChatGPT could be used to analyze large datasets of scientific papers in the biomedical field and identify trends and patterns in the data, such as emerging areas of research or common themes among different papers.

Generating questions for further research: ChatGPT could be used to suggest questions for further research in the biomedical field based on existing scientific literature, by identifying gaps in current knowledge or areas where further investigation is needed.

Generating hypotheses for scientific experiments: ChatGPT could be used to generate hypotheses for scientific experiments in the biomedical field based on existing scientific literature and data, by identifying potential relationships or associations that could be tested in future research.

 

PLEASE WATCH VIDEO

 

In this video, a bioinformatician describes the ways he uses ChatGPT to increase his productivity in writing bioinformatic code and conducting bioinformatic analyses.

He describes a series of uses of ChatGPT in his day to day work as a bioinformatian:

  1. Using ChatGPT as a search engine: He finds more useful and relevant search results than a standard Google or Yahoo search.  This saves time as one does not have to pour through multiple pages to find information.  However, a caveat is ChatGPT does NOT return sources, as highlighted in previous postings on this page.  This feature of ChatGPT is probably why Microsoft bought OpenAI in order to incorporate ChatGPT in their Bing search engine, as well as Office Suite programs

 

  1. ChatGPT to help with coding projects: Bioinformaticians will spend multiple hours searching for and altering open access available code in order to run certain function like determining the G/C content of DNA (although there are many UNIX based code that has already been established for these purposes). One can use ChatGPT to find such a code and then assist in debugging that code for any flaws

 

  1. ChatGPT to document and add coding comments: When writing code it is useful to add comments periodically to assist other users to determine how the code works and also how the program flow works as well, including returned variables.

 

One of the comments was interesting and directed one to use BIOGPT instead of ChatGPT

 

@tzvi7989

1 month ago (edited)

0:54 oh dear. You cannot use chatgpt like that in Bioinformatics as it is rn without double checking the info from it. You should be using biogpt instead for paper summarisation. ChatGPT goes for human-like responses over precise information recal. It is quite good for debugging though and automating boring awkward scripts

So what is BIOGPT?

BioGPT https://github.com/microsoft/BioGPT

 

The BioGPT model was proposed in BioGPT: generative pre-trained transformer for biomedical text generation and mining by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu. BioGPT is a domain-specific generative pre-trained Transformer language model for biomedical text generation and mining. BioGPT follows the Transformer language model backbone, and is pre-trained on 15M PubMed abstracts from scratch.

The abstract from the paper is the following:

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e. BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large-scale biomedical literature. We evaluate BioGPT on six biomedical natural language processing tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks, respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms.

Tips:

  • BioGPT is a model with absolute position embeddings so it’s usually advised to pad the inputs on the right rather than the left.
  • BioGPT was trained with a causal language modeling (CLM) objective and is therefore powerful at predicting the next token in a sequence. Leveraging this feature allows BioGPT to generate syntactically coherent text as it can be observed in the run_generation.py example script.
  • The model can take the past_key_values (for PyTorch) as input, which is the previously computed key/value attention pairs. Using this (past_key_values or past) value prevents the model from re-computing pre-computed values in the context of text generation. For PyTorch, see past_key_values argument of the BioGptForCausalLM.forward() method for more information on its usage.

This model was contributed by kamalkraj. The original code can be found here.

 

This repository contains the implementation of BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining, by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu. BioGPT is a github which is being developed by MIT in collaboration with Microsoft. It is based on Python.

License

BioGPT is MIT-licensed. The license applies to the pre-trained models as well.

Contributing

This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.

When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.

This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact opencode@microsoft.com with any additional questions or comments.

As of right now this does not seem Open Access, however a sign up is required!

We provide our pre-trained BioGPT model checkpoints along with fine-tuned checkpoints for downstream tasks, available both through URL download as well as through the Hugging Face 🤗 Hub.

Model Description URL 🤗 Hub
BioGPT Pre-trained BioGPT model checkpoint link link
BioGPT-Large Pre-trained BioGPT-Large model checkpoint link link
BioGPT-QA-PubMedQA-BioGPT Fine-tuned BioGPT for question answering task on PubMedQA link
BioGPT-QA-PubMedQA-BioGPT-Large Fine-tuned BioGPT-Large for question answering task on PubMedQA link
BioGPT-RE-BC5CDR Fine-tuned BioGPT for relation extraction task on BC5CDR link
BioGPT-RE-DDI Fine-tuned BioGPT for relation extraction task on DDI link
BioGPT-RE-DTI Fine-tuned BioGPT for relation extraction task on KD-DTI link
BioGPT-DC-HoC Fine-tuned BioGPT for document classification task on HoC link

 

So far as to date (6/12/2023) there are three papers referencing BioGPT on PubMed (abstracts and links below)

 

BioGPT: generative pre-trained transformer for biomedical text generation and mining.

Luo R, Sun L, Xia Y, Qin T, Zhang S, Poon H, Liu TY.Brief Bioinform. 2022 Nov 19;23(6):bbac409. doi: 10.1093/bib/bbac409.PMID: 36156661

We evaluate BioGPT on six biomedical natural language processing tasks and demonstrate that our model outperforms previous models on most tasks. …Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fl …

Here they show the advantages of BioGPT over BioBERT and ChatGPT in an example of text extraction and question answer

Table 7. Example of generated text

Input                                           Model                 Text

Bicalutamide                               GPT-2                 Bicalutamide, a synthetic bicalutamide derivative, was found to increase the cellular proliferation

of C. elegans cells. This effect was not observed with the other synthetic bicalutamide derivatives. This is in line with our previous work which showed that bicalutamide increases the proliferation of C. elegans cells but not in the presence of synthetic bicalutamide.

BioGPT             Bicalutamide (Casodex) is an androgen receptor (AR) antagonist approved for the treatment of metastatic castration-resistant prostate cancer (mCRPC) in patients who have progressed on or are ineligible for docetaxel chemotherapy, as well as for the treatment of early-stage prostate cancer in men who have not progressed on or are ineligible for docetaxel chemotherapy, as well as for the treatment of metastatic castration-sensitive prostate cancer (mCSPC) in men who have not progressed on or are ineligible for docetaxel chemotherapy.

Janus kinase 3 (JAK-3)                 GPT-2               Janus kinase 3 (JAK-3) mediates the conversion of glucose to glycogen in skeletal muscle. The
increase in glucose uptake by skeletal muscle is believed to be associated with a reduction in muscle protein breakdown and with the release of ketone bodies, which contribute to the metabolism of glucose.

BioGPT             Janus kinase 3 (JAK-3) is a member of the Janus kinase (JAK) family of non-receptor tyrosine kinases and plays an important role in the regulation of cell proliferation, differentiation, survival, migration and angiogenesis.

Apricitabine                                 GPT-2               Apricitabine, duloxetine and citalopram) were investigated in patients with a history of
treatment-resistant depression (n = 10). We found that treatment with the three drugs significantly decreased depressive symptoms, but not depressive symptoms over the next 12 weeks. We conclude that antidepressant drugs that reduce depressive symptoms and reduce depressive symptoms over time may be beneficial in patients with recurrent depression.

BioGPT             Apricitabine is an oral prodrug of 5-aza-2 ’-deoxycytidine (5-aza-CdR), a DNA methyltransferase (DNMT) inhibitor, which has been approved by the US Food and Drug Administration (FDA) for the treatment of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) in combination with low-dose cytarabine (Ara-C) and granulocyte colony-stimulating factor (G-CSF) for patients with intermediate-2 or high-risk MDS or AML.

Xylazine                                      GPT-2               Xylazine, the ‘active ingredient’ in ‘bath salts’ (see above) has been linked to numerous deaths,
including those of former University of California, Berkeley, professor Andrew Anglin, who posted

a video of himself having a bath filled with it.

BioGPT             Xylazine is an alpha 2-adrenoceptor agonist which has been used as a sedative and analgesic in veterinary medicine for many years, but its effects on the cardiovascular system have not been extensively studied in the dog, and its effects on the central nervous system (CNS) have not been well characterized in the dog, despite the fact that xylazine has been widely used as a sedative and analgesic in veterinary medicine for more than 30 years.

Psoralen                                      GPT-2               Psoralen, the city of the spiritualist, and had been given to him by God, who wished to show him
the way of salvation, and to draw him back to the true life of Christ, and to bring him into communion with his fellow-man.

BioGPT             Psoralen photochemotherapy (PUVA) is a well-established treatment for psoriasis, but its use is limited by the risk of skin cancer, particularly squamous cell carcinoma (SCC) of the head and neck (H & N), which is the most common site of skin cancer in the United States (US)

CP-673451                                  GPT-2                 CP-673451) and 4-5-6-3-1-2-3-4-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-

28-29-30-31-32-33-34-35-36-37-38-39-40-41-42-43-44-45-46-47-48-49-50…

BioGPT             CP-673451 is a potent, selective, and orally active inhibitor of human neutrophil elastase (HNE) and human cathepsin G (CatG) with in vitro and in vivo anti-inflammatory activity in a variety of animal models of inflammation and in a model of acute lung injury (ALI) in the rat induced by intratracheal instillation of lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-alpha), a model of acute lung injury (ALI) in which neutrophils play an important role.

BIIB-021                                     GPT-2               BIIB-021A-2-1.pdf. Wright, C. (2002). ‘The War on Terror: A Legal Theory of Terrorist Attacks,’ in
L.E.R. Wright, S.R. Warrick and J.H. Rothman (Eds.), The War on Terror: Essays in Honor of Michael T. Klare (New York: Oxford University Press), 143-57.

BioGPT             BIIB-021 is a novel, orally active, non-peptide bradykinin B2 receptor antagonist with potent and long-lasting anti-inflammatory activity in animal models of acute and chronic inflammation and in a rat model of adjuvant-induced arthritis (AIA), an animal model of rheumatoid arthritis (RA) and in a rat model of collagen-induced arthritis (CIA), an animal model of collagen-induced arthritis (CIA), in which arthritis is induced by immunization with bovine type II collagen (CII).

Note how BioGPT is more descriptive and accurate!

EGFI: drug-drug interaction extraction and generation with fusion of enriched entity and sentence information.

Huang L, Lin J, Li X, Song L, Zheng Z, Wong KC.Brief Bioinform. 2022 Jan 17;23(1):bbab451. doi: 10.1093/bib/bbab451.PMID: 34791012

The rapid growth in literature accumulates diverse and yet comprehensive biomedical knowledge hidden to be mined such as drug interactions. However, it is difficult to extract the heterogeneous knowledge to retrieve or even discover the latest and novel knowledge in an efficient manner. To address such a problem, we propose EGFI for extracting and consolidating drug interactions from large-scale medical literature text data. Specifically, EGFI consists of two parts: classification and generation. In the classification part, EGFI encompasses the language model BioBERT which has been comprehensively pretrained on biomedical corpus. In particular, we propose the multihead self-attention mechanism and packed BiGRU to fuse multiple semantic information for rigorous context modeling. In the generation part, EGFI utilizes another pretrained language model BioGPT-2 where the generation sentences are selected based on filtering rules.

Results: We evaluated the classification part on ‘DDIs 2013’ dataset and ‘DTIs’ dataset, achieving the F1 scores of 0.842 and 0.720 respectively. Moreover, we applied the classification part to distinguish high-quality generated sentences and verified with the existing growth truth to confirm the filtered sentences. The generated sentences that are not recorded in DrugBank and DDIs 2013 dataset demonstrated the potential of EGFI to identify novel drug relationships.

Availability: Source code are publicly available at https://github.com/Layne-Huang/EGFI.

 

GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information.

Jin Q, Yang Y, Chen Q, Lu Z.ArXiv. 2023 May 16:arXiv:2304.09667v3. Preprint.PMID: 37131884 Free PMC article.

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

PLEASE WATCH THE FOLLOWING VIDEOS ON BIOGPT

This one entitled

Microsoft’s BioGPT Shows Promise as the Best Biomedical NLP

 

gives a good general description of this new MIT/Microsoft project and its usefullness in scanning 15 million articles on PubMed while returning ChatGPT like answers.

 

Please note one of the comments which is VERY IMPORTANT


@rufus9322

2 months ago

bioGPT is difficult for non-developers to use, and Microsoft researchers seem to default that all users are proficient in Python and ML.

 

Much like Microsoft Azure it seems this BioGPT is meant for developers who have advanced programming skill.  Seems odd then to be paying programmers multiK salaries when one or two Key Opinion Leaders from the medical field might suffice but I would be sure Microsoft will figure this out.

 

ALSO VIEW VIDEO

 

 

This is a talk from Microsoft on BioGPT

 

Other Relevant Articles on Natural Language Processing in BioInformatics, Healthcare and ChatGPT for Medicine on this Open Access Scientific Journal Include

Medicine with GPT-4 & ChatGPT
Explanation on “Results of Medical Text Analysis with Natural Language Processing (NLP) presented in LPBI Group’s NEW GENRE Edition: NLP” on Genomics content, standalone volume in Series B and NLP on Cancer content as Part B New Genre Volume 1 in Series C

Proposal for New e-Book Architecture: Bi-Lingual eTOCs, English & Spanish with NLP and Deep Learning results of Medical Text Analysis – Phase 1: six volumes

From High-Throughput Assay to Systems Biology: New Tools for Drug Discovery

Machine Learning (ML) in cancer prognosis prediction helps the researcher to identify multiple known as well as candidate cancer diver genes

 

20 articles in Natural Language Processing

142 articles in BioIT: BioInformatics

111 articles in BioIT: BioInformatics, NGS, Clinical & Translational, Pharmaceutical R&D Informatics, Clinical Genomics, Cancer Informatics

 

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Reporter: Frason Francis Kalapurakal, Research Assistant II

Researchers from MIT and Technion have made a significant contribution to the field of machine learning by developing an adaptive algorithm that addresses the challenge of determining when a machine should follow a teacher’s instructions or explore on its own. The algorithm autonomously decides whether to use imitation learning, which involves mimicking the behavior of a skilled teacher, or reinforcement learning, which relies on trial and error to learn from the environment.

The researchers’ key innovation lies in the algorithm’s adaptability and ability to determine the most effective learning method throughout the training process. To achieve this, they trained two “students” with different learning approaches: one using a combination of reinforcement and imitation learning, and the other relying solely on reinforcement learning. The algorithm continuously compared the performance of these two students, adjusting the emphasis on imitation or reinforcement learning based on which student achieved better results.

The algorithm’s efficacy was tested through simulated training scenarios, such as navigating mazes or reorienting objects with touch sensors. In all cases, the algorithm demonstrated superior performance compared to non-adaptive methods, achieving nearly perfect success rates and significantly outperforming other methods in terms of both accuracy and speed. This adaptability could enhance the training of machines in real-world situations where uncertainty is prevalent, such as robots navigating unfamiliar buildings or performing complex tasks involving object manipulation and locomotion.

Furthermore, the algorithm’s potential applications extend beyond robotics to various domains where imitation or reinforcement learning is employed. For example, large language models like GPT-4 could be used as teachers to train smaller models to excel in specific tasks. The researchers also suggest that analyzing the similarities and differences between machines and humans learning from their respective teachers could provide valuable insights for improving the learning experience.The MIT and Technion researchers’ algorithm stands out due to its principled approach, efficiency, and versatility across different domains. Unlike existing methods that require brute-force trial-and-error or manual tuning of parameters, their algorithm dynamically adjusts the balance between imitation and trial-and-error learning based on performance comparisons. This robustness, adaptability, and promising results make it a noteworthy advancement in the field of machine learning.

References:

“TGRL: TEACHER GUIDED REINFORCEMENT LEARNING ALGORITHM FOR POMDPS” Reincarnating Reinforcement Learning Workshop at ICLR 2023 https://openreview.net/pdf?id=kTqjkIvjj7

https://arxiv.org/abs/2301.01219

Reinforcement Learning: A Survey by L. P. Kaelbling, M. L. Littman, A. W. Moore https://doi.org/10.48550/arXiv.cs/9605103

Concrete Problems in AI Safety by Dario Amodei, Chris Olah, Jacob Steinhardt, Paul Christiano, John Schulman, Dan Mané https://arxiv.org/abs/1606.06565

Other related articles published in this Open Access Online Scientific Journal include the following:

92 articles in the Category:

‘Artificial Intelligence – Breakthroughs in Theories and Technologies’ 

https://pharmaceuticalintelligence.com/category/artificial-intelligence-general/artificial-intelligence-breakthroughs-in-theories-and-technologies/

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Technion #1 in Europe in Field of AI for 2nd Straight Year

Reporter: Aviva Lev-Ari, PhD, RN

For the second year in a row, the Technion is ranked first in Europe in the field of artificial intelligence (AI) according to CSRankings, which are highly regarded for their metrics-based ranking of top computer science institutions. The repeat win further solidifies the Technion’s position as a leading institution in AI. It was also ranked 16th in the world in AI and 10th in the world in the subfield of learning systems. 

The Technion recruits researchers and students from all Technion units for interdisciplinary AI research by increasing the number of new programs and initiatives in its various fields with leading companies, top universities, and research institutions around the world. It is also establishing its own AI community to empower the student body and researchers in all fields of AI and deepening their collaborations with others doing related work.  

The Technion’s Tech.AI Center for Artificial Intelligence, established in 2020, is the greatest source of AI innovation and research on campus. Tech.AI includes approximately 150 researchers and aims to apply advanced methodologies and tools at the forefront of AI in a variety of fields including data science, medical research, mechanical engineering, civil engineering, architecture, biology, and more.  

To further facilitate AI research and collaborations, a recent agreement was signed to establish a Zimin Institute at the Technion for AI Solutions in Healthcare that will operate as part of Tech.AI. The Institute will promote interdisciplinary projects and work to develop technologies based on big data and computational learning in order to improve human health and healthcare, with an emphasis on proposals that have an applied AI component.  

https://ats.org/our-impact/technion-1-in-europe-in-field-of-ai-for-2nd-straight-year/?utm_medium=email&utm_source=ats-newsletter&utm_campaign=enews&s_src=enews

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Genomic data can predict miscarriage and IVF failure

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

Infertility is a major reproductive health issue that affects about 12% of women of reproductive age in the United States. Aneuploidy in eggs accounts for a significant proportion of early miscarriage and in vitro fertilization failure. Recent studies have shown that genetic variants in several genes affect chromosome segregation fidelity and predispose women to a higher incidence of egg aneuploidy. However, the exact genetic causes of aneuploid egg production remain unclear, making it difficult to diagnose infertility based on individual genetic variants in mother’s genome. Although, age is a predictive factor for aneuploidy, it is not a highly accurate gauge because aneuploidy rates within individuals of the same age can vary dramatically.

Researchers described a technique combining genomic sequencing with machine-learning methods to predict the possibility a woman will undergo a miscarriage because of egg aneuploidy—a term describing a human egg with an abnormal number of chromosomes. The scientists were able to examine genetic samples of patients using a technique called “whole exome sequencing,” which allowed researchers to home in on the protein coding sections of the vast human genome. Then they created software using machine learning, an aspect of artificial intelligence in which programs can learn and make predictions without following specific instructions. To do so, the researchers developed algorithms and statistical models that analyzed and drew inferences from patterns in the genetic data.

As a result, the scientists were able to create a specific risk score based on a woman’s genome. The scientists also identified three genes—MCM5, FGGY and DDX60L—that when mutated and are highly associated with a risk of producing eggs with aneuploidy. So, the report demonstrated that sequencing data can be mined to predict patients’ aneuploidy risk thus improving clinical diagnosis. The candidate genes and pathways that were identified in the present study are promising targets for future aneuploidy studies. Identifying genetic variations with more predictive power will serve women and their treating clinicians with better information.

References:

https://medicalxpress-com.cdn.ampproject.org/c/s/medicalxpress.com/news/2022-06-miscarriage-failure-vitro-fertilization-genomic.amp

https://pubmed.ncbi.nlm.nih.gov/35347416/

https://pubmed.ncbi.nlm.nih.gov/31552087/

https://pubmed.ncbi.nlm.nih.gov/33193747/

https://pubmed.ncbi.nlm.nih.gov/33197264/

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