{"topic":{"id":15441,"title":"5 challenges we could solve by designing new proteins | David Baker","slug":"topic","categoryId":4,"createdAt":"2026-01-11 06:39:55.592857","bumpedAt":"2026-01-11 12:29:36.730244","views":152,"postsCount":10,"highestPostNumber":10,"likeCount":23,"closed":false,"pinned":false,"excerpt":"最近有一个实验设计，然后是和另外一个做湿实验的小组一起做的，然后我的工作就是用类似 Diffusion Model 去对蛋白进行改造，然后看看如何改造蛋白可以获得一个可能性能更好的蛋白，然后预测出 10-20 条序列，交给做湿实验的同学去表达，验证，但是我一直觉得这东西很玄乎，因为预测永远只是预测，有可能你电脑里面跑得好好的，然后一表达就出问题然后导师说继续做一下，如果不行就换个方向 https://www.youtube.com/w…","deletedAt":null,"isAnonymous":false,"category":{"id":4,"name":"谈笑风生","slug":"general","color":"25AAE2"},"author":{"id":5151,"username":"Soyo34325","name":"Soyo34325","avatarUrl":"/uploads/image/9d/e5/9de500d3afb55c0fe71e319832f2af75532222efe94bd3de9aea21f0f5c55707.avif"},"tags":[]},"posts":[{"id":70237,"postNumber":1,"raw":"最近有一个实验设计，然后是和另外一个做湿实验的小组一起做的，然后我的工作就是用类似 Diffusion Model 去对蛋白进行改造，然后看看如何改造蛋白可以获得一个可能性能更好的蛋白，然后预测出 10-20 条序列，交给做湿实验的同学去表达，验证，但是我一直觉得这东西很玄乎，因为预测永远只是预测，有可能你电脑里面跑得好好的，然后一表达就出问题\n\n然后导师说继续做一下，如果不行就换个方向\n\nhttps://www.youtube.com/watch?v=PJLT0cAPNfs","cooked":"

最近有一个实验设计，然后是和另外一个做湿实验的小组一起做的，然后我的工作就是用类似 Diffusion Model 去对蛋白进行改造，然后看看如何改造蛋白可以获得一个可能性能更好的蛋白，然后预测出 10-20 条序列，交给做湿实验的同学去表达，验证，但是我一直觉得这东西很玄乎，因为预测永远只是预测，有可能你电脑里面跑得好好的，然后一表达就出问题

然后导师说继续做一下，如果不行就换个方向

https://www.youtube.com/watch?v=PJLT0cAPNfs

\n","createdAt":"2026-01-11 06:39:55.681365","updatedAt":"2026-01-11 06:39:55.681365","replyToPostNumber":null,"replyCount":0,"likeCount":4,"wordCount":173,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"face_holding_back_tears_hugging_face","count":1,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"}],"hasReacted":false},{"reaction":"❤️","count":4,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"},{"id":2872,"username":"芙蓉湖第一树莓果","name":"RaspberryPi"},{"id":4668,"username":"IO","name":null},{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":5151,"username":"Soyo34325","name":"Soyo34325","avatarUrl":"/uploads/image/9d/e5/9de500d3afb55c0fe71e319832f2af75532222efe94bd3de9aea21f0f5c55707.avif","admin":false,"moderator":false,"signatureRaw":"ぜーんぶ弾けなーい！","signatureCooked":"

ぜーんぶ弾けなーい！

\n"}},{"id":70239,"postNumber":2,"raw":"Bio x AI 现在应该挺常见的。\n\n远的不说，现在导师组里就有师兄在用生成模型在做细胞演化和基因表达预测任务，化学那边（我高中同学在 pku 化院）还有用生成式模型做小分子/大分子生成和性质预测的。。。我其实也有点不信这个，之前和高中同学交流，他说其实化学和生物那边很多机理人类还不是太清楚，或许大数据量加持下的 AI 确实能力大砖飞解决问题？而且，更现实的层面，AI4S 应当算是 AI 顶会里相对来说好发文章的方向 :nerd: 像是多模态生成、视频生成之类的，还是太吃组里资源、算力和操作了 :melt: \n\n个人观点是，现在生成式模型在生物/化学中的应用应该还在起步阶段，或许 5-10 年之后，确实会技术爆发。就跟 Transformer 出世 5 年之后爆发出 LLM 潮一样。\n\n# 21 世纪将是生物学的世纪！:nerd:","cooked":"

Bio x AI 现在应该挺常见的。

远的不说，现在导师组里就有师兄在用生成模型在做细胞演化和基因表达预测任务，化学那边（我高中同学在 pku 化院）还有用生成式模型做小分子/大分子生成和性质预测的。。。我其实也有点不信这个，之前和高中同学交流，他说其实化学和生物那边很多机理人类还不是太清楚，或许大数据量加持下的 AI 确实能力大砖飞解决问题？而且，更现实的层面，AI4S 应当算是 AI 顶会里相对来说好发文章的方向 🤓 像是多模态生成、视频生成之类的，还是太吃组里资源、算力和操作了 🫠

个人观点是，现在生成式模型在生物/化学中的应用应该还在起步阶段，或许 5-10 年之后，确实会技术爆发。就跟 Transformer 出世 5 年之后爆发出 LLM 潮一样。

21 世纪将是生物学的世纪！🤓

\n","createdAt":"2026-01-11 07:04:24.220214","updatedAt":"2026-01-11 07:06:02.341199","replyToPostNumber":null,"replyCount":2,"likeCount":2,"wordCount":296,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"❤️","count":2,"users":[{"id":5151,"username":"Soyo34325","name":"Soyo34325"},{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":30,"username":"一只玉米人","name":"玉米🌽","avatarUrl":"/uploads/blob/14/96/14961aeaa46ccbb75a61eec0c27b26e74fb5d1c00ccdcbbe898ca9ea37087dd6.svg","admin":false,"moderator":true,"signatureRaw":"*年月擦身过，暂且问，会更好吗？*","signatureCooked":"

年月擦身过，暂且问，会更好吗？

\n"}},{"id":70241,"postNumber":3,"raw":"[quote=\"玉米🌽, post:2, topic:15441, username:一只玉米人\"]\n做细胞演化和基因表达预测任务\n[/quote]\n\n我现在手头上就还有一个挺有意思的课题，做的是单细胞来预测下游通路的，用的就是类似 Transformer，不过我们把几个层魔改了一下\n\nTransformer 对于生物学这种长上下文的场景其实非常合适，最新的 AlphaFold3 就是魔改了 Transformer 好像（似乎 af2 就已经开始魔改加注意力了，Evoformer）\n\n不过我一直觉得生物学和计算机学界一直是脱节的，属于那种计算机界都已经老掉牙的东西，学生物的才捡起来。。。","cooked":"

\n\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t\t玉米🌽:\n\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t

\n
做细胞演化和基因表达预测任务
\n

\n\t\t\t\t\t\t

我现在手头上就还有一个挺有意思的课题，做的是单细胞来预测下游通路的，用的就是类似 Transformer，不过我们把几个层魔改了一下

Transformer 对于生物学这种长上下文的场景其实非常合适，最新的 AlphaFold3 就是魔改了 Transformer 好像（似乎 af2 就已经开始魔改加注意力了，Evoformer）

不过我一直觉得生物学和计算机学界一直是脱节的，属于那种计算机界都已经老掉牙的东西，学生物的才捡起来。。。

\n","createdAt":"2026-01-11 07:10:01.229536","updatedAt":"2026-01-11 07:10:01.229536","replyToPostNumber":2,"replyCount":2,"likeCount":2,"wordCount":183,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"hugging_face_cat","count":1,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"}],"hasReacted":false},{"reaction":"❤️","count":2,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"},{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":5151,"username":"Soyo34325","name":"Soyo34325","avatarUrl":"/uploads/image/9d/e5/9de500d3afb55c0fe71e319832f2af75532222efe94bd3de9aea21f0f5c55707.avif","admin":false,"moderator":false,"signatureRaw":"ぜーんぶ弾けなーい！","signatureCooked":"

ぜーんぶ弾けなーい！

\n"}},{"id":70243,"postNumber":4,"raw":"嗯，组里师兄之前的文章就是 single cell 的，好像这一块有不少用 flow matching 在做的","cooked":"

嗯，组里师兄之前的文章就是 single cell 的，好像这一块有不少用 flow matching 在做的

\n","createdAt":"2026-01-11 07:11:38.807705","updatedAt":"2026-01-11 07:12:19.373643","replyToPostNumber":3,"replyCount":0,"likeCount":2,"wordCount":31,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"❤️","count":2,"users":[{"id":5151,"username":"Soyo34325","name":"Soyo34325"},{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":30,"username":"一只玉米人","name":"玉米🌽","avatarUrl":"/uploads/blob/14/96/14961aeaa46ccbb75a61eec0c27b26e74fb5d1c00ccdcbbe898ca9ea37087dd6.svg","admin":false,"moderator":true,"signatureRaw":"*年月擦身过，暂且问，会更好吗？*","signatureCooked":"

年月擦身过，暂且问，会更好吗？

\n"}},{"id":70245,"postNumber":5,"raw":"[quote=\"玉米🌽, post:2, topic:15441, username:一只玉米人\"]\n像是多模态生成、视频生成之类的\n[/quote]\n\n抛开学术界的东西不谈\n我觉得假如能搞出个特别牛逼的拿来搞瑟瑟的 nsfw 大模型，应该可以搞很多钱钱\n把 admin 的审核大模型取一个反向量","cooked":"

\n\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t\t玉米🌽:\n\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t

\n\t\t\t\t\t\t\t

\n
像是多模态生成、视频生成之类的
\n

\n\t\t\t\t\t\t

抛开学术界的东西不谈
\n我觉得假如能搞出个特别牛逼的拿来搞瑟瑟的 nsfw 大模型，应该可以搞很多钱钱
\n把 admin 的审核大模型取一个反向量

\n","createdAt":"2026-01-11 07:14:21.402108","updatedAt":"2026-01-11 07:15:28.930795","replyToPostNumber":2,"replyCount":1,"likeCount":3,"wordCount":87,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"🤣️","count":1,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"}],"hasReacted":false},{"reaction":"💯️","count":1,"users":[{"id":2872,"username":"芙蓉湖第一树莓果","name":"RaspberryPi"}],"hasReacted":false},{"reaction":"mingyao","count":1,"users":[{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false},{"reaction":"❤️","count":3,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"},{"id":2872,"username":"芙蓉湖第一树莓果","name":"RaspberryPi"},{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":5151,"username":"Soyo34325","name":"Soyo34325","avatarUrl":"/uploads/image/9d/e5/9de500d3afb55c0fe71e319832f2af75532222efe94bd3de9aea21f0f5c55707.avif","admin":false,"moderator":false,"signatureRaw":"ぜーんぶ弾けなーい！","signatureCooked":"

ぜーんぶ弾けなーい！

\n"}},{"id":70246,"postNumber":6,"raw":"我的一个非 CS 专业高中同学就在本地部署了 stable diffusion 用来跑瑟图 :rofl: \n瑟瑟是第一生产力！ :rofl:","cooked":"

我的一个非 CS 专业高中同学就在本地部署了 stable diffusion 用来跑瑟图 🤣
\n瑟瑟是第一生产力！ 🤣

\n","createdAt":"2026-01-11 07:15:59.284824","updatedAt":"2026-01-11 07:16:12.537499","replyToPostNumber":5,"replyCount":1,"likeCount":3,"wordCount":37,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"🤩️","count":1,"users":[{"id":5151,"username":"Soyo34325","name":"Soyo34325"}],"hasReacted":false},{"reaction":"😉️","count":1,"users":[{"id":5351,"username":"Xrystal-line","name":"羽流弦ノ迹"}],"hasReacted":false},{"reaction":"🤣️","count":1,"users":[{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false},{"reaction":"❤️","count":3,"users":[{"id":5151,"username":"Soyo34325","name":"Soyo34325"},{"id":5351,"username":"Xrystal-line","name":"羽流弦ノ迹"},{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":30,"username":"一只玉米人","name":"玉米🌽","avatarUrl":"/uploads/blob/14/96/14961aeaa46ccbb75a61eec0c27b26e74fb5d1c00ccdcbbe898ca9ea37087dd6.svg","admin":false,"moderator":true,"signatureRaw":"*年月擦身过，暂且问，会更好吗？*","signatureCooked":"

年月擦身过，暂且问，会更好吗？

\n"}},{"id":70247,"postNumber":7,"raw":"我第一次接触 Stable Diffusion 也是为了画瑟瑟，23 年吧\n那时候还买不到显卡，当时专门买了张计算卡 P4 来画图\n接触了 LoRA 和微调之类的东西\n当时效果不太好","cooked":"

我第一次接触 Stable Diffusion 也是为了画瑟瑟，23 年吧
\n那时候还买不到显卡，当时专门买了张计算卡 P4 来画图
\n接触了 LoRA 和微调之类的东西
\n当时效果不太好

\n","createdAt":"2026-01-11 07:17:25.61955","updatedAt":"2026-01-11 07:17:25.61955","replyToPostNumber":6,"replyCount":0,"likeCount":2,"wordCount":61,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"🥰️","count":2,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"},{"id":7981,"username":"TwlnfuSprig","name":null}],"hasReacted":false},{"reaction":"❤️","count":2,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"},{"id":7981,"username":"TwlnfuSprig","name":null}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":5151,"username":"Soyo34325","name":"Soyo34325","avatarUrl":"/uploads/image/9d/e5/9de500d3afb55c0fe71e319832f2af75532222efe94bd3de9aea21f0f5c55707.avif","admin":false,"moderator":false,"signatureRaw":"ぜーんぶ弾けなーい！","signatureCooked":"

ぜーんぶ弾けなーい！

\n"}},{"id":70263,"postNumber":8,"raw":"脑电脑机接口那块也差不多，两年前在脑信号处理用 transformer 的 paper 就很先进了，现在倒是有在弄脑电大模型这种说法","cooked":"

脑电脑机接口那块也差不多，两年前在脑信号处理用 transformer 的 paper 就很先进了，现在倒是有在弄脑电大模型这种说法

\n","createdAt":"2026-01-11 10:38:39.588833","updatedAt":"2026-01-11 10:38:39.588833","replyToPostNumber":3,"replyCount":1,"likeCount":1,"wordCount":48,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"❤️","count":1,"users":[{"id":5151,"username":"Soyo34325","name":"Soyo34325"}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":2872,"username":"芙蓉湖第一树莓果","name":"RaspberryPi","avatarUrl":"/uploads/image/b2/80/b280dd91d55893347ec240a10b09e7fda3d482025dc73802407bf3d8b14c4144.avif","admin":false,"moderator":false,"signatureRaw":"Hard time comes again and never leave.","signatureCooked":"

Hard time comes again and never leave.

\n"}},{"id":70264,"postNumber":9,"raw":"前几天还在和师兄聊\n以后假如都接入脑机系统，然后给你装个反诈中心\n那就真的是「big brother is watching you」","cooked":"

前几天还在和师兄聊
\n以后假如都接入脑机系统，然后给你装个反诈中心
\n那就真的是「big brother is watching you」

\n","createdAt":"2026-01-11 11:08:50.777946","updatedAt":"2026-01-11 11:08:50.777946","replyToPostNumber":8,"replyCount":1,"likeCount":3,"wordCount":41,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"🤣️","count":1,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"}],"hasReacted":false},{"reaction":"mingyao","count":1,"users":[{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"}],"hasReacted":false},{"reaction":"😰️","count":1,"users":[{"id":7981,"username":"TwlnfuSprig","name":null}],"hasReacted":false},{"reaction":"❤️","count":3,"users":[{"id":30,"username":"一只玉米人","name":"玉米🌽"},{"id":5905,"username":"PipaQinse233","name":"PipaQinse233"},{"id":7981,"username":"TwlnfuSprig","name":null}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":5151,"username":"Soyo34325","name":"Soyo34325","avatarUrl":"/uploads/image/9d/e5/9de500d3afb55c0fe71e319832f2af75532222efe94bd3de9aea21f0f5c55707.avif","admin":false,"moderator":false,"signatureRaw":"ぜーんぶ弾けなーい！","signatureCooked":"

ぜーんぶ弾けなーい！

\n"}},{"id":70266,"postNumber":10,"raw":"侵入式现在都没法准确读取信息吧，感觉写入更不现实 :joy:","cooked":"

侵入式现在都没法准确读取信息吧，感觉写入更不现实 😂

\n","createdAt":"2026-01-11 12:29:36.730244","updatedAt":"2026-02-24 13:10:32.701084","replyToPostNumber":9,"replyCount":0,"likeCount":1,"wordCount":25,"liked":false,"bookmarked":false,"polls":[],"reactions":[{"reaction":"🥺️","count":1,"users":[{"id":5151,"username":"Soyo34325","name":"Soyo34325"}],"hasReacted":false},{"reaction":"❤️","count":1,"users":[{"id":5151,"username":"Soyo34325","name":"Soyo34325"}],"hasReacted":false}],"wiki":false,"version":1,"publicVersion":1,"deletedAt":null,"isAnonymous":false,"user":{"id":4668,"username":"IO","name":null,"avatarUrl":"/uploads/image/86/f2/86f267c0aaa73835a999b7cc3a7e7a701605574eda9a2c2a56f5ddbbba64d1a9.avif","admin":true,"moderator":false,"signatureRaw":"","signatureCooked":null}}],"hasMore":false,"lastReadPostNumber":8,"hasUrlPostNumber":true}