20251023Thu transformer, part 2

  == pre-class to do: 

post video:

calendar email invitation: 

homework assignment, data camp, 

socrative sign in

update Canvas course materials, update learning objectives. assignments as needed:

Test-run code: skip. 

kindle book. using ipad to highlight key points. 

== In-class to do: 

clean up destktop space, calendars, 

ZOOM, live transcript (start video recording). 

Socrative sign in, 

transformer gpt.ipynb on vertex ai, 

 decoder only

 causal masks, 

 temperature 

student presentation: Google Day practice

breakout rooms:   course project. 

 https://www.politico.com/newsletters/future-pulse/2025/10/22/arpa-h-new-director-00618080

How Alicia Jackson Could Redefine ARPA-H’s AI Future

Alicia Jackson’s DARPA roots could profoundly reshape how ARPA-H approaches artificial intelligence — especially generative AI in the life sciences.

While POLITICO reports that the Trump administration cut several ARPA-H AI programs in areas like AI-driven cancer detection and preventive care, that doesn’t mean a retreat from AI. It signals a strategic pivot — from broad, exploratory projects to mission-focused, biologically grounded applications.

---

🔹 1. From Algorithms to Living Systems

At DARPA’s Biological Technologies Office, Jackson led visionary programs such as Living Foundries and BRICS, advancing programmable biology and biosafety.

Her philosophy treats AI as a design engine — a tool for creating biological systems, not just interpreting them.

Jackson’s Focus	How Generative AI Fits In
Programmable biology	AI models that design new enzymes, antibodies, or pathways.
Biomanufacturing efficiency	Reinforcement learning to optimize cell or microbial production.
Predictable, controllable systems	AI that forecasts biological stability and detects anomalies in real time.

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🔹 2. Translating AI into the Real World

Jackson’s entrepreneurial work — from Evernow to Drawbridge Health — points to a leader focused on translation and commercialization.

Expect ARPA-H to favor AI that accelerates real-world deployment, not theoretical modeling.

Likely directions:

• Digital biomanufacturing twins for faster FDA qualification

• Human-in-the-loop generative design for explainable AI innovation

• Regulatory-ready AI models aligned with FDA’s evolving digital-health framework

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🔹 3. Safety, Robustness, and Governance at the Core

Jackson’s history with Safe Genes and BRICS highlights her awareness of biosecurity and dual-use risks.

Her ARPA-H will likely push for “safe and governed” AI, emphasizing:

• Explainable generative models for biology

• Ethical-control frameworks for AI that manipulates living systems

• Red-teaming and validation pipelines — directly inspired by DARPA safety protocols

In practice, that means generative tools will need built-in containment logic to prevent unintended or dangerous outputs.

---

🔹 4. What Future ARPA-H AI Projects Might Look Like

ARPA-H Priority Area	AI Application Example	Strategic Outcome
Rapid Bio-Design Platforms	Foundation models for proteins and RNA	Faster molecule discovery for health and defense
Scalable Biomanufacturing	Generative control of microbial or cell-free systems	On-demand vaccines, hormones, or nutrients
Neuro-Restoration Interfaces	Generative neural encoding	Brain recovery and adaptive prosthetics
Women’s Health & Aging	Personalized AI for hormonal and aging biomarkers	Precision-health insights with consumer impact
AI Safety in Biotechnology	Red-team and governance frameworks	Mitigate dual-use and biosecurity risks

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🔹 5. The Bigger Picture

Under Jackson’s leadership:

• AI won’t vanish — it will integrate deeply into bioengineering.

• Generative AI will fund tangible biological prototypes, not abstract tools.

• Open-ended “AI-for-everything” research will give way to DARPA-style challenges — measurable, outcome-driven, and safety-conscious.

In short, ARPA-H’s next AI chapter will likely merge engineering discipline with biological imagination — turning AI into a creative partner for the life sciences, not just an observer.

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influenza virus, known as D/HY11,

 A team of researchers at the Changchun Veterinary Research Institute in China has zeroed in on a specific strain of the influenza virus, known as D/HY11, which emerged in cattle in northeast China in 2023.

model the evolution and specici jump using viralGPT. 

policy map

 policy map

policymap.com

https://www.policymap.com/

maternal vulnerability

 maternal vulnerability

https://mvi.surgohealth.com/

BMS program

 

BMS meeting. 

 Robert Bruno, 3D bioprint and cancer

 Lifang Yang

 Larry Sanford

 Frank Lattanzio

 Patrick Sachs

 Siqi Guo

 Ebony Clark

 Lisa Shollengerger

 Peter Mollica

• Lifang Yang: Focuses on fundamental and translational cancer research, specifically cancer pathogenesis, biomarker development, and therapeutic approaches. Her lab studies tumor cells, tumor microenvironment, extracellular vesicles, proteomics, and cancer disparities to advance precision oncology through multi-omics and bioinformatics approaches.
• Frank Lattanzio: Connected to bioelectrics research, including applications of nanosecond pulsed electric fields (nsPEFs) in cancer treatment and cellular electropermeabilization mechanisms.
• Patrick Sachs: Associated with biomedical and translational sciences, likely focusing on biomedical engineering and tumor microenvironment studies combined with 3D bioprinting and cancer research models.
• Siqi Guo: Involved in bioelectric research, including DNA vaccination delivery, electrotransfer, and electroporation-mediated gene transfer techniques; associated with cellular and molecular response to electric fields.

• Siqi Guo is a Research Associate Professor affiliated with the Frank Reidy Research Center for Bioelectrics. His grants include a commercial contract worth about $102,900 (2016-2017) for studying nanosecond electric pulses (NSEPS) as an ablation-immunotherapy for advanced pancreatic cancer. His work focuses on cancer, biotechnology, and bioelectric therapies like nano-pulse stimulation and gene electrotransfer for cancer treatment. He leads projects advancing novel immunotherapy techniques based on electric pulse technology.
• Lifang Yang, listed as an instructor at Eastern Virginia Medical School collaborating with ODU, shares in recent multidisciplinary seed funding ($42,000) supporting research on synergistic effects of nano-pulse treatment combined with cold plasma reactive species for cancer treatment. Her expertise centers on cancer pathogenesis, tumor microenvironment, extracellular vesicles, and biomarker discovery aiming to improve precision oncology through multi-omics and bioinformatics.

20251016Thu Transformer

== pre-class to do: 

post video

calendar email invitation: 

socrative sign in

update Canvas course materials, update learning objectives. assignments as needed:

kindle book. 

== In-class to do: 

clean up destktop space, calendars, 

ZOOM, live transcript (start video recording). 

** Google Day presentation; 

Socrative sign in, 

student presentation; 

breakout rooms:   course project poster work; 

lect 6, engery based model

   == pre-class to do: 

post video of lect 4 LSTM

calendar email invitation: 

homework assignment, data camp, 

socrative sign in

update Canvas course materials, update learning objectives. assignments as needed:

Test-run code: skip. 

kindle book. using ipad to highlight key points. 

== In-class to do: 

clean up destktop space, calendars, 

ZOOM, live transcript (start video recording). 

Socrative sign in, 

student presentation; Terry and ?? 

breakout rooms:   course project