I'd read these 15 papers before taking this course, they cover EVERYTHING from RLHF to recursively self-improving agents.
(optional, but they just make everything click faster imo)
links below! 👇
1. InstructGPT
- SFT → reward modeling → PPO.
- Human preference data + KL regularization.
- The full RLHF stack.
- Reproduce the pipeline conceptually
2. Deep RL from Human Preferences
- Pairwise comparisons.
- Reward model training.
- Behavior without hand-specified rewards.
- The foundation for RLHF.
3. Proximal Policy Optimization Algorithms
- Policy gradients and clipped objectives.
- Importance sampling ratios.
- Advantage estimation.
- Reproduce PPO on a small environment.
4. Direct Preference Optimization: Your Language Model is Secretly a Reward Model
- Derivation of DPO from RLHF.
- Preference-based training without explicit PPO.
- Reference policy and implicit reward modeling.
- Reproduce DPO.
5. DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models
- GRPO algorithm.
- Group-relative advantage calculation.
- Critic-free RL.
- Reproduce GRPO.
6. Let's Verify Step by Step
- Process reward models (PRMs).
- Step-level vs. outcome-level supervision.
- Verifying intermediate reasoning.
- Train a small PRM.
7. DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning
- RLVR and R1-Zero's emergent reasoning.
- Cold-start SFT, rejection sampling, and RL.
- Distillation of reasoning models.
- Reproduce a small RLVR experiment.
8. DAPO: An Open-Source LLM Reinforcement Learning System at Scale
- Improvements to GRPO.
- Dynamic sampling and clipping.
- Token-level policy optimization.
- Large-scale RL engineering.
9. Scaling LLM Test-Time Compute Optimally can be More Effective than Scaling Model Parameters
- Inference-time compute allocation.
- Best-of-N sampling and search.
- Verifier-guided reasoning.
- Compute scaling tradeoffs.
10. Tülu 3: Pushing Frontiers in Open Language Model Post-Training
- Full open post-training recipe.
- SFT, DPO, RLVR.
- Dataset construction and evaluation.
- How to assemble an end-to-end post-training stack.
11. ReAct: Synergizing Reasoning and Acting in Language Models
- Reasoning/action loops.
- Tool-use architecture.
- Action-observation feedback.
- Implement a ReAct agent.
12. Reflexion: Language Agents with Verbal Reinforcement Learning
- Episodic memory.
- Self-reflection after failures.
- Feedback-based improvement without weight updates.
- Implement a reflection loop.
13. Voyager: An Open-Ended Embodied Agent with Large Language Models
- Skill generation.
- Skill libraries.
- Ind feedback.
- Open-ended learning in an environment.
14. Self-Taught Optimizer (STOP): Recursively Self-Improving Code Generation
- Recursive code generation.
- Self-modifying optimization systems.
- Evaluating whether self-improvement actually works.
- Reproduce a bounded self-improvement loop.
15. Darwin Gödel Machine: Open-Ended Evolution of Self-Improving Agents
- Agents modifying their own code.
- Evolutionary search over agent designs.
- Empirical evaluation of self-modifications.
- The distinction between agent improvement and model-weight improvement.
Big little announcement: @karinanguyen and I are excited to announce a brand new course on Full-Stack Post-Training, RL & RSI at @UCBerkeley.
If you are a Berkeley student and want to learn about the frontier, enroll for the next semester.
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1. InstructGPT: alphaxiv.org/abs/2203.02155
2. Deep RL from Human Preferences: alphaxiv.org/abs/1706.03741
3. PPO: alphaxiv.org/abs/1707.06347
4. DPO: alphaxiv.org/abs/2305.18290
5. DeepSeekMath (GRPO): alphaxiv.org/abs/2402.03300
6. Let's Verify Step by Step: alphaxiv.org/abs/2305.20050
7. DeepSeek-R1: alphaxiv.org/abs/2501.12948
8. DAPO: alphaxiv.org/abs/2503.14476
9. Scaling LLM Test-Time Compute: alphaxiv.org/abs/2408.03314
10. Tülu 3: alphaxiv.org/abs/2411.15124
11. ReAct: alphaxiv.org/abs/2210.03629
12. Reflexion: alphaxiv.org/abs/2303.11366
13. Voyager: alphaxiv.org/abs/2305.16291
14. STOP: alphaxiv.org/abs/2310.02304
15. Darwin Gödel Machine: alphaxiv.org/abs/2505.22954
no filler, no nonsense: these are the 15 videos that took me from zero GPU knowledge to GEMM optimization research:
watch them in this order (links below👇):
1. GPU Architecture Explained by ExplainingComputers
Overview: A visual intro to GPU hardware and parallel execution.
- GPU versus CPU: throughput-oriented versus latency-oriented design.
- Streaming Multiprocessors (SMs) and CUDA cores.
- SIMT execution: threads grouped into warps of 32.
- GPU memory hierarchy and hardware parallelism.
2. CUDA MODE Lecture 3: Getting Started With CUDA by GPU MODE
Overview: A practical intro to CUDA programming and writing GPU kernels.
- Host versus device: CPU launches the work, GPU executes it.
- Kernel launch syntax and thread indexing.
- Mapping data elements to threadIdx, blockIdx, and blockDim.
- Basic GPU programming from Python.
3. CUDA MODE Lecture 4: Intro to Compute and Memory Architecture by GPU MODE
Overview: A hardware intro to the compute and memory design behind kernel performance.
- Compute versus memory: throughput limits versus bandwidth limits.
- GPU memory hierarchy: global memory, shared memory, registers, and caches.
- Memory bandwidth and compute throughput.
- How daexecution time.
4. Memory Coalescing by NVIDIA Developer
Overview: A visual intro to how GPU threads access memory efficiently.
- Coalesced versus uncoalesced access patterns.
- Warp-wide memory transactions: threads in a warp combine their loads.
- Strided and contiguous memory layouts.
- Transaction efficiency and wasted bandwidth.
5. CUDA MODE Lecture 9: Reductions by GPU MODE
Overview: A practical intro to parallel reduction algorithms on the GPU.
- Parallel sum and max reduction: combining N values into one in log(N) steps.
- Warp-level reductions using shuffle instructions.
- Shared-memory reductions and thread synchronization.
- Handling non-power-of-two inputs and reduction tails.
6. The Roofline Model by Berkeley HPC
Overview: A performance model for finding hardware bottlenecks.
- Arithmetic intensity: FLOPs per byte of memory traffic.
- Peak compute throughput versus peak memory bandwidth.
- Compute-bound versus memory-bound: which roof limits the kernel.
- Estimating achievable kernel performance.
7. CUDA Performance Checklist by GPU MODE
Overview: A practical checklist for diagnosing and optimizing kernel performance.
- Memory coalescing and access patterns.
- Occupancy versus register pressure: more registers per thread means fewer resident warps.
- Control divergence: threads in a warp taking different branches.
- Kernel bottleneck diagnosis.
8. Nsight Compute Introduction by NVIDIA Developer
Overview: A practical intro to profiling individual GPU kernels.
- Kernel-level profiling and hardware performance metrics.
- SM throughput, memory occupancy.
- Warp stall reasons: why warps wait instead of issuing instructions.
- Roofline analysis and bottleneck identification.
9. Nsight Systems Introduction by NVIDIA Developer
Overview: A system-level view of the full CPU-GPU timeline.
- CUDA API calls, kernel launches, and memory transfers.
- CPU launch overhead and GPU idle gaps.
- Stream execution and operation overlap.
- Synchs and pipeline analysis.
10. CUDA MODE Lecture 14: Practitioner's Guide to Triton by GPU MODE
Overview: A practical intro to writing high-performance kernels in Triton.
- Triton versus CUDA: block-level versus thread-level programming.
- Program IDs, blocked tensors, and tile-based execution.
-Array dimensions.
- Tuning block sizes, warps, and memory layouts.
11. Fused Softmax in Triton — GPU programming tutorial channel
Overview: Implements softmax efficiently by fusing multiple operations into a single GPU kernel.
- Numerically stable softmax using row-wise max subtraction.
- Reduction for maximum and normalization denominator.
- Fusion of max, exp, sum, and division.
- Eliminating intermediate global-memory writes and kernel launches.
12. FlashAttention From Scratch in Triton by GPU programming tutorial channel
Overview: A practical intro to building an IO-aware attention kernel.
- Tiled attention: splitting Q, K, and V into blocks that fit in SRAM.
- Online softmax: running max and sum updated block by block.
- HBM versus SRAM: keeping intermediates on-chip to cut memory traffic.
- IO complexity and memory-efficient attention.
13. CUDA Streams and Asynchronous Execution by NVIDIA Developer
Overview: A practical intro to asynchronous GPU execution and pipeline throughput.
- CUDA streams: ordered queues of GPU operations.
- Asynchronous memory copies with pinned host memory.
- Overlapping computation and data transfer; synchronization, events, and inter-stream dependencies.
14. Hopper TMA / WGMMA Deep Dive by NVIDIA Developer
Overview: A hardware intro to Hopper's data movement and Tensor Core mechanisms.
- Tensor Memory Accelerator (TMA): hardware-driven multidimensional copies into shared memory.
- WGMMA: matrix multiply-accumulate across 4 warps.
- Producer-consumer pipelines: load warps versus compute warps.
- Asynchronous execution and latency hiding.
15. CUDA MODE Lecture 23: Tensor Cores by GPU MODE
Overview: A hardware intro to how Tensor Cores accelerate matrix multiplication.
- Tensor Core matrix multiply-accumulate operations.
- FP16, BF16, TF32, and lower-precision formats.
- Matrix tile layouts and Tensor Core execution.
- Precision, throughput, and performance trade-offs.
1. GPU Architecture Explained — ExplainingComputers
youtube.com/results?search_q…
2. CUDA MODE Lecture 3: Getting Started With CUDA — GPU MODE
youtube.com/watch?v=4sgKnKbR…
3. CUDA MODE Lecture 4: Intro to Compute and Memory Architecture — GPU MODE
youtube.com/watch?v=lTmYrKwj…
4. Memory Coalescing — NVIDIA Developer
youtube.com/results?search_q…
5. CUDA MODE Lecture 9: Reductions — GPU MODE
youtube.com/watch?v=09wntC6B…
6. The Roofline Model — HPC educational resources
youtube.com/results?search_q…
7. CUDA MODE Lecture 8: CUDA Performance Checklist — GPU MODE
youtube.com/watch?v=SGhfUhlo…
8. Introduction to Nsight Compute — NVIDIA Developer
youtube.com/results?search_q…
9. Introduction to Nsight Systems — NVIDIA Developer
youtube.com/results?search_q…
10. Lecture 14: Practitioners Guide to Triton — GPU MODE
youtube.com/watch?v=DdTsX6DQ…
11. Fused Softmax in Triton — GPU programming tutorial
youtube.com/results?search_q…
12. Flash Attention Derived and Coded From First Principles With Triton — Triton tutorial
youtube.com/watch?v=zy8ChVd_…
13. CUDA Streams and Asynchronous Execution — NVIDIA Developer
youtube.com/results?search_q…
14. Hopper TMA / WGMMA Deep Dive — GPU programming tutorials
youtube.com/results?search_q…
15. Lecture 23: Tensor Cores — GPU MODE
youtube.com/watch?v=hQ9GPnV0…
small robot sims on GPU spend most of their time launching kernels.
so i built a compiler (borrowing ideas from @hyperstition_cc's work) that reads a MuJoCo file and writes one fused GPU kernel.
results on a T4:
• matches MuJoCo's physics
• 17-143× faster than MJX
• small articulated robots, no contact (yet)
1. fusion alone makes identical code 3-4× faster
same equations, the only change is going from many kernels per step to 1:
• cartpole + controller: 3.4-3.6× (0.0138 → 0.0039 ms)
• 2-link arm + controller: 3.1-3.4× (0.0145 → 0.0043 ms)
• ball + floor contact: 4.0-4.1× (0.0136 → 0.0033 ms)
unfused, fused and multi-step versions agree to within ~3e-8, so fusing doesn't change the physics. vs MJX: 1.6e-7 (cartpole) and 5.2e-8 (arm) at step 100, ball within 3.67 mm during the bounce and 0.01 mm after.
2. running many steps in one kernel adds another 3-15×, while the physics is cheap
• cartpole: 0.0039 → 0.0006 ms (~6.5× over fused)
• chain5 (5 joints): 0.0104 vs 0.0107 ms, tep does enough math, launch overhead stops mattering.
3. the compiler works on models it was never hand-tuned for
• mass matrix, bias forces and accelerations match MuJoCo to 1e-13 to 1e-16 (arm2, chain5, and a branching tree with sliding joints)
• the generated float32 Warp kernel matches mj_step to ~6e-8 after one ps, it stays within MuJoCo's own sensitivity to a 1e-6 nudge on all 3 models
4. same input files, generated kernels vs MJX (1 env / 4,096 / 16,384):
• arm2: 44× (0.159 → 0.0036 ms) / 64× / 124×
• chain5: 17× (0.178 → 0.0104 ms) / 40× / 112×
• tree: 24× (0.178 → 0.0073 ms) / 61× / 143×
5. MJX on small models is mostly launch overhead
• 94 kernels per step
• ~0.14 ms per step whether you run 1 env or 1,024
• roughly 1.5 µs per launch, doing almost no physics
this is NOT a mujoco replacement (yet haha), just an experiment so far. please let me know where I made mistakes!
10 things worth building with megakernels right now, and each one pushes real research forward!:
1. a real time world model
- feed in frames + action inputs, predict the next latent states
- hyperkernel fuses the rollout loop to cut inference latency
2. a genomics research assistant
- visualize embeddings from a DNA language model
- compare variant effect predictions across sequences
- one interface for researchers to probe their results
3. a GPU-accelerated protein structure explorer
- run ESMFold predictions in the browser with optimized inference
- compare predicted structures and confidence scores side by side
- an interactive tool for exploring how proteins fold
4. an autonomous driving simulator
- run a vision model on simulated road frames, predict vehicle actions
- hyperkernel speeds up the perception pipeline
- visualize predicted trajectories and decisions in real time
5. an AI agent with long-term memory
- an agent that remembers its research across multiple days
- hyperkernel fuses memory-related ops to make local inference faster
- the memory architecture is where the real research lives
6. a learned physics id dynamics and soft-body interactions with learned models
- benchmark against a conventional physics engine
- hyperkernel accelerates the learned approximation
7. a scientific discovery platform
- pick a model and run simulations for any scientific question
- analyze the results and generate a research report
- hyperent inference backend
8. a real-time voice assistant
- streaming speech recognition and generation with natural interruptions
- fully local inference at very low latency
- hyperkernel's moshi work is a reference for fast speech-model execution
9. a molecular simulation explorer
- interactive visualization of molecular behavior
- ML-based predictions with GPU acceleration
- one platform for computational biology research
10. a mini AI inference platform
- open-source serving system with model selection and performance profiling
- hyperkernel provides the high-performance execution layer
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this week in AI was WAY bigger than you realize
here are the top 11 releases that directly affect jobs in kernel engineering, security research, sales, even chemical engineering:
1. Together Compiler (TKCC)
AI agents continuously rewrite, test, and optimize GPU inference kernels
• up to 2.6× higher tokens/sec vs optimized open-source engine configs
• 1.7× throughput over available megakernels (Llama 1B, batch size 1)
• 252× higher experiment throughput vs baseline agentic optimization systems
• already serving production workloads
together.ai/blog/together-co…
2. Scientist World
turns research papers into executable environments with reproduced baselines
• 1,000 verified environments
• frontier AI scientists beat the reproduced human methods in 74% of evaluated improvement/innovation cases
• 158% boost in a small model's research ideation after training on these environments
arxiv.org/abs/2611.08478
3. SwarmEvolve
hundreds of cheap agents share KV caches and search for better programs in latent space, without decoding every idea into text
• tested across 21 math discovery and scientific computing problems
• hit in a median of 3–8 min the scores other frameworks needed 60 min to reach
• Qwen3 8B improved on solutions originally found by AlphaEvolve
arxiv.org/abs/2611.08483
4. TCSExam
benchmark for theoretical CS research: theorem proving, solver engineering, constructions, open conjectures
• 100 expert-reviewed tasks
• outputs checked by Lean or executable validators
• GPT-6 Astra leads Full at 71.9, Opus 5.5 leads Lite at 72.3
arxiv.org/abs/2611.07962
5. SPAR
self-evolving B2B sales agent that treats selling strategies as testable hypotheses, remembers each merchant, and updates its playbook using causal attribution
• live A/B test on Alibaba's 1688 platform, 200,000+ merchants
• 15.8% conversion lift
• 35.8% growth in high-intent merchants
arxiv.org/abs/2611.01695
6. OpenAI Linux Kernel Autonomous Pipeline
autonomous vulnerability discovery and patch generation for the Linux kernel
• 2,308 candidate findings
• 1,724 vulnerabilities dynamically reproduced
• 948 local privilege-escalation exploits, plus candidate patches for maintainer review
• ~$1.2M in API costs
openai.com/index/a-thousand-…
7. VFlash
visual planning model that predicts points, bounding boxes, and trajectories jointly instead of one coordinate token at a time
• lower prediction error than autoregressive decoding across 2D and 3D robotics tasks
• ~25× faster 3D point-motion generation (preliminary)
• 70.2% avg success across four MolmoSpaces suites vs 62.6% baseline
arxiv.org/abs/2611.08449
8. ChemE-as-Code
open-source platform letting LLM agents do chemical engineering calcs, process simulation, plant layout, HAZOP, and life-cycle assessment through checkable tools
• preliminary ammonia engineering package for $224 in API costs
• calculations run outside the LLM, with provenance tracking and automated consistency checks
arxiv.org/abs/2611.07947
9. GuidedWAM
training-free guidance for driving world action models. it injects differentiable objectives during sampling, so you skip retraining for every new objective
• tested on three frozen, public world action models
• +1.8 to 3.6 EPDMS on the NAVSIM v2 hard split (avg over 3 seeds)
• under 10% extra sampling time per step
arxiv.org/abs/2611.07912
10. Wave Forcing
long-video generation method that co-designs training, inference, and execution for better temporal consistency and throughput
• on Wan2.1-T2V-1.3B, quality comparable to Rolling Forcing with 5 denoising steps
• 134.8 end-to-end FPS on 8 H200s (4-step)
• up to 2.53× throughput over matched context-parallel baselines (DiT-only tests)
arxiv.org/abs/2611.00859
11. Persistent Retrieval for Conversational Agents
retrieval subagents that keep their history across multi-turn conversations and hand evidence straight to the main agent
• 43.3% fewer agent-model tokens vs skill-based retrieval
• 45% lower estimated API costs
• 9.1% faster average response time
arxiv.org/abs/2611.07899
the pattern this week: AI is getting really good at the optimization loop first. kernels, program search, sales playbooks, retrieval
if part of your job is "try something, measure it, try again", that's the part to start learning to automate yourself
CAVEATS SO THERE IS NO FEAR-MONGERING:
1. results are company-reported
what it automates: parts of GPU kernel optimization and inference performance engineering
2. benchmark-specific. promising evidence for automated research, and scientists are still very much needed
what it automates: parts of ML research (paper reproduction, experimental iteration, method improvement)
3. a concrete program-search result. general scientific autonomy is a much bigger claim
what it automates: parts of computational algorithm search and optimization
4. t's an eval benchmark. stronger evidence than unverified math claims, and theoretical computer scientists are still essential
what it automates: routine formal proof assistance and verified mathematical construction
5. one company's sales environment. still one of the strongest real-world deployments on this list
what it automates: parts of sales outreach, follow-up, and playbook optimization
6. these are validated exploit demos and patch candidates. maintainer-approved merged fixes are a separate step. controlled campaign
what it automates: parts of vulnerability discovery, reproduction, and patch development
7. simulated task suites so far
what it automates: parts of visual planning and trajectory prediction engineering
8. the authors say the design has yet to be independently reviewed by an engineer
what it automates: parts of chemical engineering calculations, simulation setup, and documentation
9. a technical improvement to driving models. driving engineers stay in the loop
what it automates: parts of autonomous-driving model tuning and control optimization
10. meaningful systems research. video production pros are still very much in the picture
what it automates: parts of video-generation systems engineering and optimization
11. vs a non-persistent retrieval subagent it's faster but uses more tokens and costs more
what it automates: parts of retrieval pipeline design and maintenance for conversational agents
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you can run real physics simulators on a laptop in 2026!
here are the 10 i'd actually use for AI research and world models, ranked by how good they are for experimenting:
1. Newton: robotics physics backed by DeepMind, Disney Research and NVIDIA
2. MuJoCo: best overall, easiest to get running
3. NVIDIA Warp: write your own physics kernels in Python
4. PhiFlow: differentiable fluid sims you can train a neural net through
5. Genesis: multi-physics engine built for embodied AI
6. Taichi: for inventing new physics (granular, elastic, MPM)
7. PhysicsNeMo: PINNs, neural operators, surrogate models
8. DeepXDE: neural nets that solve differential equations
9. JAX MD: differentiable molecular dynamics
10. OpenFOAM: serious engineering CFD, steepest setup
the one to install fastest (and the two i'd build research on) are next👇
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if you only try one now, make it MuJoCo
pip install mujoco, paste a 15 line script, and you're watching a sphere fall under gravity in a 3D viewer within 5 minutes
for real research i'd pick Genesis + Warp. Genesis lets AI agents act inside simulated worlds, Warp lets you invent your own solver
one caveat: running a simulator on a laptop is easy. training a big learned physics model still wants a real GPU or cloud compute
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I think I found the new best method for ideation @ambitionlabsinc
just getting started, more soon
i’ve been hacking on the 6th idea from here, I found it pretty interesting
want a demo? let me know! it’s in the works, but i’d love to know more people into making faster and cheaper physics-based simulations
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i’ve been hacking on the 6th idea from here, I found it pretty interesting
want a demo? let me know! it’s in the works, but i’d love to know more people into making faster and cheaper physics-based simulations
10 things worth building with megakernels right now, and each one pushes real research forward!:
1. a real time world model
- feed in frames + action inputs, predict the next latent states
- hyperkernel fuses the rollout loop to cut inference latency
2. a genomics research assistant
- visualize embeddings from a DNA language model
- compare variant effect predictions across sequences
- one interface for researchers to probe their results
3. a GPU-accelerated protein structure explorer
- run ESMFold predictions in the browser with optimized inference
- compare predicted structures and confidence scores side by side
- an interactive tool for exploring how proteins fold
4. an autonomous driving simulator
- run a vision model on simulated road frames, predict vehicle actions
- hyperkernel speeds up the perception pipeline
- visualize predicted trajectories and decisions in real time
5. an AI agent with long-term memory
- an agent that remembers its research across multiple days
- hyperkernel fuses memory-related ops to make local inference faster
- the memory architecture is where the real research lives
6. a learned physics id dynamics and soft-body interactions with learned models
- benchmark against a conventional physics engine
- hyperkernel accelerates the learned approximation
7. a scientific discovery platform
- pick a model and run simulations for any scientific question
- analyze the results and generate a research report
- hyperent inference backend
8. a real-time voice assistant
- streaming speech recognition and generation with natural interruptions
- fully local inference at very low latency
- hyperkernel's moshi work is a reference for fast speech-model execution
9. a molecular simulation explorer
- interactive visualization of molecular behavior
- ML-based predictions with GPU acceleration
- one platform for computational biology research
10. a mini AI inference platform
- open-source serving system with model selection and performance profiling
- hyperkernel provides the high-performance execution layer
10 things worth building with megakernels right now, and each one pushes real research forward!:
1. a real time world model
- feed in frames + action inputs, predict the next latent states
- hyperkernel fuses the rollout loop to cut inference latency
2. a genomics research assistant
- visualize embeddings from a DNA language model
- compare variant effect predictions across sequences
- one interface for researchers to probe their results
3. a GPU-accelerated protein structure explorer
- run ESMFold predictions in the browser with optimized inference
- compare predicted structures and confidence scores side by side
- an interactive tool for exploring how proteins fold
4. an autonomous driving simulator
- run a vision model on simulated road frames, predict vehicle actions
- hyperkernel speeds up the perception pipeline
- visualize predicted trajectories and decisions in real time
5. an AI agent with long-term memory
- an agent that remembers its research across multiple days
- hyperkernel fuses memory-related ops to make local inference faster
- the memory architecture is where the real research lives
6. a learned physics id dynamics and soft-body interactions with learned models
- benchmark against a conventional physics engine
- hyperkernel accelerates the learned approximation
7. a scientific discovery platform
- pick a model and run simulations for any scientific question
- analyze the results and generate a research report
- hyperent inference backend
8. a real-time voice assistant
- streaming speech recognition and generation with natural interruptions
- fully local inference at very low latency
- hyperkernel's moshi work is a reference for fast speech-model execution
9. a molecular simulation explorer
- interactive visualization of molecular behavior
- ML-based predictions with GPU acceleration
- one platform for computational biology research
10. a mini AI inference platform
- open-source serving system with model selection and performance profiling
- hyperkernel provides the high-performance execution layer
We invented a recursive megakernel generator called Hyperkernel, the most complete solution to megakernels and GPU efficiency.
Hyperkernel-generated megakernels achieve state of the art performance on 11 different domains: inference (DeepSeek, Kimi and GLM), pretraining (Qwen), hardware fault recovery, robotics (π₀-FAST, ACT) diffusion and real time world models (Matrix-Game), full self driving (OpenPilot), voice models (Moshi), genomics (Evo 2) and protein folding (ESMFold).
All of this in a single kernel launch.
For context, Hyperkernel generated fully optimized megakernels for robotics, genomics and voice in under 50 minutes, and doubled the efficiency for >5 models generally using only about 60-100 lines of code per megakernel. This speaks to the unparalleled standard for code quality in the automated generations.
Our first release today open sources the megakernels themselves. Over the next couple weeks, we will release the entire Hyperkernel stack, along with the complete serving stack for Kimi and GLM (20-30% inference efficiency gains across all concurrencies).
Out of the box GPU machinery performs terribly for unorthodox research. We built Hyperkernel only 20 days ago for internal use; but given its multi-modality, we have decided to open source it.
Creative research should not be bottlenecked by the lack of dedicated infra teams. Hyperkernels offer a one stop shop infra stack for all research. We would love for the open source community to add to it :)
GitHub repo: github.com/Hyperstitioncc/Hy…
NOTE: We primarily use NVIDIA B300s, but our kernel generation extends to other hardware (B200s, AMD, TPUs).
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We absolutely crush NVIDIA and achieve the best low latency inference for DeepSeek v4.1 Flash.
Compared with NVIDIA’s published vLLM results, Hyperkernel delivers:
• 36.7% higher per-user generation speed at concurrency 1.
• 28.2% higher per-user speed while serving two users, versus NVIDIA serving one.
• 15% higher per user speed while serving four users, versus NVIDIA serving one.
• 90.6% higher per-user generation speed at concurrency 4, compared with the highest published C4 AgentX interactivity for TP4 B300s.
• 28.5% higher per-user generation speed at concurrency 8, compared with NVIDIA's published result.
• 36% faster median per-request decode speed.
these 10 papers are what AI for biology the coolest field in 2026
if you work anywhere near biology, this is your reading list. a lot of this work is already being tested in real labs!
links to the papers below! 👇
1. Evo 2 (Nature, Mar 2026)
• genomic foundation model trained on ~9 trillion DNA base pairs, modeling sequences across all domains of life.
• predicts the effects of genetic variation, including clinically relevant variants. AI moves from single proteins to whole-genome patterns.
2. AlphaGenome (Nature, Jan 2026)
• ingests up to 1M base pairs and predicts thousands of regulatory signals: gene expression, chromatin accessibility, RNA splicing.
• gives a mechanistic read on how a tiny non-coding mutation can cascade into disease.
3. Robin, multi-agent scientific discovery (Nature, 2026)
• an agent system that generates hypotheses, mines literature, proposes experiments, interprets results and updates its beliefs.
• closest thing yet to AI acting as the scientist. experimentally validated therapeutic candidates in a lab-in-the-loop workflow.
4. AutoDNA (Nature, Nov 2026)
• couples AI with automated lab instruments to run biomolecular operations with minimal human intervention.
• AI orchestrating physical experiments end to end. this points at labs that run research around the clock.
5. AlphaGenome Atlas (preprint, Sep 2026)
• in silico mutagenesis of the entire human genome: predicted effects for billions of variants.
• a massive prioritization resource for non-coding variants, potentially surfacing overlooked genetic explanations for rare diseases.
6. Claude uplifting biomolecular modeling (Anthropic, Sep 2026)
• Claude optimized 30+ specialized biological AI models, reportedly ~4x faster on average while retaining identical outputs.
• AI accelerating the infrastructure other AI uses to do biology. a compounding loop.
7. Pinal (Nature, Oct 2026)
• 16B-parameter foundation model that translates natural-language descriptions of protein function into candidate designs.
• scientists can state the biological goal in plain language. results are computational so far, so wet-lab validation is the next test.
8. Towards a virtual yeast (Nature, Jul 2026, perspective)
• proposes an AI system integrating genetic, metabolic and structural processes to simulate yeast-cell behavior.
• a virtual cell lets you test hypotheses computationally before paying for the physical experiment.
9. AI-driven digital organism (Nature Medicine, Aug 2026, perspective)
• interconnected foundation models representing biology from molecules to cells to whole organisms.
• a roadmap for predicting biological outcomes across every level of complexity.
10. Generalist biological AI (Nature Biotechnology, Mar 2026, review)
• surveys systems that jointly model DNA, RNA, proteins and cellular systems as one language of life.
• the clearest map of where general-purpose biological foundation models are heading.
links to the papers, same order:
1. Evo 2
alphaxiv.org/abs/2603.01234
2. AlphaGenome
doi.org/10.1038/s41586-025-1…
3. Robin
doi.org/10.1038/s41586-026-1…
4. AutoDNA
doi.org/10.1038/s41586-026-1…
5. AlphaGenome Atlas
doi.org/10.64898/2026.09.16.…
6. Claude uplifting biomolecular modeling
anthropic.com/research/claud…
7. Pinal
doi.org/10.1038/s41586-026-1…
8. Virtual yeast
doi.org/10.1038/s41586-026-1…
9. Digital organism
doi.org/10.1038/s41591-026-0…
10. Generalist biological AI
doi.org/10.1038/s41587-026-0…
these 10 GPU optimization papers are why your model runs fast today
the engineers who actually read these are the ones who'll be writing your kernels in 2 years.
links to the papers below! 👇
1. FlashAttention (2022)
• IO-aware exact attention: tiles Q/K/V into on-chip SRAM and uses online softmax to avoid materializing the quadratic attention matrix in HBM.
• an incredible example of how optimizing data movement can unlock longer contexts and faster Transformers.
2. FlashAttention-2 (2023)
• redesigns work partitioning across thread blocks and warps, improving occupancy while cutting non-matmul FLOPs and shared-memory communication.
• makes attention substantially better at actually using the GPU's compute capacity. around 2× faster than the original in the paper's benchmarks.
3. Stream-K (2023)
• partitions aggregate GEMM inner-loop work into balanced chunks, reducing the wave-quantization inefficiency of fixed output-tile scheduling.
• especially elegant for matrix shapes that would otherwise leave a partially occupied final wave of thread blocks.
4. PagedAttention (2023)
• brings virtual-memory-style paging to KV-cache management, with noncontiguous physical blocks and flexible cache sharing.
• foundational to vLLM: reduces memory waste so serving systems can fit larger batches.
5. FlashAttention-3 (2024)
• exploits Hopper's asynchronous Tensor Cores and TMA through warp specialization, overlapping data movement with computation and interleaving matmul with softmax.
• adds an FP8 path with block quantization and incoherent processing. serious hardware-algorithm co-design.
6. Tiled GEMM / Tensor Core dataflow (foundational technique)
• stages matrix tiles through shared memory and registers, reusing operands across Tensor Core multiply-accumulate operations.
• the foundation underneath so much of this list. a family of techniques, so this entry has no single canonical paper.
7. Online normalizer calculation for softmax (2018)
• updates the running maximum and normalization sum as elements stream through, reducing memory passes while preserving numerical stability.
• a beautifully compact building block for memory-efficient attention.
8. MARLIN (2024)
• combines low-bit weight storage with higher-precision computation, using asynchronous loads and carefully pipelined dequantization to feed Tensor Cores efficiently.
• makes weight-only quantization useful for batched inference, with substantial speedups extending beyond single-user decoding.
9. Ring Attention (2023)
• distributes sequence blocks across devices and circulates KV blocks in a ring, overlapping communication with blockwise attention computation.
• scales context capacity across GPUs while preserving exact attention.
10. FlashInfer (2025)
• combines customizable attention kernels with load-balanced scheduling for dynamic serving workloads and heterogeneous KV-cache layouts.
• tackles the messy inference conditions: variable sequence lengths and changing request batches.
links to the papers, same order:
1. FlashAttention
alphaxiv.org/abs/2205.14135
2. FlashAttention-2
alphaxiv.org/abs/2307.08691
3. Stream-K
alphaxiv.org/abs/2301.03598
4. PagedAttention
alphaxiv.org/abs/2309.06180
5. FlashAttention-3
alphaxiv.org/abs/2407.08608
6. Tiled GEMM / Tensor Core dataflow
no single paper. FlashAttention above is one concrete example of IO-aware tiling.
7. Online normalizer calculation for softmax
alphaxiv.org/abs/1805.02867
8. MARLIN
alphaxiv.org/abs/2408.11743
9. Ring Attention
alphaxiv.org/abs/2310.01889
10. FlashInfer
alphaxiv.org/abs/2501.01005
1
10
683
these 10 GPU optimization papers are why your model runs fast today
the engineers who actually read these are the ones who'll be writing your kernels in 2 years.
links to the papers below! 👇
1. FlashAttention (2022)
• IO-aware exact attention: tiles Q/K/V into on-chip SRAM and uses online softmax to avoid materializing the quadratic attention matrix in HBM.
• an incredible example of how optimizing data movement can unlock longer contexts and faster Transformers.
2. FlashAttention-2 (2023)
• redesigns work partitioning across thread blocks and warps, improving occupancy while cutting non-matmul FLOPs and shared-memory communication.
• makes attention substantially better at actually using the GPU's compute capacity. around 2× faster than the original in the paper's benchmarks.
3. Stream-K (2023)
• partitions aggregate GEMM inner-loop work into balanced chunks, reducing the wave-quantization inefficiency of fixed output-tile scheduling.
• especially elegant for matrix shapes that would otherwise leave a partially occupied final wave of thread blocks.
4. PagedAttention (2023)
• brings virtual-memory-style paging to KV-cache management, with noncontiguous physical blocks and flexible cache sharing.
• foundational to vLLM: reduces memory waste so serving systems can fit larger batches.
5. FlashAttention-3 (2024)
• exploits Hopper's asynchronous Tensor Cores and TMA through warp specialization, overlapping data movement with computation and interleaving matmul with softmax.
• adds an FP8 path with block quantization and incoherent processing. serious hardware-algorithm co-design.
6. Tiled GEMM / Tensor Core dataflow (foundational technique)
• stages matrix tiles through shared memory and registers, reusing operands across Tensor Core multiply-accumulate operations.
• the foundation underneath so much of this list. a family of techniques, so this entry has no single canonical paper.
7. Online normalizer calculation for softmax (2018)
• updates the running maximum and normalization sum as elements stream through, reducing memory passes while preserving numerical stability.
• a beautifully compact building block for memory-efficient attention.
8. MARLIN (2024)
• combines low-bit weight storage with higher-precision computation, using asynchronous loads and carefully pipelined dequantization to feed Tensor Cores efficiently.
• makes weight-only quantization useful for batched inference, with substantial speedups extending beyond single-user decoding.
9. Ring Attention (2023)
• distributes sequence blocks across devices and circulates KV blocks in a ring, overlapping communication with blockwise attention computation.
• scales context capacity across GPUs while preserving exact attention.
10. FlashInfer (2025)
• combines customizable attention kernels with load-balanced scheduling for dynamic serving workloads and heterogeneous KV-cache layouts.
• tackles the messy inference conditions: variable sequence lengths and changing request batches.
links to the papers, same order:
1. FlashAttention
alphaxiv.org/abs/2205.14135
2. FlashAttention-2
alphaxiv.org/abs/2307.08691
3. Stream-K
alphaxiv.org/abs/2301.03598
4. PagedAttention
alphaxiv.org/abs/2309.06180
5. FlashAttention-3
alphaxiv.org/abs/2407.08608
6. Tiled GEMM / Tensor Core dataflow
no single paper. FlashAttention above is one concrete example of IO-aware tiling.
7. Online normalizer calculation for softmax
alphaxiv.org/abs/1805.02867
8. MARLIN
alphaxiv.org/abs/2408.11743
9. Ring Attention
alphaxiv.org/abs/2310.01889
10. FlashInfer
alphaxiv.org/abs/2501.01005
i keep coming back to the systems work behind AI in biology
Evo 2 uses StripedHyena 2 to model DNA at single-nucleotide resolution with a 1 million-token context window
the architecture details are a pretty natural rabbit hole after optimizing GPU kernels
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StripedHyena 2 mixes short explicit, medium regularized and long implicit convolution operators with attention.
the paper reports up to 3x higher throughput than highly optimized Transformer baselines at 40B parameters and 1M context.
that's a concrete systems result worth digging into.
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the biological evaluation i find interesting: zero-shot variant-effect prediction using changes in sequence likelihood.
how much does a mutation change the probability assigned to the surrounding DNA?
they evaluate those scores against measured effects, including BRCA1 saturation mutagenesis data.
paper: nature.com/articles/s41586-0…
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my favorite papers that i’ve read over the past month (biased)
links below! 👇
1. Qwen-CUA: Native Computer Use for (almost) Everything - I like qwen, and I love computer use. no brainer.
2. FreeToken: Efficient Edge-Native MoE Serving with Bandwidth-Adaptive Execution - as an avid @ollama user, I had to check out the competition. This did. NOT disappoint.
3. Prime Agent: A Self-Improving RLM Harness - I love long horizon research, this is probably my favorite paper on it.
4. KernelFoundry: Hardware-aware evolutionary GPU kernel optimization - when I got into the open kernel challenge, this is the first paper I read when I hit a roadblock.
5. Human Learning about - wanted to check out @raphaelroux’s work, probably my favorite paper over the past 3 months
last but not least… shoutout @askalphaxiv. I read all the papers through their mobile app on the way to school every day. all love!
1. alphaxiv.org/overview/2608.0… alphaxiv.org/overview/2608.0…
2. alphaxiv.org/overview/2608.1… alphaxiv.org/overview/2608.1…
3. alphaxiv.org/overview/2608.2… alphaxiv.org/overview/2608.2…
4. alphaxiv.org/overview/2603.1… alphaxiv.org/overview/2603.1…
5. alphaxiv.org/overview/2406.0… alphaxiv.org/overview/2406.0…
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