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Alameda, California, United States
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2K followers
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RJ Honicky posted thisAgents for science are pathologically bad at converging. Always hedging, caveats becomes a new analysis branch, unlikely failure modes gets chased down. This is good for rigor, but I quickly lose track of all the branches. I'm working on a UI that looks like git commit tree, including merges, to help with this. Part of our agentic UI that some of our customers are interested in. How to to make the judgement call and move on? How to decide when there is enough evidence to actually conclude something?
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RJ Honicky reposted thisRJ Honicky reposted thisAt MiraOmics we have developed H&E whole slide image analytics stack. The best part! We did not use ANY manual annotation to train our models. Everything was 100% automated! End-to-end the analysis for 120 images took 1 week. This framework means that we can take histology whole slide image, identify Tumor cells, TME region and Normal regions. We can further identify Cell types, and group them into Niches, we can group niches into tumor subtypes. An important subtype for colorectal cancer is: MSI (microsatellite instability) vs MSS (microsatellite stable). This stratification is a very important problem since different drug treatments are required for each. For example, MSI is responsive to checkpoints. Here we show both kinds of tumor sample from TCGA. We are working on using our niche detection algorithm and cell type composition to stratify the two types. Are you a pharma translational or a pathology expert? Do you want to apply this method to your H&E slides for patient stratification? Don't hesitate to reach out today!
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RJ Honicky reposted thisRJ Honicky reposted thisAt MiraOmics, we wanted to find out if we can stratify MSI/MSS colorectal cancer based on cell types from H&E ALONE. It turns out that we can! This classifier has been built using enrichment of cell types. MSI (microsatellite instability) colorectal cancer is responsive to checkpoint inhibitors, while MSS is not. Being able to stratify is incredibly valuable in informing treatment options. This relatively simple model gives a much greater-than-chance prediction of MSI/MSS while shedding light on MSI biology. This workflow was 100% automated with no manual annotation of underlying data. Our AI system has used cell classification to identify the MSI/MSS status. Do you want to use this system to stratify your patients? We would love to work with you. Please don't hesitate to reach out today! Do you have other ideas for cancer types that would be interesting to investigate? Please DM or reply in the comments.
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RJ Honicky shared thisIs vH&E model training data good enough to augment real H&E data? How do can you even tell if it's reasonable? In this image, the real eosin (E in H&E) was washed out by the something in the processing, so we are reconstructing a virtual H&E using immunoflorescent stains. The image shows a QC check I did to make sure all the pockets reflect real empty areas vs. failure of the stains to capture tissue. Middle: green is airways, magenta is blood vessles Right: Red is capillary walls of alveoli (air sacks), green is more vessel markers I'll let you know if it works :)
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RJ Honicky reposted thisRJ Honicky reposted thisAt MiraOmics we have developed H&E whole slide image analytics stack. The best part! We did not use ANY manual annotation to train our models. Everything was 100% automated! End-to-end the analysis for 120 images took 1 week. This framework means that we can take histology whole slide image, identify Tumor cells, TME region and Normal regions. We can further identify Cell types, and group them into Niches, we can group niches into tumor subtypes. An important subtype for colorectal cancer is: MSI (microsatellite instability) vs MSS (microsatellite stable). This stratification is a very important problem since different drug treatments are required for each. For example, MSI is responsive to checkpoints. Here we show both kinds of tumor sample from TCGA. We are working on using our niche detection algorithm and cell type composition to stratify the two types. Are you a pharma translational or a pathology expert? Do you want to apply this method to your H&E slides for patient stratification? Don't hesitate to reach out today!
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RJ Honicky shared thisI'm increasingly using ad-hoc GUIs to accomplish bio tasks Claude and Codex This is an annotation gui in which I am teaching Astra to more effectively segment some tricky heart cells. I mark errors with errors and bounding boxes, add a note, and then pass them to Agent which then refines its recipe. This is a natural way to dialogue with AI, and is more visual and appropriate for a lot of bio tasks.
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RJ Honicky shared thisBio-lab automation is having a moment (thanks Anthropic) With Anthropic's announcement of the (potentially) CRISPR-like function they discovered, a lot of attention is suddenly on the fact that generating hypotheses is cheap, validating them is expensive. Lila Sciences, NOETIK, Xaira Therapeutics, Radical AI, Periodic Labs, Octant and many others have been building the infrastructure to collect data at high throughput. With the physical world being a hard constraint, experiments having an intrinsic duration, this seems like a wide moat to cross for Anthropic. Here's a cool clip from our episode with Andrew Beam and Rafael Gómez Bombarelli on Lila Sciences' system. Links below 👇
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RJ Honicky shared thisI review slides visually and quantitatively by swapping views This internal MiraTyper tool allows us to look at our annotations overlayed on an H&E, and also ask quantitative questions so we can make sure our labels make sense. And then we can swap back and see individual cells that match our criteria in the context of the slide again! This really helps us understand our data (and our models!) We starting to roll this out to customers. Let me know if you want a demo
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RJ Honicky reposted thisRJ Honicky reposted thisIn my hands, Claude Code is getting better at manually gating cells. I've been testing this since Opus 4.5. Here, I built a manual gating interface so I could watch Claude gate in real time. It was done on the Samusik_01 CyTOF dataset (mouse bone marrow). I ran it in two settings: with and without the visual gating strategy from the X-shift paper (Figure S5, Samusik et al, Nat. Methods 2016). The run with the image also had the reference population counts. Ground truth was the manual gates that are in the Samusik dataset. With the gating strategy image, it got 98% of assigned cells right. Without it, it got 85% of assigned cells right. This suggests that the model can take gating strategy information (visual, tree) and use it. Another observation, and I saw this in earlier experiments with Opus 4.5, is that in the latter case, there were a high number of cells labeled "unassigned" (55.3%) in comparison to the "ground truth" gates (38.8%). Most of these additional unassigned cells were monocytes. I haven't scrutinized each gate yet. I found many to be pretty good, but others to be a bit coarse-grained. What this means for you: the latest Claude Opus seems to have had a major upgrade in capabilities in my hands. I can say the same about GPT Codex, though I have not done this exact test yet. The results here suggest that AI gating assistants, (or God forbid: vibe gating) might be around the corner. Try this on your cells. Try the harder populations. See where the "edge cases" are. Make note of them. The bigger picture is that the models are at a point now where you should be testing their capabilities against your datasets. Know what they can do, and know where their failure modes are. Re-test with each new model. Leaders of research teams need to encourage this. There is a lot of upside coming, but also a lot of potential for catastrophic failure if you don't check every assumption. If there is anything you want to test, but you don't have the time or resources to do so, just let me know. I hope you all had a nice summer.
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RJ Honicky liked thisRJ Honicky liked thisWhen I showed Sam Altman my vision for TypeSafe AI, he told me to stop working on RLHF and work on my idea instead. But it still took me 2 years to start Jev… We’d just released InstructGPT, which took 50% of the LLM market almost immediately. I remember thinking, “Is this AGI? It's superhuman at instruction in, instruction out.” Looking back, it was obviously not the case 🤣 The “value creation” went largely toward copywriting (what we now call AI slop websites). The model was clearly suuuper smart, but something was missing for it to unlock true value. I went back to the drawing board and worked backwards from an AI-based economic revolution and realized we had to optimize models for machines not humans. I wrote a doc explaining my thoughts and showed it to Sam. He told me I should drop what I’m working on and work on that instead. I was at OpenAI at the time working on other projects, so didn’t get the time to explore the idea. I later spoke to other companies about starting a lab focused on this. I asked straight up, “What would be faster, a lab in your company or my own startup?” The answer was "startup" every time… At that point I was like, “F*ck it.” I picked up the phone to call Erik Spock Gafni and Sasha Sheng, and within 2 weeks TypeSafe was born. Full story here: https://lnkd.in/gz4TSx4d
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RJ Honicky reacted on thisRJ Honicky reacted on thisA first glimpse. A mother’s face. A family’s smile. A child’s tears of wonder. What more could we ask for? Celebrate life. Celebrate the little miracles. ❤️ Some moments simply leave you #speechless. 🥲❤️ Some moments simply bring us joy like this one. 🥲❤️ A small #child, who had never been able to see, opened his #eyes for the #firsttime after #surgery—and the very first faces he saw were those of his #mother and #family. I am sure, if this moment doesn’t bring tears to your eyes, what else will bring you tears in your life? 🥹 This #video shows us the power of a heartfelt bonding between a mother and her child. Imagine seeing your mother for the very first time. Imagine discovering the #world through your own eyes. Imagine the #happiness of recognizing the people who have always loved you. That is life. That is happiness. That is love. That is hope. We spend so much of our lives chasing #success, #money, #titles, and #achievements. Yet sometimes, the most #pricelessmoments are the simplest ones. Respects to every #mother on the earth, respect women, respect every girl. #Life #Happiness #Hope #Gratitude #Humanity #Inspiration #LifeLessons #ThankfultoGod #Tuesdayvibes #vibes #motivational #motivation #miracles #ThankyouDoctors #EyeCare #darkness #lighting #light #firsttime #learninglessons #dailylearning #learneveryday #care #motherscare #bond #bonding #motherisgod #woman #womanpower #empathy #JOY #empathetic #tearsofjoy #joyful #greatfamily #wonderfulmoments #wonderfulmoment #thankfultoGod #godisgreat #motherisgreat #bethankfultogod #everydaymiracles #positive https://lnkd.in/drRdUzfh
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RJ Honicky liked thisRJ Honicky liked thisTarana Wireless FWA technology already supports the 6GHz band. With the UK opening access to the upper portion, the extra bandwidth will allow Tarana to increase FWA capacity to gigabit speeds, making the wireless technology "fibre-class" broadband. https://lnkd.in/gnGZ9_uP
Publications
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Workload Modelling of Stateful Protocols Using HMMs
Proceedings of the 31th International Computer Measurement Group Conference
Supporting stateful protocols like CIFS and NFSv4 in a workload model (or a benchmark) requires accurate capture of the order of operations observed in various traces as this has a significant impact on the performance of the storage device. One common tool for analyzing streams of discrete values that depend on an underlying stateful process is a Hidden Markov Model (HMM). This paper clearly illustrates how HMMs can be used effectively to capture the state behavior of CIFS and NFSv4 traffic.
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Keith Townsend
The Advisor Bench • 16K followers
Enterprise AI has a equipment problem, not a compute problem. I contributed to a new 3-part series on the Intel community blog: "From Gold Rush to Factory: How to Think About TCO for Enterprise AI." The core idea: most organizations are still in gold-rush mode — buying GPUs before understanding the work. But the enterprises getting real ROI from AI are thinking like factory operators. Match the equipment to the job. Build repeatable workflows. Optimize the CPU-to-GPU ratio by workload, not by hype. One story from the piece that still gets me: a genomics company deployed high-end GPUs to meet a seven-day SLA. Got results in under a minute. Impressive — until someone asked if a two-hour completion on CPUs would suffice. It did. The GPUs were decommissioned. That's not an edge case. It's closer to the norm than most want to admit. The constraint isn't compute. It's the lack of a system for matching the job to the right equipment. Part 1 is live now. Parts 2 and 3 are coming. https://lnkd.in/gQX_pe_2 cc: Rahul Awasthy Lynn Comp
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John Werner
Link Ventures • 34K followers
Today's article in my AI column – at Google Bay View, a panel discussed wafer-scale chips, data center and fabrication bottlenecks, costly movement of model weights, and the risk of overheated investment. Despite those challenges, the panelists expect AI infrastructure to underpin economic change. https://lnkd.in/g9CNCasG
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Andrew Feldman
Cerebras Systems • 59K followers
OpenAI’s OSS-120B is the premier open-source model. How many of the five fastest inference providers serve it on GPUs? One. And they’re in fifth place. Performance data (OpenRouter, 10/21/25): - Cerebras: 2,838 tokens/sec per user - Groq: 915 tokens/sec per user - SambaNova: 851 tokens/sec per user - Google Vertex: 516 tokens/sec per user - Fireworks: 494 tokens/sec per user (GPU-based) Speed tells the story. The fastest inference in the world doesn't run on GPUs. Check out the uptime data as well. Cerebras and Google get perfect uptime scores.
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Richard Lynes
Genesis AiX • 854 followers
Executive Thesis — Earth as the Ultimate Compute Substrate AI compute demand is rising at a rate that outpaces the physical limits of surface-level data centers. Thermal density, grid constraints, water scarcity, and land-use conflicts are converging into a single bottleneck: the inability to dissipate heat at the rate AI generates it. Some propose escaping Earth’s constraints entirely — most notably Elon Musk’s long-term vision of orbital compute platforms. While elegant in theory, orbital compute is economically and operationally non-viable for at least the next half-century. https://lnkd.in/eHgNB6cZ #SupercriticalCO2 #sCO2 #ThermalManagement #DataCenterCooling #AdvancedCooling #SubsurfaceDataCenters #UndergroundDataCenters #AIInfrastructure #ComputeInfrastructure #HighPerformanceComputing #HPC #EnergyEfficiency #SustainableInfrastructure #DigitalInfrastructure #DataCenterInnovation #InfrastructureDesign #PatentPending #DeepTech #ClimateTech #NextGenInfrastructure #EngineeringInnovation #SystemsArchitecture #FutureOfCompute #ResilientInfrastructure #TrustedInfrastructure
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Moshe Tanach
NeuReality • 8K followers
NVIDIA-Groq $20B is a thought provoking deal – but where does the real value lives? The news around NVIDIA acquiring Groq is worth pausing on, not just as an impressive M&A headline, but as a signal of where real value in AI infrastructure is being created. First, kudos to Jonathan Ross and the entire Groq team. For me, beyond the hardware story that is debatable in my opinion, what Groq truly delivered was a robust, production-grade inference deployment and serving stack. That’s the hard part many underestimated and still do. Shipping impressive latency benchmarks is one thing; operationalizing newly announced models at scale, reliably and fast, is a different game. A lot of companies over the past years explored SRAM-based architectures, in-memory compute, and other novel XPU architectures. Far fewer succeeded in building a repeatable end-to-end inference deployment stack that deliver fast transition from model arrival to scaled production. Groq did. And it’s not surprising that NVIDIA recognized that value. When we started NeuReality, right from the first customers’ tour we concluded that software stack and AI serving is where we should start from since efficient compute is the goal but software is the mean to deliver it to customers with Ease-of-use and TTM. So we started with defining our Inference Serving Stack and our Scale-Out Networking Stack. Where our paths diverge is in philosophy. Groq chose full vertical integration, eliminating supply chain intermediaries, building the hardware and the software, and selling tokens directly to end users while we took a different approach of productizing the inference software and hardware infrastructure, making it work across any GPU or XPU, and enabling others - hyperscalers, silicon vendors, Neoclouds, and enterprises to unlock that same deployment velocity with their choice of XPU without locks. Different strategies. Same technology focus and realization. Designing silicon is impressive. Turning it into a real, deployable inference platform is rare. That’s the hard part -- and that’s where durable value lives. https://lnkd.in/dy6_89dA
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John Byrd
Gigantic Software, LLC • 3K followers
Zero plus zero equals two. Not in some toy project. In Berkeley SoftFloat -- the IEEE 754 math library reference implementation. It's inside QEMU and most x86 emulators, and it's the oracle that hardware teams verify chip designs against. If you've ever emulated a CPU or validated a chip design in the last decade, Berkeley SoftFloat did the floating-point math. I found seven wrong results across five of six arithmetic operations in the 80-bit extended precision format. The one Intel invented for the x87 FPU in 1980. Some other fun highlights: - 0.5 + 0.5 = 3 - A huge finite number plus zero = infinity - Infinity x 0 = infinity (and no error raised) - Two tiny numbers added together = zero These aren't rounding errors. These are completely wrong answers for valid inputs. The root cause: the x87's 80-bit format has an explicit "integer bit" that every other IEEE format hides. This creates encodings -- unnormals, pseudo-denormals, pseudo-infinities -- where the bit says one thing and the exponent says another. The original 8087 handled all of them correctly. SoftFloat hasn't since its 2011 rewrite. Nobody noticed because the test suite has a structural blind spot. The test generator only produces the encodings that SoftFloat itself would output... the "nice" ones where the integer bit is consistent with the exponent. It never generates the inputs that trigger the bugs. I patched the generator to cover the full input space and failures lit up everywhere. I never would have found any of this if I hadn't been writing my own floating-point library from scratch. When my results disagreed with SoftFloat, I assumed I was wrong. Over and over. I'd go back to my code, recheck my math, trace through my logic... because the reference implementation couldn't possibly be wrong. That's what "reference" means. But the reference was wrong, and I wasn't, and suddenly... Suddenly I was very sad. SoftFloat is supposed to be "the thing that is correct." It's the ultimate tech industry oracle, the final reference on one plus one. TestFloat tests hardware against SoftFloat. FPGA developers validate against SoftFloat. When your personal deity lies, when addition and subtraction themselves dissemble, the epistemological foundation shifts under you. You can't trust the thing you trusted, and now you have to ask what else you can't trust. What makes my situation lonelier is that finding the bug doesn't feel like a win, because it shouldn't have been there in the first place. I wasn't looking for SoftFloat bugs. No one gives you an award for breaking addition and subtraction. I was trying to validate my own work and the ground moved, and now I just feel like I'm waiting for the next earthquake. https://lnkd.in/g67ZCkMu https://lnkd.in/gG7DC-26 https://lnkd.in/g9rJs6ej https://lnkd.in/gV28f9vp https://lnkd.in/g3EPE_wW
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Adam Roe
ZLABS Agency • 8K followers
AI Inference Leaps with Cerebras-AWS; World Models Surge in Funding. Frontier Hardware and Model Innovations Reshape AI Landscape At a glance: AWS announced on March 16, 2026, the deployment of Cerebras CS-3 systems within AWS Bedrock, delivering the industry's fastest AI inference using open-source large language models alongside Amazon’s proprietary Nova models. This partnership introduces a disaggregated architecture that pairs AWS Trainium chips for the prefill phase of AI generation with Cerebras' Wafer-Scale Engine for the decode phase, achieving a fivefold increase in token throughput. The setup optimizes high-speed inference by assigning specialized hardware to distinct computational stages, enabling enterprises in logistics and finance to process complex queries at unprecedented speeds without compromising accuracy. Read full brief: https://lnkd.in/gSRyC9i6
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Guilherme Marshall
20 years' experience in… • 3K followers
ExecuTorch 1.0 is here - bringing a unified PyTorch workflow to billions of Arm-based edge devices. For those building at the edge, that means: 🚀 Faster, simpler development and deployment 📱 Greater reach for apps and workloads ⚡ Higher performance and efficiency across Arm CPUs, GPUs, and NPUs With Arm KleidiAI, CMSIS-NN, and TOSA integrations in ExecuTorch, it’s now easier than ever to bring high-performance AI to life everywhere.
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