Speaker unverified: evaluation

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…e evaluate all these different models. And so you just know when AlphaFold3 was trained, you know, when you’re, you intentionally trained to the same date or something like that. Exactly. Right. Yeah. And so this is kind of the way that you can somewhat easily kind of compare these models, obviously, that assumes that, you know, the training. You’ve always been very passionate about validation. I remember like DiffDoc, and then there was like DiffDocL and DocGen. You’ve thought very carefully about this in the past. Like, actually, I think DocGen is like a really funny story that I think, I don’t know if you want to talk about that. It’s an interesting like... Yeah, I think one of the amazing things about putting things open source is that we get a ton of feedback from the field. And, you know, sometimes we get kind of great feedback of people. Really like... But honestly, most of the times, you know, to be honest, that’s also maybe the most useful feedback is, you know, people sharing about where it doesn’t work. And so, you know, at the end of the day, it’s critical. And this is also something, you know, across other fields of machine learning. It’s always critical to set, to do progress in machine learning, set clear benchmarks. And as, you know, you start doing progress of certain benchmarks, then, you know, you need to improve the benchmarks and make them harder and harder. And this is kind of the progression of, you know, how the field operates. And so, you know, the example of DocGen was, you know, we published this initial model called DiffDoc in my first year of PhD, which was sort of like, you know, one of the early models to try to predict kind of interactions between proteins, small molecules, that we bought a year after AlphaFold2 was published. And now, on the one hand, you know, on these benchmarks that we were using at the time, DiffDoc was doing really well, kind of, you know, outperforming kind of some of the traditional physics-based methods. But on the other hand, you know, when we started, you know, kind of giving these tools to kind of many biologists, and one example was that we collaborated with was the group of Nick Polizzi at Harvard. We noticed, started noticing that there was this clear, pattern where four proteins that were very different from the ones that we’re trained on, the models was, was struggling. And so, you know, that seemed clear that, you know, this is probably kind of where we should, you know, put our focus on. And so we first developed, you know, with Nick and his group, a new benchmark, and then, you know, went after and said, okay, what can we change? And kind of about the current architecture to improve this pattern and generalization. And this is the same that, you know, we’re still doing today, you know, kind of, where does the model not work, you know, and then, you know, once we have that benchmark, you know, let’s try to, through everything we, any ideas that we have of the problem. oday, you know, kind of, where does the model not work, you know, and then, you know, once we have that benchmark, you know, let’s try to, through everything we, any ideas that we have of the problem. And there’s a lot of like healthy skepticism in the field, which I think, you know, is, is, is great. And I think, you know, it’s very clear that there’s a ton of things, the models don’t really work well on, but I think one thing that’s probably, you know, undeniable is just like the pace of, pace of progress, you know, and how, how much better we’re getting, you know, every year. And so I think if you, you know, if you assume, you know, any constant, you know, rate of progress moving forward, I think things are going to look pretty cool at some point in the future. ChatGPT was only three years ago. Yeah, I mean, it’s wild, right? Like, yeah, yeah, yeah, it’s one of those things. Like, you’ve been doing this. Being in the field, you don’t see it coming, you know? And like, I think, yeah, hopefully we’ll, you know, we’ll, we’ll continue to have as much progress we’ve had the past few years. So this is maybe an aside, but I’m really curious, you get this great feedback from the, from the community, right? By being open source. My question is partly like, okay, yeah, if you open source and everyone can copy what you did, but it’s also maybe balancing priorities, right? Where you, like all my customers are saying. I want this, there’s all these problems with the model. Yeah, yeah. But my customers don’t care, right? So like, how do you, how do you think about that? Yeah. e you, like all my customers are saying. I want this, there’s all these problems with the model. Yeah, yeah. But my customers don’t care, right? So like, how do you, how do you think about that? Yeah. So I would say a couple of things. One is, you know, part of our goal with Bolts and, you know, this is also kind of established as kind of the mission of the public benefit company that we started is to democratize the access to these tools. But one of the reasons why we realized that Bolts needed to be a company, it couldn’t just be an academic project is that putting a model on GitHub is definitely not enough to get, you know, chemists and biologists, you know, across, you know, both academia, biotech and pharma to use your model to, in their therapeutic programs. And so a lot of what we think about, you know, at Bolts beyond kind of the, just the models is thinking about all the layers. The layers that come on top of the models to get, you know, from, you know, those models to something that can really enable scientists in the industry. And so that goes, you know, into building kind of the right kind of workflows that take in kind of, for example, the data and try to answer kind of directly that those problems that, you know, the chemists and the biologists are asking, and then also kind of building the infrastructure. And so this to say that, you know, even with models fully open. You know, we see a ton of potential for, you know, products in the space and the critical part about a product is that even, you know, for example, with an open source model, you know, running the model is not free, you know, as we were saying, these are pretty expensive model and especially, and maybe we’ll get into this, you know, these days we’re seeing kind of pretty dramatic inference time scaling of these models where, you know, the more you run them, the better the results are. But there, you know, you see. You start getting into a point that compute and compute costs becomes a critical factor. And so putting a lot of work into building the right kind of infrastructure, building the optimizations and so on really allows us to provide, you know, a much better service potentially to the open source models. That to say, you know, even though, you know, with a product, we can provide a much better service. I do still think, and we will continue to put a lot of our models open source because the critical kind of role. I think of open source. Models is, you know, helping kind of the community progress on the research and, you know, from which we, we all benefit. And so, you know, we’ll continue to on the one hand, you know, put some of our kind of base models open source so that the field can, can be on top of it. And, you know, as we discussed earlier, we learn a ton from, you know, the way that the field uses and builds on top of our models, but then, you know, try to build a product that gives the best experience possible to scientists.…

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