AI与生物学:弥合鸿沟,加速发现
Mark: 这是一个,我认为,人工智能(AI: Artificial Intelligence,模拟人类智能的机器或程序)将发挥巨大作用的领域。
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this is a a a space that I mean that there's just going to be a huge amount of leverage with AI.
然而,在这个领域,围绕工具构建似乎仍需投入更多努力。这有点不可思议,我们现在身处2025年,但生物学领域还没有像化学元素周期表那样的等效工具。我们认为,这可能是需要构建的最重要的一套工具。当我们最初设定本世纪末治愈和预防所有疾病的目标时,说实话,大多数科学家都无法正视我们。
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It still seems like there could be a lot more effort in this space around building tools and it's kind of this crazy thing that we're you know here in you know 2025 and there's not the kind of periodic table of elements equivalent for biology. We think that this is like probably one of the most important sets of tools that you need to build. When we first set out that the goal to cure and prevent disease by the end of the century, people like honestly most scientists couldn't look at us with a straight face.
主持人: 这太疯狂了。
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>> And that's crazy.
Mark: 是的。这是真的,因为如果你只是决定把钱花在资助全国每个实验室的下一个最佳研究项目上,那么这条路是行不通的。我认为,生物学界的人认为这雄心勃勃得有些疯狂。而人工智能(AI)领域的人则觉得,这有点无聊,它会自动发生。我知道,这就像是,好吧,两者之间存在一些需要弥合的鸿沟。
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>> Yes. And it was true because if you just decided to spend the money funding the next best grant for every single lab in the country, like you there was no pathway to that being true. The biology folks, I think, looked at it as if it were crazy ambitious. And then the AI folks are like, well, that's kind of boring. That's just automatically going to happen. I know. It's like, okay, there's something in between there that needs to be bridged.
陈-扎克伯格倡议的使命与策略
主持人: 马克、普莉希拉,欢迎来到a16z播客。
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>> Mark Priscilla, welcome to the Asz podcast.
Priscilla: 谢谢邀请。
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>> Thanks for having us.
Mark: 是的,很高兴来到这里,很兴奋。
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>> Yeah, great to be here. Excited.
主持人: 好的。很高兴能邀请到你们。你们正在做一些令人兴奋的事情。
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>> All right. Excited to have you. You're doing exciting stuff.
Mark: 是的。为此,差不多十年前,你们启动了陈-扎克伯格倡议(Chan Zuckerberg Initiative, CZI: 马克·扎克伯格和普莉希拉·陈创立的慈善组织),其使命和宗旨是在本世纪末治愈、预防和管理所有疾病。
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>> Yeah. Well, to that end, almost a decade ago, you guys started the Chan Zuckerberg initiative with the mission and intent to cure, prevent, manage all disease by the end of this century.
你们本可以投入时间和资源去做很多事情。我们来谈谈,是什么促使你们选择这项使命?普莉希拉,不如我们从你开始,听听你的故事。
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There's a lot of missions that you guys could have poured your time and resources into. Why don't we talk about take us behind the conversations of why you guys picked this one? Maybe Priscilla, why don't we start with with you and you hear your side of the story.
Priscilla: 当我谈到我们如何从事基础科学研究时,人们总是感到惊讶。
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>> It always surprises people when I talk about how we work in basic science research.
我曾是一名儿科医生,人们总以为这一定与医学有关。对我来说,你知道,我之所以选择医学,是因为我想改善人们的生活。我想有所作为,我想能够帮助他人。我想,在加州大学旧金山分校(UCSF: University of California, San Francisco,一所顶尖的医学研究机构)接受儿科医生培训时,我遇到了很多病人,坦白说,还有很多小孩子和家庭,我们根本不知道他们的问题出在哪里。如果他们足够幸运,可能能说出一个特定的基因名称。或者他们可能被归入一堆其他疾病中,然后会有一份通用的PDF文件打印出来,上面写着“这就是我们所知道的”。然后,作为实习医生或住院医生,我的工作就是尝试将几行信息转化为我们应该如何照护病人。对我来说,那是我真正意识到基础科学力量的时候,以及我们如何需要通过基础科学来推动可能性的前沿,没有它,我认为就没有希望的管道。
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Um, I trained as a pediatrician and people always think like, oh, it must be about medicine. And for me, it w, you know, I went into medicine because I wanted to improve people's lives. I wanted to make a difference. I wanted to be able to help others. And I think training as a pediatrician at UCSF, I met a lot of patients and frankly like little kids and families for which like we just had no idea what the problem was. and they might have like a specific gene that they could name if they were lucky. Um, or they could be grouped into a bunch of other diseases and there'd be a general sort of PDF they'd print out like this is what we know. And then it was my job as an intern or resident to try to translate like like a few lines of information to how we were supposed to take care of the patient. And for me, that's when I really like realized the power of basic science and how we need to work on basic science to advance the forefront of what's possible and without that there's sort of I think of it as the pipeline of hope.
主持人: 是的。那你们为什么认为可以治愈所有疾病呢?因为那是一个非常激进的目标。
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>> Yeah. And why did you think um you could cure all disease? Because that's like a very like aggressive goal.
Priscilla: 嗯,你想回答这个问题吗?
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>> Um do you want to do you want to answer that one?
Mark: 是的。嗯,嗯,我的意思是,明确地说,我们不会治愈所有疾病。我的意思是,我们的策略是帮助科学家和科学界治愈所有疾病。所以,这项策略实际上是为了加速基础科学的进展,我们当时的理论是,如果你回顾科学史,大多数重大突破基本上都伴随着新工具的发明,以全新的方式观察现象。对吧?想想显微镜这样的东西,对吧?能够观察细菌,或者在其他领域,望远镜,或者……
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>> Yeah. Well, well, I mean we're not going to cure all diseases to be clear. I mean the the strategy is to help scientists and the scientific community cure all diseases. So the strategy is really one of accelerating the pace of basic science and the theory that we had was if you look at the history of science most major breakthroughs are basically preceded by the invention of a new tool to observe phenomena in a new way. Right? So think about things like the microscope, right? Being able to observe bacteria or you know other fields, the telescope or
主持人: 嗯,你知道,但这……
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>> um you know, but it's
Mark: 仅仅举一个工程学的例子,你知道,如果没有这些工具,就像你写代码却无法单步调试和排查问题一样,对吧?所以,嗯,那就像是过去的日子。
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>> just to use an engineering example, you know, it's without those kind of tools, it's kind of like you're coding without being able to step through the code and debug things, right? So it's um that's like the old days
主持人: 当你……
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>> when you
Mark: 所以,我们在这方面的整体方法基本上是,让我们帮助构建能够加速整个领域发展的工具。我认为这有一个非常适合的利基市场,因为如果你看看科学领域的资金运作方式,你知道,绝大多数资金来自政府和美国国立卫生研究院(NIH: National Institutes of Institutes of Health,美国主要的生物医学研究机构)的拨款。这些资金被分成相对较小的拨款,允许个体研究人员通常研究相当短期的项目。嗯,而开发这些新型工具,无论是成像技术,还是现在大量构建像虚拟细胞模型这样的人工智能(AI)相关事物,通常周期更长,开发成本也更高。所以,想想看,这可能需要大约一亿到十亿美元的投入,在10到15年的时间里,然后你尝试解锁这些工具,并将它们提供给科学界,以加速其发展速度。所以,这大概就是我们的理论。
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>> so so our our whole approach on this is basically let's help build tools that will accelerate the pace of the whole field and I think that that there's a niche that I think fits that because if you look at how funding works in science you know the vast majority of funding comes from the government and NIH grants. it's parcled out into these relatively small grants that allow individual investigators to investigate usually pretty near-term things. Um, and the development of these kind of new types of tools, whether it's imaging or building now a lot of AI things like virtual cell models, um, are longer term, often times more expensive to develop. So think about like on the order of a hundred you know maybe you know hundred million to a billion dollars over a um over a 10 to 15 year period and then you you try to unlock those tools and give them to the scientific community to accelerate the pace. So that's that's kind of the the theory
慈善事业的独特价值:构建共享工具
主持人: 对,而且在很多方面,你似乎不会因为这些工具而获得认可。我的意思是,我们已经注意到,我们有公司在使用你们的工具,他们对此非常满意。但是,嗯,你知道,我甚至不知道情况是这样。所以,
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>> right and and there it seems like there's also something that that's is you don't really get credit for the tools in a lot of ways. I mean, we've been noted, well, we have companies that use your tools and they're very happy about it. But, um, you know, I didn't even know that that was the case. And so,
Priscilla: 这就是为什么它是慈善事业。
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>> that's why it's philanthropy.
主持人: 是的。嗯,确实如此,但大多数人做慈善也是为了获得认可。我的意思是,你知道,这在某种程度上也是其中一部分。那么,我想你们有没有考虑过这一点,或者你们只是觉得,不,这会奏效的,如果它奏效了,那就是我们所需要的一切了。
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>> Yeah. Well, it is, but most people do philanthropy to get credit, too. I mean, you know, like that's a you know, that that's kind of a part of it. So, how did you I guess did you think about that or were you just like, no, like this is going to work and if it works, that's all we need.
我们非常专注于如何真正让每一位科学家变得更好,以及超越科学领域,比如初创公司和初创公司创始人,因为关键是我们无法独自完成这项工作。当我们最初设定本世纪末治愈和预防疾病的目标时,说实话,大多数科学家都无法正视我们。
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We're super focused on like actually making every scientist better and and beyond science like startups, startup founders because I the point is we can't do this alone. And when we first set out that the goal to cure and prevent disease by the end of the century, people like honestly most scientists couldn't look at us with a straight face
主持人: 太疯狂了。
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>> and crazy.
Mark: 是的。这是真的,因为如果你只是决定把钱花在资助全国每个实验室的下一个最佳研究项目上,那么这条路是行不通的。但如果你强迫人们真正思考这个问题,比如“实现这一目标最可靠的途径是什么?”以及“这条可靠途径的障碍是什么?”那么我们就能有所进展,对吧?他们会说,嗯,比如没有共享工具,或者我们没有在大型项目上工作,也没有构建正确的数据集。然后我们就会想,好吧,那我们就可以开始为此做些事情了。嗯,所以这就是构建共享工具的想法的来源,因为现在科学界没有人……
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>> Yes. And it was true because if you just decided to spend the money funding the next best grant for every single lab in the country like you there's no pathway to that being true. But if you forced people to really think about this and like okay what is the most credible pathway to doing this and what are the barriers to that credible pathway then we sort of got somewhere right? They were like, well, like there's no shared tools or like we don't have we're not working on big projects and building the right data sets. And we're like, okay, well then we can start doing something about that. Um, and so that's where the idea of building shared tools cuz no one right now in the science.
主持人: 嗯,这太有趣了。所以基本上,你们说我们要治愈所有疾病,然后他们说,
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>> Well, that's so interesting. So basically, you're like, we're going to cure all disease and they're like,
Mark: 是的,做不到。为什么做不到?嗯,因为我们没有工具。好的,这是一个相当酷的逻辑链。
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>> yeah, can't be done. Why can't it be done? Well, because we don't have the tools. Okay, that's pretty that's a pretty cool sequence.
Mark: 是的。是的。我的意思是,还有一件有趣的事情是,我认为生物学界的人认为这雄心勃勃得有些疯狂。然后人工智能(AI)领域的人则觉得,这有点无聊,它会自动发生。我知道,这就像是,好吧,两者之间存在一些需要弥合的鸿沟。如果你能利用现代人工智能(AI)工具来构建生物学家所需的工具。所以,这是我们思考工作方式的一个重要部分,嗯……
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>> Yeah. Yeah. I mean, there's also this funny thing where the the biology folks, I think, looked at it as if it were crazy ambitious. And then the AI folks are like, well, that's kind of boring. That's just automatically going to happen. I know it's like, okay, there's something in between there that needs to be bridged. And if you can like kind of use the the kind of modern AI tools in order to build the types of tools that biologists need. So that's a big part of how we think about our work is um
主持人: 人工智能(AI)一定是史上最被高估也最被低估的技术,两者同时存在。太奇怪了。
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>> AI has got to be the most overestimated and underestimated technology ever like simultaneously. So weird.
我的意思是,是的,我们可能像早期的互联网一样,但我们认为我们自己以及我们在生物中心(Biohub: Chan Zuckerberg Initiative资助的生物医学研究机构)所做的工作,是前沿生物学与前沿人工智能(AI)的结合,对吧?所以,有一些实验室在从事前沿人工智能(AI)研究,他们基本上,你知道,正在构建最先进的模型。嗯,然后还有很多生物研究机构,它们实际上在做非常前沿的……
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I mean, yeah, we'll probably like the internet early on, but but we kind of think about ourselves and the work that we're doing at the Biohub as frontier biology paired with frontier AI, right? So, there's there are labs that do frontier AI that uh basically, you know, are building the most advanced models. Um and then there are lots of biological research organizations that that effectively do very leading edge
Mark: 研究,以构建,嗯,你知道,要么发现新的数据集,要么应对某些挑战。
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>> research to build um you know to either discover new data sets or or or looking to certain challenges.
主持人: 但到目前为止,还没有人尝试同时做这两件事。当你看看,我的意思是,即使是像AlphaFold(DeepMind开发的人工智能程序,用于预测蛋白质三维结构)这样的惊人成就,它也是基于几十年前产生的公共数据集构建的,对吧,嗯……
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>> But so far there hasn't been anyone who's tried to do both of those at once. And when you look at I mean even something like AlphaFold which is amazing right it's it was built off of this data set that was a public data set that had been produced decades ago right and um
Mark: 我认为,如果你将这两者结合起来,就有机会为训练人工智能(AI)模型生产特定数据集,以构建能够执行特定功能的虚拟细胞。
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>> what what I think you have the opportunity to do if you do both of those together is produce specific data sets for the purpose of training AI models to build virtual cells that can do specific things
主持人: 对。
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>> right
Mark: 所以我认为这是一个非常有趣的领域。
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>> so I think that that's like a a pretty interesting zone to be in
Mark: 在我们所做的一切工作中。你知道,实际上,当我们启动CZI时,我们实际上专注于多个领域,而我们发现,科学研究的回报是迄今为止最大的。所以,我们一次又一次地加倍投入,直到现在,我们已经投入了十年,生物中心(Biohub)确实是我们目前慈善事业的主要焦点。
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>> and of all the things that that we've uh that we've worked on. You know, actually when when we started CZI, we we kind of actually focused on a number of areas and what we found is just that the science research has had by far the biggest return. So, we've just doubled down on it over and over and over until now we're at the point that, you know, we're 10 years in and Biohub is really the like main focus of of our of our philanthropy at this point.
主持人: 嗯,但是,是的,我的意思是,这基本上就是重点。也许你们没有给自己足够的肯定,因为你们似乎在说:“嗯,有小规模的科学研究,我们不想做那个。还有百年尺度的科学研究,那看起来时间跨度很长,但可实现,也很有野心。”但你们实际上已经确定了,我认为这非常棒,宏大的科学挑战,
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>> Um, but yeah, I mean, that's kind of that's basically the focus. Maybe you're not giving yourselves enough credit because you're sort of saying, "Well, there's bite-size science. We didn't want to do that. There's century scale science and that seemed like a long time horizon, but achievable, ambitious." But you've actually identified, you know, which I think is really fantastic, grand scientific challenges
Mark: 它们恰好介于两者之间。它们是10到15年的时间跨度,至少根据你们沟通它们的方式以及你们激励……
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>> that are right in between. They're 10 to 15 year horizons, at least per kind of the way you communicate about them and the way you energize
主持人: 科学界对它们的热情。10到15年是一个有趣的时间跨度,有点像风险投资公司的项目周期,也像一个团队可以共同工作的时间长度。我想知道你们是如何得出这个数字的,以及你们是如何考虑在每个10到15年的周期中承担的挑战的,因为你们宣布这些挑战的方式,让它们变得具体、可实现,并且建立了很高的信誉。
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>> the scientific community about them. 10 to 15 is kind of an interesting time horizon sort of like similar to the time horizon of a venturebacked company similar to the time horizon on which a team can work together for that period of time I think it's how did you get to that number and then how are you thinking about the challenges that you take on in each 10 to 15 year wave because that's concrete achievable you know you build a lot of credibility around it the way that you've announced those challenges
Priscilla: 嗯,我很好奇你们是怎么想的,但对我们来说,当我们审视10到15年时间跨度的宏大挑战时,它必须是那种你一看就觉得“我看到了路径”的项目。
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>> well I'm curious how you guys think about it but for us when we looked at the grand challenges for on the 10 to 15 year time horizon it needs to be like when you look at it you're like I see a path
主持人: 对。
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>> right
Priscilla: 并非所有问题都需要我们来解决,事实上,如果所有问题都解决了,那感觉就应该直接……
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>> not everything needs to be solved for us to take it on in fact if everything's solved then that feels like that should just go
主持人: 足够有野心。
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>> ambitious enough
Priscilla: 是的,就像你们说的,我们有一些风险偏好,对吧?所以我们希望做那些有可靠途径、有人能掌舵的项目。而且要有足够的模糊性,让我们觉得可以承担这种风险,如果成功了,回报甚至可能超出预期。我们在生物中心(Biohub)中对此进行建模的方式是,我们有三个生物中心。我们在旧金山、芝加哥和纽约各有一个。纽约的生物中心专注于细胞工程。你知道,我们能否工程化细胞,让它们进入体内检测信号、读取信息或执行特定动作。在芝加哥,我们正在构建组织,并研究组织内的细胞间通信。而在旧金山,我们正在研究深度成像和转录组学(Transcriptomics: 研究细胞内所有RNA分子的科学)。
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>> yeah like you like we we have we have some risk appetite right so we want things where we're like there's a credible pathway someone who is at the helm who can do this And there's enough ambiguity where we feel like we could take on that risk and if we do it like the the returns could be higher than even expected and the way we modeled that from you know in the biohubs is we we have three biohubs. We have one in San Francisco, one in Chicago, one in New York. The one in New York works on cell engineering. You know can we engineer cells to go in and detect signals, read it out or to take certain actions. In Chicago, we're building tissues and looking at uh tissue cell communications within tissues. And then in San Francisco, we're looking at deep im imaging and uh transcrytoics.
这些工作地点的选择并非偶然。我们还会考虑合作大学,因为有人来到生物中心进行协作、跨学科的工作,并且不受传统实验室的束缚。但我们也会利用这些学术机构中支持这项工作的实验室。所以,嗯,这就是我们选择宏大挑战和地点的考量。然后,大型语言模型(LLMs: Large Language Models,基于海量文本数据训练的深度学习模型)和人工智能(AI)的介入,这种叠加效应变得非常有趣,因为我们当时已经在构建工具来测量有趣的数据,构建数据集,但我们还不太清楚如何利用它们。嗯,当大型语言模型(LLMs)出现时,我们觉得,哇,我们现在可以理解所有这些数据了。我很好奇你们如何看待治疗领域的成功。所以,你知道,我们非常关注理解生物学,有时我们会投资那些希望解锁全新生物学领域、我们尚不清楚病因的疾病的初创公司。然后还有另一群人,他们会说,嘿,好的,既然我们明白了问题所在,那就来解决它吧。嗯,让我们用药物介入。让我们用一种新型化学物质,一种新型抗体。你们认为陈-扎克伯格生物中心(CZI Biohub)在未来10、20、50年,在你们所促成的新药方面,成功会是什么样子?
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And that work the locations are not by accident. We also look at the partner universities because we have folks who come to the biohubs to do this work collaborative, interdisciplinary um and sort of unconstrained by the traditional lab. But we also build off of the labs at these academic institutes that support the work. And so uh that's how we sort of choose the grand challenge and um and the locations. And then the sort of layering and the uh large language models and AI coming into the picture has been so interesting because we were already building tools to measure interesting data building the data sets but we didn't really know what to do with them yet. Um and large language models coming onto the scene we're like wow we can make sense of all of this now. I'm curious what you view success as in the therapeutic realm. So, you know, we think a lot about understanding biology and sometimes we bet on startups that want to unlock completely new biological areas, diseases where we don't know what's going wrong. And then there's another group of folks who kind of say, hey, okay, now that we understand what's going wrong, let's fix it. Um, let's come in with a drug. Let's come in with a new type of chemistry, a new type of antibbody. How do you what do you think success for the CZ Biohub looks like 10, 20, 50 years from now in terms of the new medicines that you've enabled?
Priscilla: 我们希望看到一个社区爆发式增长,他们正在构建这些,嗯,就是部署精准医疗(Precision Medicine: 根据个体基因、环境和生活方式差异为病人量身定制治疗方案)的新浪潮。就像我们,我认为无论是罕见病还是常见病,我们实际上都在讨论被我们笼统归类为个体生物学的现象。嗯,而且我们通常不知道它是如何发生的,对吧?我们知道你存在这种突变,或者最糟糕的噩梦是,你有一个意义不明的变异。那到底意味着什么?
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>> We want there to be like an explosion of a community who are building these um just the new wave of what it means to be deploying precision medicine. like we like I think for rare diseases and common diseases alike, you're really talking about individual biology that we sort of lump together. Um and uh they and we often don't know how it happens, right? We know that you have this mutation or the worst nightmare is you have a variant of unknown significance. What does that even mean?
主持人: 可怕的我们。
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>> The horrible us.
Priscilla: 是的。可怕。你就像是告诉某人你好像知道些什么,但我们不知道它意味着什么。但如果你看看我们如何能够研究变异并观察单细胞转录组学,我们开始能够说,好的,这个变异实际上影响了这组下游细胞,然后我们开始观察表达的蛋白质,以及它与健康细胞看起来有什么相似或不同之处。然后你就可以开始靶向治疗了。好的,比如,我们把那个作为一个靶点。而且你既能知道你想要构建的靶点的特异性,这基于连接突变与蛋白质表达的能力,也能预测脱靶效应。副作用是什么?因为你还会知道这种药物在身体其他部位可能与什么相互作用。所以这些都是罕见的,而且我真的认为大多数疾病都应该被视为罕见病,因为我们每个人的生物学特征都不同,而现在我们只是被笼统归类,对吧?我们根据年龄、人口统计学、血统被归类,如果我们足够幸运能达到那种理解水平的话。但实际上,我们每个人的生物学特征都不同,比如说,如果你看看高血压或抑郁症,我们基本上都是通过试错法,说‘我们试试那种药,看看会发生什么’。但真正应该发生的是,通过观察个体生物学特征,能够精准、准确、快速地治疗人们。我们希望赋能基础科学,如果人们能利用我们构建的模型来开发所需的诊断工具和治疗方法,我们会非常高兴。
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>> Yes. Horrible. And you're like you tell someone you kind of know something but we don't know what it means. But if you look at the way we've been able to look at variants and look at single cell transcrytoics, we're starting to be able to say, okay, this variant actually impacts this set of downstream cells and then we start looking at the proteins that get expressed and how it looks similar or different to what a healthy cell would look like. Then you can start targeting. Okay, like let's look at that as a target. And you both know the specificity of the target you want to build based on the ability the ability to connect mutation to protein expression as well as to be able to predict off target effects. What are the side effects? Because you also know where else that drug will be able to interact with the body. And and so those are rare like and and but I really think most diseases should be thought of as rare diseases because each one of our biology is different and right now we just get lumped right we get lumped based on age demographics ancestry if we're lucky uh to have that level of understanding but truly each one of our biology is different and say like if you look at hypertension or depression like we kind of just go by trial and error and saying like let's just try that drug and see what happens. happens. But what should really happen is being able to precisely and accurately and quickly treat people by looking at individuals biology. We want to enable the basic science and we would be thrilled if people picked up the models that we build to be able to build the diagnostics, the therapeutics that need to come.
数据集与工具的开源力量
主持人: 你们构建了令人惊叹的数据集。我必须说,我的意思是,你们可能听不到来自初创公司、制药公司和研发社区的反馈,但它们确实存在,因为你们致力于开源,所以人们可能不会都撰写论文,但他们正在使用这些工具。嗯,我们投资组合中有一家初创公司正在研究特发性肺纤维化(Idiopathic Pulmonary Fibrosis, IPF: 一种慢性、进行性、致命性的肺部疾病,病因不明)。这个名字就说明了这种疾病有多么令人困扰。它是特发性的,我们不知道它为什么会发生。IPF就是这样命名的。所以,你知道,他告诉我,他利用你们的细胞基因图谱来观察数百万个患病和未患病患者的单细胞,试图精确定位成纤维细胞,深入研究成纤维细胞及其基因表达。这试图,你知道,利用这些信息来指导,嘿,在这种本质上是奇怪的、特发性起源的疾病中,我可以在哪里寻找新的药物靶点。所以,嗯,我认为有一大批创新者热爱这些工具、可视化、查询系统,以及你们为使数据极易获取而构建的软件方法。所以,
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>> You've built amazing data sets. I have to say like I mean you may not hear the feedback from the startup community and the pharma community and the R&D community but it's there because you've committed to open source and so people may not be they may not all be writing papers but they are using those tools. Um there's a startup in our portfolio working on idiopathic pulmonary fibrosis. The name tells you how vexing the disease is. It's idiopathic. We don't know why it happens. The IPF is named that way. And so, you know, he was telling me that he used your cell by gene atlases to look at millions of single cells in patients with disease, without disease, try to pinpoint the fibroblasts, double click on the fibroblasts and their gene expression. It's try to, you know, use that to inform, hey, where could I go after a new drug target in this disease that's fundamentally a strange clump of idiopath, you know, idiopathic um origin. So um I think there's a huge there's a huge group of innovators who are who love the tools, the visualizations, the query systems and really the software approach that you built to making that data incredibly accessible. So
Mark: 不过,Cell by Gene(一个用于单细胞数据注释和共享的工具)的诞生几乎是个意外。
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>> cell by gene is like almost an accident though.
主持人: 告诉我们更多。
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>> Tell us more.
Mark: 那么,你想分享一些关于Cell by Gene的信息,还是我来开始?嗯,我的意思是,我不知道你想深入哪个部分,但总的来说,细胞图谱的工作,我的意思是,这有点不可思议,我们现在身处2025年,但生物学领域还没有像化学元素周期表那样的等效工具,对吧?所以,很多灵感来源于此,就是,好吧,我们如何通过在生物中心(Biohub)的工作以及其他拨款,能够汇集并标准化一种格式,从而拥有所有这些数据。当我们刚开始时,我们甚至没有想到要用它来构建虚拟细胞模型。我认为这只是随着人工智能(AI)工作的进展才逐渐成为焦点,但这确实是一件非常令人兴奋的事情。我们当然应该花大量时间在虚拟细胞模型上,但我不太确定你想在细胞图谱方面了解什么。
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>> So do you want to share a little bit about cellene or do you want me to start? Well, I mean, I don't know which part you want to get into, but I mean, but the cell atlas work overall, I mean, it's kind of this crazy thing that we're, you know, here in, you know, 2025 and there's not the kind of periodic table of elements equivalent for biology, right? So, that was sort of a lot of the inspiration of it was all right, how do we both through work that we're going to do in the Biohub and through other grants um be able to pull together and standardize a format where you can have all this data. And when we were starting off, we didn't even necessarily have in mind that we were going to use that to build virtual cell models. I think that's sort of just come into focus as the AI work has advanced, but that's a very exciting thing. We should definitely spend a bunch of time on the virtual cell models, but I'm not sure what you wanted to get into on the cell atlas.
Priscilla: 嗯,单细胞工作是我们十年前启动的首批RFA(Request for Applications: 资助申请请求)之一,当时我们觉得,好的,我们认为这是可行的。我们实际上资助了其方法学研究,以标准化其执行方式。那是十年前的事了。然后我们资助了一些实验室开始构建那个数据集。但我们当时想,有数百万甚至数十亿种不同的细胞类型和排列组合。我们该怎么做呢?而且,嗯,特别是在一项新兴技术的情况下。所以我们最终资助了一些团队,他们开始工作,然后他们告诉我们他们遇到了一个问题。他们的工作流程中存在一个瓶颈,因为他们无法足够快地注释数据。嗯,所以我们构建了Cell by Gene,它是一个注释工具。这是其最初的来源。所以我们构建了这个注释工具,让从事单细胞科学研究的人能够轻松地注释数据。然后我们将收集到的数据公开发布,以便人们可以共享。但由于每个人都开始使用相同的注释工具,所以每个人都在相同的数据格式上实现了标准化。
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>> Well, the single cell work is was one of our first RFAS 10 years ago we started and we were like, okay, we think this is possible. We actually funded the methodology for it to to standardize how it was going to be done. So that was 10 years ago. And we then were we seated a few labs to start building out that data set. But we were like there are like millions or billions of different cell types and different permutations. Like how are we going to do this? And um especially with like a burgeoning technique. And so we ended up um seating a few groups and they started doing work and then they told us they had a problem. There was a uh there was a bottleneck in their workflow because they couldn't annotate the data fast enough. Um and so we built cell by gene was an annotation tool. That's the original source of this. So we built the annotation tool to make it easy for people to who are doing single cell science to be able to annotate the data. And then we put we put the data that we collected publicly so people could share. But because everyone started using the same annotation tool, everyone was standardized then on the same data formats
Mark: 然后围绕这个工具开始形成一个社区,他们想要回馈并构建这个图谱。所以现在十年后,数百万个细胞已经被构建成这个共享资源,供整个科学界使用。我们只资助了大约25%。75%来自更广泛的社区,他们认为这很有用,而且有一个简单的方法可以让我们标准化并构建相同的元数据。
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>> and then there started being a a community around the tool and they wanted to share back and build the atlas. So now after 10 years there are millions of cells that have been built into this uh shared resource for the entire scientific community. We only funded about 75% of it. Sorry that's wrong. We've only funded 25% of it. 75% came from the broader community saying this is useful and there's an easy way for us to standardize and build the same metadata.
主持人: 没错。
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>> That's right.
Mark: 这就像一个有趣的,你称之为网络效应,对吧?
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>> It's like an interesting what you'd call a network effect, right?
主持人: 是的。我正要说这听起来像互联网。是的。
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>> Yeah. I was going to say it sounds like the internet. Yeah.
Mark: 为注释而来,为虚拟细胞模型留下。
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>> Come for the annotation, stay for the stay for the virtual cell model.
Priscilla: 嗯,当我们开始这项工作时,让所有参与者都采用一致的格式非常重要。这样它就可以被使用和移植。然后一旦这种方式流行起来,成为完成任务的方法,其他人就觉得它很有价值。
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>> Well, it was very important when we were getting started with the work to have everyone who was doing it have a consistent format. So that way it could be used and portable. And then once that kind of took off as as the way that it would get done, then other people just found it valuable.
主持人: 是的。甚至相对于以前的数据库,比如GIO等等,它们根本没有那么标准化或经过质量控制。
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>> Yeah. And even relative to prior data bases like GIO and and whatnot, they're just simply not as standardized or QC.
Priscilla: 是的。控制。
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>> Yeah. Control.
主持人: 是的。
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>> Yeah.
虚拟细胞:生物学研究的未来
主持人: 让我们来谈谈虚拟细胞。这是你们将重点关注的重大挑战之一。嗯,也许可以谈谈它的前景或希望,以及可能面临的一些挑战或我们目前的进展。
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>> Let's get into virtual cells. One of the the great challenges that the grandchild you would focus on. Um maybe talk about what is the promise or the hope and maybe some of the challenges or where we're at with it.
Mark: 是的。我的意思是,我们认为这在目前将是最重要的工具之一,基本上是构建从蛋白质到细胞内不同结构,再到整个虚拟免疫系统或不同层级结构的层次体系。我们认为这最终将成为一套非常重要的工具,让人们能够有效地为不同的科学工作生成假设。嗯,你知道,甚至在你真正进行完整实验之前,你就可以对它的运行方式进行一些估算。它将对普莉希拉几分钟前谈到的某些精准医疗类型的例子有所帮助,但我们认为这可能是你需要构建的最重要的一套工具之一,而且它不是单一的东西,对吧?所以可以从不同的角度来处理这个问题,细胞图谱数据有助于在细胞层面理解事物。嗯,我们目前正在做的一件非常重要的事情是,有一家很棒的公司Evolutionary Scale,他们拥有一批曾在Meta从事蛋白质折叠模型研究的科学家,现在正加入生物中心(Biohub),而其负责人亚历克斯·里夫斯(Alex Reeves)实际上将担任整个科学项目的负责人,这实际上很有趣。
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>> Yeah. I mean, we think that one of this is going to be one of the most important tools at this point is basically building up the kind of hierarchy from proteins to um to just different structures within the cell to whole to like whole like a virtual immune system or different levels of hierarchy. And we think that this is going to end up being like a very important set of tools for people to effectively generate hypotheses for for different science work. um you know even before you get to the point where you're really running full experiments in it you can come up with some um estimate of how that might run um it will be useful for some of the precision medicine type um examples that Priscilla was talking about a few minutes ago but we think that this is like probably one of the most important sets of tools that you need to build um and it's not a single thing right so there's different angles to to come at this from the cell atlas data is helpful for understanding things on a cellular level. Um, one of the the kind of most important things that we're doing right now, the the um there's this this great company, Evolutionary Scale, who actually had a bunch of researchers who'd formerly worked at Meta on protein folding models, um, is joining a Biohub and and Alex Reeves, the the, uh, leader of it, is actually going to be the the kind of head of the whole science program, which is actually kind of interesting.
Mark: 是的。当你想到人工智能(AI)和生物学结合在一起,实际上是由一个懂生物学的人工智能(AI)专家来领导,而不是一个对人工智能(AI)有所了解的生物学家来领导时,我认为这多少说明了我们认为这些事物的相对重要性所在。但我的意思是,我们基本上认为,你知道,就像普莉希拉之前提到的不同生物中心(Biohub)一样。那么,纽约的细胞工程工作将基本上使你能够拥有可以记录身体周围正在发生的各种事情的细胞,并共享这些数据,然后你可以将其构建成模型。芝加哥生物中心(Biohub)能够记录炎症,嗯,并基本上研究它,以帮助理解,嗯,比如那个。那是一个不同的数据集。我们有成像研究所,我们刚刚训练了第一批围绕它的模型,这些是第一个空间模型,用于理解细胞在不同状态下的外观,最终就像你在行业方面对语言模型有一个类比一样,你拥有不同的能力,然后随着时间的推移,你将它们训练成模型,它变得越来越通用。
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>> Yeah. when you think about it where it's like you have AI and biology coming together and really it's like an AI person who understands biology is running it rather than a biologist who has some understanding of AI. I think just kind of speaks a little bit to where we think the the relative um weight of these things is. But I mean we basically view, you know, like Priscilla was saying with the different biohubs. Then New York doing cellular engineering will basically make it so that you can have cells that can record different things that are going on around the body and and share that data and then you can build that into models. The Chicago Biohub being able to record inflammation um and and basically study that in order to kind of help understand um like that. That's a that's a different data set. We have the imaging institute which is we just trained our our first set of models around that which are the first like spatial models around understanding like the way that that kind of cells look in different states and eventually just like you have this analogy on the um kind of the industry side around language models where you have different capabilities and then over time you train them into models and it gets more and more general.
主持人: 这就是这里的想法。
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>> That's kind of the idea here.
所以我们将围绕重大的生物学挑战来建设生物中心(Biohub)。生物中心(Biohub)将构建工具,生成新颖的数据集。我们将基于这些数据构建模型,然后最终将模型组合成一个日益通用的虚拟细胞视图,这将对科学家以及希望从事药物研发的初创公司和企业都有用,尽管这不是我们整个工作的一部分,但我认为这显然是需要发生的非常重要的一部分。
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So we'll we'll we'll build the biohubs around grand biological challenges. The biohubs will build tools that will generate novel data sets. We will build models based on those and then eventually combine the models into an increasingly general view of a virtual cell that will be useful um both for scientists and hopefully startups and companies that are working on finding drugs which is not our part of the whole thing but but I think is obviously a really important part of what needs to happen.
主持人: 是的。你知道,你们在做投资时总是考虑风险,我认为使用虚拟细胞模型进行虚拟生物学的承诺是,你实际上可以承担风险更高的想法。现在,比如,拨款很难获得,湿实验室的工作既昂贵又缓慢,而且不仅仅是钱的问题,还有时间。所以你必须选择一些你认为有一定成功可能性的项目,以维持你的实验室生涯。因此,这自然会促使人们承担一些风险,但不是很多风险,因为他们需要确保在一定时间内达到一定的成功率,以获得终身教职或发表论文,或者完成他们需要做的任何事情。但如果你有一个虚拟细胞模型,可以模拟高质量的生物学过程,那么你就可以在计算端开始测试和调整,提出风险更高的问题,那些在实验室中进行会耗费大量时间和资源的事情,并且在投入时间和金钱进行湿实验室实验之前,实际上可以在模拟环境中看看是否有前景。
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>> Yeah. And you know, you guys think about risk all the time in terms of when you make investments like I think the promise of being able to do virtual biology using a virtual cell model is you can actually take on riskier ideas. right now like grant funding can be hard to come by and the wet lab work is expensive and slow and it's not just you know money it's also time and so you have to choose something that you think is going to have some likelihood of success to keep your lab career going and so it naturally lends people to take on like some risk but not a lot of risk because they need to make sure that they are hitting like a certain percentage of the time to make tenure or publish or whatever they need to do. But if you had a virtual cell model where you could simulate really highquality biology, you could actually then start testing and tinkering on the computational side and like ask riskier questions, things that would have been expensive and t costly in terms of time and resources to do in the lab and actually see if there is promise doing the experiments in silicone before you make the time and money investment in the wet lab.
主持人: 你们认为它有点像一个模式生物吗?
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>> Do you think of it kind of like a model organism?
Priscilla: 是的。就像它是新的果蝇。
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>> Yeah. like it's the new fruit of fly.
主持人: 是的。我本来想问,考虑到细胞的复杂性,你们认为这个模型能达到多高的准确度?我的意思是,假设你们能让它完美准确地代表一个细胞,但虚拟细胞需要多高的准确度才能有用呢?
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>> Yeah. I was going to ask given the complexity of a cell, like how close um like how accurate do you think you'll get the model too? I mean just assuming I mean maybe you get it to like a perfectly accurate representation of a cell, but like how accurate to be useful with the virtual cell have to be?
Priscilla: 我认为它显然会不断迭代,变得越来越好,因为现在我们,我们现在仍然只是在谈论转录组学。我们正在扩展到观察细胞的不同方式,但你会获得越来越高的准确性,但我认为它不需要100%准确才能有用,因为你只是想在前端稍微降低一些风险。嗯,你降低的风险越多,效率显然就越高,但即使你只获得方向性信号,它也会很有用。是的,我确实如此。我们确实把它看作一个模式生物,但它以一种对人体具有忠实度的方式存在,就像你知道的,我不想……
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>> I think it will obviously iterate and get better and better because right now we we like right now we're still just talking about uh transcrytoics. are expanding into different ways of looking at the cell, but you get more and more accuracy and but I don't think it needs to be 100% accurate to be useful because you just want to be able to derisk the idea on the front end a little bit. Um, and the more and more you derisk it, the the more efficient it gets obviously, but it will be useful if you even get directional signal. And yes, I do. We do think about it like as a a model organism, but in a way that's like has fidelity to the human body, like you know, like I don't want to
主持人: 所有模型都是错的,但有些是有用的。
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>> All models are wrong. Some are useful.
Priscilla: 是的。
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>> Yeah.
主持人: 这有望在某些方面具有实用性。
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>> This is hopefully has has utility on certain access.
Mark: 没错。就像语言模型一样,你构建了特定的功能。所以它不是,例如,你知道,我们正在发布的一个模型是Variant Former(一种预测基因变异影响的模型),对吧?基本上,你知道,它被训练在一系列有效的配对数据上,你有一个细胞,你对它施加CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats: 一种基因编辑技术)编辑,然后你观察另一端会发生什么,所以它基本上能够做出那种预测,比如,如果你对一个细胞进行这种编辑,很可能会发生什么。嗯,另一个模型是扩散模型(Diffusion Model: 一种生成式AI模型,通过逐步去噪生成数据),基本上你可以描述你希望它模拟的细胞类型,它就会生成一种合成的细胞模型。嗯,再次强调,我的意思是,这很有趣,因为正如普莉希拉之前所说,每个人都是不同的,不同的细胞也有不同的,你知道,你希望能够模拟这些罕见的配置。嗯,至少拥有一个这种可能外观的合成版本是很有趣的,然后你可以针对它进行测试。我认为冷冻电镜模型(Cryo-EM Model: 基于冷冻电子显微镜数据构建的分子结构模型)很有趣,因为它是空间性的。所以它能让你感觉到,你可以拥有所有这些不同的模型,它们能让你基本上观察不同类型的事物,然后你只需随着时间的推移训练它们,让它们变得越来越通用。
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>> Exactly. And just like the language models, you build in specific capabilities. So it's not so for example, you know, one of the models that uh we're we're publishing is is variant former, right? basically you know makes it so that um it's trained on a bunch of effectively pairs of you you have a cell you apply crisper to it in a place you see what comes out at the other side so it's it basically is able to make that kind of a prediction like okay if you have this edit that you're doing to to a cell what is likely going to happen um another one of the models is it's this diffusion model basically you can describe a type of cell that you would like it to simulate and it will just produce a kind of synthetic model of of of the cell Um, again, I mean, it's kind of interesting because to Priscilla's point before about how everyone is different and and like and different cells have have kind of um, you know, you want to be able to simulate these kind of rare configurations. Um, having at least a synthetic version of what that could look like is interesting and then you can test against that. The cryo model I think is interesting because it's spatial. So it kind of gives you a sense of there are all these different models that you can have that allow you to um basically look at different kinds of things and then you just train them in to be increasingly general over time.
主持人: 哇。非常有趣。那么这种建模技术基本上是大型语言模型(LLMs)吗,或者说,是否存在一个推理模型?它只是……
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>> Wow. Very interesting. And is the is the modeling technology basically LLMs or like like is there is there a reasoning model? Is it like a just
Mark: 哦,这实际上,是的。我知道这也很吸引人,因为其中一个新模型,嗯,我认为这个模型还处于非常早期,但它基本上是第一个基于生物学的推理模型。所以,这个想法是,嗯,是的,你实际上拥有这些以不同方式模拟世界模型的模型,然后你希望它不仅能够,嗯,仅仅吐出相关性,对吧,就它发现了什么而言,而是能够真正地推理事物将如何演变以及为什么会发生。嗯,我认为那个模型还处于相当早期,但它在概念上很有趣,我认为这显然将是一个重要的方向。
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>> Oh, that's actually Yeah. I know that's a fascinating one too and because one of the new models um I think this one is very early but it's um it's it's basically the first reasoning model over biology. So the the idea is that um yeah, you you you effectively have these models that that kind of simulate world models in different ways and then you want it to be able to not just um be able to spit out correlations, right, in terms of like what it's found, but actually be able to kind of reason through how things would would evolve and why things would happen. Um I think that one's quite early but it's uh but it is interesting conceptually as what I think is clearly going to be an important direction
主持人: 嗯,就这些模型如何演变而言。
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>> um in terms of how these models evolve.
主持人: 是的。不,因为我当时在想,你知道,如果它不起作用,你接下来的问题就是为什么?
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>> Yeah. No it because that's what I was thinking you know that if it doesn't work the next question you have is why?
Mark: 是的。
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>> Yeah.
主持人: 你知道,就像……
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>> You know like
Mark: 但我认为你在推理中发现的类比……
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>> but I think what you find in reasoning the the analogy
主持人: 你对你的假设深信不疑。嗯,是的。当然。当然。是的。我的意思是,嗯,
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>> you're married to your hypothesis. Well, yeah. Sure. Sure. Yeah. I mean, the the uh
Mark: 是的。我以为你是在说,如果推理模型不起作用,为什么?我的意思是,我认为,不,我的意思是,语言模型对此的类比是,你需要更好的世界模型或更好的预训练模型,才能使推理效果良好。但是,但是,是的,你只是构建更多……
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>> Yeah. I thought I thought you're saying if if the reasoning model doesn't work, why? I mean, I think the kind of way in No, it's I mean, the language model analogy for that would be you need better kind of world models or or better pre-trained models in order to get the reasoning to be good. But, but it's yeah, you just you build more
主持人: 你在其中构建了更多的功能。而且我认为可能还有一个顺序。
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>> you build more capabilities into it. And I think that there's probably an order, too.
Mark: 所以亚历克斯(Alex Reeves)和Evolutionary Scale团队所做的工作,很多都与蛋白质有关,嗯,这很有趣,因为这显然比细胞数据、细胞图谱的分辨率更小,但是……
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>> So the work that Alex and the evolutionary scale folks worked on is a lot of it is protein um which is interesting because that's at a kind of smaller resolution obviously than the cellular data the cell atlas but
Mark: 假设的一部分是,你可以观察所有这些不同的细胞,并且可以模拟它们的行为方式,但除非你真正对细胞的子组件将如何相互作用有这种分层理解,否则你的理解将是肤浅的。
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>> part of the hypothesis is that you can look at all these different cells and you can kind of simulate how they might behave but you're going to have a somewhat shallow understanding unless you actually have this hierarchical understanding of what um how the sub components of the cells are going to interact.
所以,
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So
Mark: 我们的观点是,你基本上想要构建一个最先进的蛋白质模型,然后让它成为最先进的细胞模型的一部分,一旦你拥有了它,你就可以构建像虚拟免疫系统这样的东西,它允许你模拟,嗯,更复杂的系统。但这有点像是构建这些虚拟模型的分层方法。这很有道理,因为当你进入个性化领域时,你会发现常见的蛋白质组合成一个独特的细胞。所以这从系统角度来看,这使得它更易于管理。这很有道理。有趣。
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>> our view is that you basically want to build up a state-of-the-art protein model and then have that be a part of the state-of-the-art cellular model and then once you have that you build things like the virtual immune system which allows you to simulate um much more complicated systems. But it's sort of this like hierarchical approach to building up these these uh virtual models. That makes a lot of sense because also as you get into personalization, you've got like common proteins combining into a unique cell. So that makes it like from a systems standpoint that makes it like much more manageable. That that makes a lot of sense. Interesting.
Mark: 是的。
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>> Yeah.
主持人: 是的。这非常引人入胜。
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>> Yeah. Know it's it's it's very fascinating stuff.
Mark: 是的。
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>> Yeah.
CZI的未来:统一的生物中心与加速目标
主持人: 那么你们这周要宣布一些大新闻。想给我们一个预告吗?
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>> So you guys are announcing some big news this week. Do you want to give us a sneak preview?
Priscilla: 嗯,我,大新闻是,嗯,我们正在思考如何作为一个团队走到一起。
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Well, I the big news is uh thinking about how we are going to be coming together as one team.
嗯,你知道,过去我们运营过生物中心(Biohub),也开发过软件,还做过一些人工智能(AI)研究,但所有这些都有些分散。但现在,在亚历克斯(Alex Reeves)的领导下,我们将作为一个整体的生物中心(Biohub)走到一起,成为一个运营型慈善机构,共同为实现一个单一目标而从事科学研究,以及我们如何在人工智能(AI)和生物学的交叉点上真正推动生物学和研究的发展。
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Um and you know in the past we have done we've run biohubs and we've done built software we've done some AI research but all of it has been really thinking about has been a little bit decentralized but now under Alex's leadership we are going to come together as the biohub a uh an operating philanthropy where we are doing the science um in service of a singular goal together and how do we actually advance the state of biology and research um at the intersection of AI and biology.
主持人: 太棒了。亚历克斯(Alex Reeves)很棒。所以,
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>> Amazing. Alex is amazing. So,
Mark: 是的。不,他很棒。然后,然后另一件事是我之前提到的那部分,就是,是的。我的意思是,CZI已经专注于许多不同的事情。我们只是随着时间的推移发现,我们觉得我们能够在科学领域做出最大的贡献。所以,我们一直在加倍投入,我们将继续在教育领域开展工作。我们将继续支持当地社区以及这些不同的部分。但展望未来,生物中心(Biohub)将真正成为我们慈善事业的主要推动力,我们对此感到非常兴奋,因为我认为,你知道,当我们开始时……
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>> yeah. No, he's great. And then and then the other thing is that the piece that that I mentioned earlier, which is just Yeah. I mean, CCI has focused on a number of different things. We've really just found over time that we we feel like we've been able to make the biggest difference in science. So, we've just kept on doubling down on it and we're going to continue doing work in education. We're going to continue supporting local communities and and in those different pieces. But going forward, the biohub is really going to be the main thrust of our philanthropy and we're very excited about that because I think that this is there there has been you know when we started
Mark: 我们的使命是看看我们能否帮助科学界在本世纪末治愈和预防疾病。我确实认为,随着人工智能(AI)的进步,这应该能够大大提前实现,这是一个非常有价值、重要且令人兴奋的目标,我们认为我们在生态系统中拥有独特的地位,可以帮助赋能他人在这方面取得快速进展。
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>> the mission to see if we could help the scientific community cure and prevent diseases by the end of the century. I do think with the advances in AI that should be possible to do significantly sooner and that is a very worthy and important and very exciting goal that we think we kind of have a unique place in the ecosystem that we can help empower others to make fast progress on that.
主持人: 所以,显然,从管理、沟通成本等方面来看,去中心化有很多优势,那么你们通过在顶层增加这种新的层级/统一化,试图增加什么?输出是什么?然后,我想,这又会带来哪些复杂性呢?因为这,嗯,抱歉问了一个CEO式的问题。
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So there there's obviously like plenty of advantages to decentralization from a management communication overhead and so forth and so like what are you trying to add by adding this kind of new layer/unification on top like what what are the outputs and then I guess what are the complexities to that because that's um I'm sorry to ask a CEO question.
Priscilla: 不不,我的意思是,我非常,你想先说吗,然后我再补充。
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>> No no I I mean I'm like super you want to go for it then I can jump in.
Priscilla: 是的。显然,有很多优秀的团队在从事前沿人工智能(AI)研究,也有很多团队在从事卓越的前沿生物学研究,而我们认为我们能做的独特之处在于将这两者结合起来。我们已经资助了数据集,也构建了数据集,我们现在正在构建仪器设备,以便能够观察细胞,无论是组织细胞间的通信,还是我们的冷冻电镜(Cryo-EM: 一种电子显微镜技术,用于观察生物分子在近原子分辨率下的结构),通过它我们可以观察到近原子级别的细胞。所以我们不仅能够构建数据集,还能根据我们认为必要的方式来塑造和形成它们,以补充现有的知识体系。我们有优秀的团队在做这项工作,我们正在构建这些人工智能(AI)模型。所以,之所以要一起做,是因为这样我们就能真正完成这个飞轮,比如,你知道,模型在这个领域似乎存在一些空白和盲点。好的,我们该和谁交流?我们如何构建下一个数据集?而且你知道我们在实验室里看到了这一点,元数据将非常丰富,我们可以将其反馈到我们进行建模的方式中。
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>> Yeah. So there are obviously amazing groups doing frontier AI and a lot of groups doing uh great frontier biology and where we think we can do uniquely is actually tie these two together and we are we've funded data sets we've built data sets we're like building the instrumentation now to be able to look at the cell whether it's you know for at the tissue cell communication our cryoEM where we can look at the cell at nearly atomic level. So we have the ability to not only build the data sets but actually shape and form them the way we want based on what we see as necessary to complement the existing body of knowledge. And so we have amazing teams doing that work and we're building these AI models. And so what the reason to do it together is then we can actually complete the flywheel like you know the model is looking like it has some gaps and blind spots in this area. Okay, who do we talk to? How do we build um the next data set? And you know we're seeing this in the lab like the metadata is going to be so rich that we can feed back into the way that we do this modeling. Yeah.
Mark: 我认为这将是极其强大的。而且它不仅仅是,你知道,写下规范然后说‘请交付这个’。这些人需要并肩工作,共同塑造彼此的工作,这样才能真正,嗯,成为越来越准确的人类细胞运作模型。
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I think it's going to be incredibly powerful. And it's it's more than it's more than just like, you know, writing down a spec and saying like please deliver this. Like these people need to be sort of working shouldertoshoulder and shaping uh each other's work for this to actually um be the more and more accurate model of how the human cell works.
主持人: 嗯,是的。这太有趣了,因为这正是人工智能(AI)领域给我们行业带来的最大惊喜,暂且不谈生物学,那就是领域特定模型非常有趣,最初的论点是有些人工智能(AI)会变得非常聪明,在所有方面都比所有人更聪明,但是,嗯……
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>> Well, yeah. It's so interesting because that is exact like that's has been the biggest surprise in the industry for us in AI world like forget biology for one second is that the domain specific models have been like super interesting like the original thesis were like there's just some AIs are get so smart they're going to be smarter than everybody at everything but um
Mark: 就像视频模型一样,每个视频模型在某些方面表现最佳,但并非所有方面都最佳。所以,知道你正在解决什么问题,在人工智能(AI)中反而变得非常重要,嗯,因为你实际上可以获得更好的结果。
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>> like on video models like every video model is best at something but not everything And so knowing what problem you're solving actually turns out to be sort of ironically very important in AI um because you can actually get to a way better result.
主持人: 是的。
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>> Yes.
Mark: 如果你把两者结合起来,是的,我们一次又一次地看到这一点,嗯,以一种……
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>> If you put the two together like yeah we're we're seeing that over and over over again uh in a way that that is
主持人: 我会说这与整个叙事非常反直觉。
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>> I would say very counterintuitive to the whole narrative kind of going into it.
Mark: 而在生物学领域,过去的情况是,或者至少,你知道,一个假设是数据集不在互联网上。所以你需要领域特定模型的部分原因在于数据集不是公开的。
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>> And in biology it used to be the or at least you know one assumption was well the data sets aren't on the internet. So part of the reason you need a domain specific model is that the data sets are not public.
主持人: 你们也通过创建大量数据的开源访问来逆转这一趋势,即使如此,听起来你们仍在押注我们在其他行业看到的趋势,但数据注释和数据管理的方式仍然会有细微差别。
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you guys are kind of bucking that trend too by creating a lot of open- source access to the data and then even then it sounds like you're betting you know on the trend that we're seeing in other industries but still there will be nuance in how you annotate that data curate that data
Mark: 嗯,还有你如何与科学家交流,对吧?因为你不仅要了解数据和模型等等,而且我们不断发现,对话最终变得非常非常重要,对吧?
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>> well and how you talk to a scientist right like so because you have to not only know the the data and the model and so forth but like the conversation is what we keep finding out ends up being very very important right
主持人: 如此丰富和重要,你实际上……
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>> so rich and so important how you actually
Mark: 科学家不会像,你知道,我跟ChatGPT聊天那样去和它交流。所以,这是你可以交流的果蝇。
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>> a scientist isn't going to talk to it like you know I talked to chat at GPT or whatever. So, this is the fly you can talk to.
主持人: 是的。是的。是的。那真的非常令人兴奋。
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>> Yeah. Yeah. Yeah. That that's really that's super exciting.
Priscilla: 而且用户界面实际上非常重要。嗯,你提到了,嗯,你们有一位创始人正在使用Cell by Gene。那个用户界面是故意设计的,不需要有计算或非常深厚的生物学背景就能使用,因为你希望来自不同领域的人来审视这个问题。就像是,看这里,帮助我们解决这里的问题。因此,以一种没有很高门槛的方式构建用户界面,让人们能够探索、学习并将其知识带回自己的工作,这是有意的。我们真的希望,当我们构建这些虚拟模型时,嗯,我们能达到一个境地,让人们的进入门槛越来越低,让他们可以说,你知道,我对此有一些了解,也许我可以贡献一些力量。嗯,一个非常相关的例子是,我认为免疫学与神经退行性疾病有很大关系,对吧,但是……
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>> And the user interface is actually really important. Um you talked about uh you guys have a founder who's using Cell by Gene. That user interface was intentionally designed to not need to have a computational or really a very deep biological background to be able to use because you want people coming from different fields to look at the problem. It's like look here, help us solve problems here. And so building that user interface in a way where it's not a very high barrier to entry to be able to poke around and learn something and bring knowledge back to your work, that's intentional. And we're really hoping when we build these virtual models um that we get to a place where we can allow a lower and lower barrier entry for people to say like you know like I have some knowledge about this maybe I can contribute. Um a very pertinent example is turns out I think immunology has a ton to do with neuro degeneration right but
主持人: 免疫学似乎是所有这些背后的推手,所以它可能是你们百年愿景的一部分。
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>> seems like immunology is behind all this so might be part of your century vision.
Priscilla: 嗯,所以你需要能够让免疫学家介入,理解神经退行性疾病,并理解他们的世界如何融入其中。因此,你越是降低进入门槛,就越能让人们以一种真正协作和跨学科的方式思考。
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>> Uh so you need to be able to allow the immunologists to come in and understand neuro degeneration and understand how their world fits in. And so the more you lower the barrier to entry allows people to actually think in a sort of truly collaborative and interdisciplinary way.
主持人: 那么生物中心(Biohub)会作为一个团队成长吗?比如,你们会在生物中心(Biohub)内部雇佣更多人,还是会转向一种网络模式,拥有更多站点、更多实验室、更多社区驱动的数据集?比如,重点是什么?或者两者兼有?
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So will the Biohub grow as a team? Like will you employ more people at the Biohub proper or are you moving towards more of a network model with more sites, more labs, more communitydriven data sets? Like which which is the thrust? Or maybe it's both.
Mark: 可能两者兼有。我们随着时间增加了新的生物中心(Biohub)。嗯,然后我们也在建立更多这样的中央人工智能(AI)团队。
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>> Probably a little of both. And we've added new biohubs over time. Um and then we're also building up more of this like central AI team.
主持人: 酷。所以,嗯,但我认为这些关于如何建立组织的管理问题非常引人入胜,我们很多方法都受到……
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>> Cool. So um but I don't I think that these organizational questions of how do you set this up are fascinating and a lot of our approach is sort of informed by
Mark: 该领域其他机构正在做什么的启发,因为我,你有点把科学看作是一个投资组合,对吧?社会有一个它正在努力做的事情的投资组合,就慈善事业而言,你希望……
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what the rest of the field is doing because I you kind of think about science as it's this portfolio right society has a portfolio of stuff that it's trying to do and as in terms of philanthropy you want to
Mark: 通过找出还有哪些领域代表不足,来尽可能地发挥增益作用。所以科学默认是非常去中心化的,对吧?这就像拨款的运作方式,以及我认为科学家默认想要的工作方式。
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>> be the most additive that you can be by trying to figure out what else is underrepresented. So science by default is very decentralized, right? It's like kind of the the way that granting has worked, the way that I think scientists by default want to work.
主持人: 嗯……
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>> Um
Mark: 所以我认为我们发现很多的是,找出鼓励协作的方法,嗯,这些方法看起来很简单,但以前并没有发生,却能释放巨大的价值。所以第一个生物中心(Biohub),我们在那里做了两件有趣的事情。一个就是加州大学旧金山分校(UCSF)、斯坦福大学(Stanford: Leland Stanford Junior University,世界顶尖私立研究型大学)和加州大学伯克利分校(Berkeley: University of California, Berkeley,世界顶尖公立研究型大学)之间的合作,所有这些不同地方都有非常聪明的人,他们以前理论上可以找到合作的方式,但实际上并没有一个正式的框架让他们这样做,而这只是允许了更多的合作。
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>> so I think a lot of what we've found is that figuring out ways to encourage collaboration in um ways that otherwise seem very simple but weren't happening before can unlock a lot of value. So the very first Biohub what we did there were two kind of interesting things. One was it was this collaboration between UCSF, Stanford and Berkeley and there are all these really smart people at all these different places who previously I guess in theory they could have figured out a way to work together but there was not really a formal construct for them to do that and this just allowed a lot more collaboration.
主持人: 嗯哼。
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Mhm.
Mark: 另一个是跨学科。基本上是让生物学家和工程师坐在一起,这种观点认为这两个学科需要……
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>> The other one is cross- discipline. Basically having biologists sit next to engineers and this view that like these two disciplines are things that need to um and I I don't know. I mean I'm sure you know you've seen this in a lot of in a lot of the companies but like
主持人: 有这么多有趣的……
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>> it's there's so many interesting
Mark: 在公司里,他们总是喜欢把他们分开。
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>> in the companies they always like set them apart.
主持人: 嗯,这很有趣。不,有趣的是,仅仅通过让两个团队坐在一起,你就能解决多少组织问题,对吧?这就像,无论组织结构图是什么,或者其他什么,都无关紧要。就像你们需要坐在一起,直到你们把这件事做好,然后……
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>> Well, it's interesting. No, it's interesting how many organizational questions or problems you can fix just by having two teams sit together, right? It's like it doesn't matter what the or chart is or like whatever. It's like you guys need to sit next to each other and until you get this thing to work and
Mark: 嗯……
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>> um
主持人: 那是我真正相信的。所以,
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>> that's something I really believe in. So,
Mark: 而且你有10到15年。
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>> and you have 10 you have 10 to 15 years.
主持人: 嗯,不,这就像沟通普遍是一个被低估的问题。是的。嗯,在构建任何东西或解决任何问题时都是如此。所以,
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>> Well, no, it's all like communication is such an underrated problem in general. Yeah. Uh in in all kinds of in building anything or solving anything. So,
Mark: 这很棒。
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>> that's a that's pretty neat.
主持人: 是的。是的。这其实是很简单的事情,但我认为,嗯……
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>> Yeah. Yeah. And it's it's just really kind of simple stuff, but but I think it's um
Mark: 它作为一种模式是新颖的。其中一件事是,我们现在已经复制了这种模式……
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>> it's sort of novel as a model. And one of the things that's so we've now copied this
Mark: 从第一个生物中心(Biohub)到生物中心网络,并将其扩展到其他模型,但看到其他在该领域工作的人也采用类似的模型,这也很棒,因为它是一个非常直观的东西。
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>> from the first Biohub to the Biohub network and expanded it to other models, but it's also just been neat to see um other folks who are working in the field also adopt similar models because it's a pretty intuitive thing.
主持人: 但你知道,在某个时候你会达到一个阶段,你知道,实际上拥有去中心化的工作也非常好,对吧?所以不应该是,我们并不是说所有科学都应该这样运作。我们只是说,这里有它的空间。它可以释放巨大的价值,因为它出于某种原因一直不是默认模式。
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>> But you know, at some point you'll reach the point where you know, actually it's really good to have decentralized work too, right? So it shouldn't be that like we're not saying that this is like the way that all science should work. We're just saying that there's a space for this. It can unlock a lot of value because it for whatever reason hasn't been the default.
Priscilla: 是的。而且我们仍然依赖于……
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>> Yeah. And we still rely on like
主持人: 是的。麻省理工学院(MIT)实验室里有关于这方面的著名故事。他们就是这样发明激光等的,他们把来自不同部门的一群人放在同一个……
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>> Yeah. There's famous like stories in the MIT lab about that. That's how they invented lasers and so forth is they put a bunch of people from different departments in the same
Mark: 实验室。是的。嗯,实际上,物理学是我们获得很多灵感的地方。就像物理学历史上一直都是这样,实验室围绕着大型项目和大型共享资源聚集。嗯,我们,你知道,我们相对集中,但我们仍然依赖许多正在进行精确前沿工作或补充工作的实验室,共同支持这项事业。就是这样。但关于你的扩展问题,还有一个想法是,这也许就像是现代人工智能(AI)实验室。我们本身并没有大量扩展占地面积,但我们正在扩展我们的计算能力。
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>> the lab. Yeah. Well, actually physics is where we got a lot of the inspiration. like physics has just historically been like labs have just rallied around big projects and big shared resources. Um and we will you know we are relatively centralized but we still depend on a lot of labs who are doing sort of exact frontier work or complimentary work to come together to support this. There's that. But one more thought on your expansion question is like and maybe this is like the uh modern AI lab. We are not expanding like a lot of square footage per se, but we're expanding our compute.
主持人: 嗯……
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>> Um
Mark: 是的。
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>> yeah,
主持人: 研究人员不想要为他们工作的员工。他们不想要空间。是的。他们只想要GPU(Graphics Processing Unit: 图形处理器,常用于AI计算),
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>> the research they don't want employees working for them. They don't want space. Yeah. They just want GPUs,
Mark: 代理。所以从某种意义上说,那就是新的实验室空间。嗯,它比湿实验室空间昂贵得多。
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>> agents. So it's just like in a sense that's new lab space. Um it's much more expensive than wet lab space.
主持人: 你们在这方面一直很有创意。即使在过去几年里,你们也创造了分享计算资源的方式。你们让学术实验室能够,你知道,嗯,我忘了你们项目的名字,有点像……
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>> And you guys have always been creative on that. Even in the last few years, you've created ways to share access to compute. You've enabled academic labs to you know um I forgot the name of your program kind of like
Mark: 驻地科学家之类的。
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>> scientists and residents or something like that
主持人: 租赁式的酒店模式。
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rental kind of hoteling.
Mark: 核心是集群。嗯,你知道,如果你看看单个实验室,他们会有……
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>> The core of it is clusters. um you know if you look at individual labs they'll have like
主持人: 比如一个大型实验室会有几十个GPU。
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>> like a large lab would have tens of GPUs
Mark: 嗯,我们是第一个真正构建大规模计算集群的,嗯,现在是上千个,我们计划扩展到万级,那显然需要不同类型的项目,你能够提出不同类型的问题。嗯,而且,这是一个我们使用的资源,但我们也邀请科学家申请,说‘你有什么问题,嗯,可以使用这么多的资源,并能够,嗯,以这种方式促成合作’。
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>> um and we were the first to really build a large scale compute cluster um a thousand now we're we have plans to move to the 10,000 range and that one requires a different type of project obviously you're are able to ask different types of questions um and uh it's a resource that we use but also we've invited scientists to apply and say like what question do you have that uh could use this amount of resource and be able to uh stem uh sort of seed collaborations that way
主持人: 所以,如果有一位科学家正在听,他没有受雇于生物中心(Biohub)或在生物中心(Biohub)工作,但想与生物中心(Biohub)合作,
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>> and so if a scientist is out there listening like who's not employed by the biohub or working at the biohub but wants to collaborate with the biohub
Mark: 你们将创造有趣的……
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>> that you're going to create interesting
主持人: 有趣的途径。
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>> interesting doors
Mark: 来利用这些资源,这太棒了。
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>> to utilize the resources that's awesome
Mark: 是的,我的意思是,GPU在某种程度上是零和的,对吧。但数据不是。所以……
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>> yeah I mean the GPUs are somewhat zero sum Right. So that the data isn't. So
主持人: 是的。说得有理。
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>> Yeah. Fair enough.
展望未来:耐心与紧迫并存
主持人: 是的。所以你们即将庆祝这项工作十周年,嗯。展望未来,你们还能告诉我们些什么,无论是你们对未来的思考,还是指导你们未来成长和演进的原则或北极星?
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>> Yeah. So you're about to celebrate 10 years um doing this. As as you look out in the years to come, what else can you tell us about either things that you're thinking about for the future or maybe even principles or a northstar that's going to guide how you guys grow and evolve going forward?
Priscilla: 你知道,过去十年真的很有趣,因为我最初几年完全羡慕那些在营利性公司工作的人,因为那里有如此清晰的反馈。比如,市场会告诉你,无论是私有的还是公开的,它都会告诉你你是否做得好。
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You know, it's been really interesting in the past 10 years because I actually spent the first few years completely envious of people working for for-profit companies because there's so much clarity. Like the market will tell you whether or not it's private or public will tell you if you're doing a good job.
主持人: 如果他们认为你做得好,
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>> If they think you're doing a good job,
Priscilla: 如果他们认为,他们不总是对的。
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>> if they think you're they're not always right.
主持人: 他们不总是不同。但我仍然羡慕,因为我渴望那种反馈,比如我做得好不好?
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>> They're not always different. But I was still envious cuz that was I was like I craved that feedback like am I doing a good job?
Priscilla: 你知道,十年过去了,我们之所以加倍投入生物学领域,不仅是因为我们实现了我们承诺要做的事情,而且当我们开始这些项目时,它实际上带来的成果超出了我们的预期。然后我就觉得,好的,这是一个我可以抓住的信号,这是一个我们可以真正继续加倍投入并做更多事情的信号。所以我认为,嗯,就是要继续容忍早期的模糊性,当你觉得‘好吧,我要做更多这样的事情’的时候。嗯,而且,嗯,要有耐心,但同时也要愿意拥有长远的眼光,但又不能缺乏紧迫感。因为正是这一路上的所有迭代,才让我们达到了今天这个境地,你知道,我们已经准备好利用人工智能(AI)和大型语言模型(LLMs)所构建的数据集,这都归功于我们一直在做的工作。所以,能够在这种模糊性中,有时在缺乏明确信号的情况下,继续朝着一个宏大目标前进,我认为我们已经为此奠定了基础。
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And you know 10 years in you the reason why we're doubling down on biology is like not only did we achieve what we said we were going to do and when we set out to set out on these projects it actually delivered more than we thought we were going to. And I was like okay that's a signal I can latch on to and like that's a signal I we can really continue doubling down and doing more of that. And so I think it's uh continuing to tolerate the early ambiguity when you're like, "Okay, I'm gonna do more of this." Um and uh and being patient, but uh uh being willing to have a long time horizon, but be impatient at the same time. because it's all those iterations along the way that have sort of allowed us to get to this place where you know to get lucky ready having built data data sets to take advantage of AI and large language models that's because of all the work that we have been doing and so being able to continue moving forward in this ambiguity and sometimes lack of signal on a big goal like I think we've sort of set the DNA for that.
主持人: 太棒了。
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>> Amazing.
Priscilla: 哦,不是双关语。
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>> Oh, no pun intended.
Mark: 是的。但我们能看到有多少人使用这些工具以及反馈。
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>> Yeah. But we get to see how many people use the tools and the feedback.
主持人: 是的。是的。
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Yeah. Yeah.
主持人: 是的。你们有客户,这很酷。
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>> Yeah. You have customers which is pretty cool.
Priscilla: 是的。
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>> Yeah.
主持人: 对于慈善事业来说。这太棒了。
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>> For philanthropy. Like that's awesome.
Mark: 是的。不,构建工具的乐趣之一就是你可以看到……
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>> Yeah. No, it's it's one of the fun things about building tools is like you kind of get to see
主持人: 是的。
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>> Yeah.
Mark: 人们觉得这些工具有多大价值?人们是否使用这些工具来发表重要的研究成果?
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>> How valuable do people find the tools? Do people use the tools in order to publish important work?
主持人: 对。对。对。对。是的。嗯,我的意思是,我们的反馈是它们很棒。
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>> Right. Right. Right. Right. Yeah. And well, I mean our feedback is they're awesome.
Mark: 反馈。
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>> Feedback
主持人: 而且顺便说一句,它们是完全独特的。所以,
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and and completely unique by the way. So like
Mark: 另一件事是,如果你没有这个,你会用什么?就像什么都没有。
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>> the the other thing is like what would you use if you didn't have this? It's like there's nothing.
主持人: 不。是的。这确实是一种空白。我的意思是,需要存在一个完整的链条,从加速基础科学到资助很多人使用它,然后你可以进入生物技术公司,它们基本上可以开始研究新颖疗法,然后是制药公司大规模生产这些疗法。然后,在公共卫生领域的另一端,慈善事业也有其空间,基本上是将这些疗法推广给世界上的每一个人。但这是一个领域,人工智能(AI)将在这里发挥巨大的杠杆作用,而且,嗯,是的,它仍然看起来在这个领域,围绕工具构建和更好地加速整个过程,可以投入更多的努力。
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>> No. Yeah. It's a real it's a real kind of void. I mean there's this whole pipeline that that needs to exist from accelerating basic science to funding a lot of people to use it to then you can get into the biotechs that basically can start to work on on on basically coming up with novel therapies and then you get the pharma companies that do them at scale. And then there's a space for philanthropy on the other side of public health of basically taking the the therapies and and kind of bring them out to everyone in the world. But this is a a space that and that there's just going to be a huge amount of leverage with AI and it is um yeah it's it still seems like there could be a lot more effort in the space around building tools and just accelerate the whole thing a lot better.
主持人: 是的。我确实认为这是你们完全独特的地方。对。其他事情有其他人可以做,但没有人做……
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>> Yeah. And I do think it is the place where you are completely unique. Right. The other things there are other people who can do that but there's nobody doing what
Mark: 那有很好的创始人市场契合度。
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>> that's got good good founder market.
主持人: 是的。创始人市场契合度。我的意思是,如果我们不存在,那会是个问题吗?是的。像这些问题,嗯,作为风险投资人,真的会让你……
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>> Yes. Founder market fit. I mean if we didn't exist would it be a problem? Yes. Like those questions uh really land you know as a VC
Mark: 就像我们其中一个是工程师,另一个是科学家医生。
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>> like one of us as an engineer the other one scientist doctor.
主持人: 是的,对这个方向非常满意。
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>> Yeah very happy this direction.
Mark: 是的。
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>> Yeah
主持人: 我们非常感谢你们,不仅是为了我们的公司,也是为了我们人类,嗯,感谢你们从事这项工作。这是了不起的工作。谢谢你们。
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>> we thank you very much not only for our companies but for us as humans um for working on this work. It's amazing work. Thank you.
Priscilla: 谢谢你们。
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>> Thank you guys.
Mark: 非常感谢。
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>> Thank you so much.