name: brunlab-apr24 class: title, middle ## Generative and active machine learning for drug discovery Alex Hernández-García (he/il/él) .turquoise[[Yves Brun's Lab, Université de Montréal](https://brunlab.com/) · April 26th 2024] .center[ <a href="https://mila.quebec/"><img src="../assets/images/slides/logos/mila-beige.png" alt="Mila" style="height: 4em"></a> <a href="https://www.umontreal.ca/"><img src="../assets/images/slides/logos/udem-white.png" alt="UdeM" style="height: 4em"></a> ] .smaller[.footer[ Slides: [alexhernandezgarcia.github.io/slides/{{ name }}](https://alexhernandezgarcia.github.io/slides/{{ name }}) ]] --- ## Traditional discovery cycle .context35[The climate crisis and health challenges demand accelerating scientific discoveries.] -- .right-column-66[<br>.center[]] .left-column-33[ <br> The .highlight1[traditional pipeline] for scientific discovery: * relies on .highlight1[highly specialised human expertise], * it is .highlight1[time-consuming] and * .highlight1[financially and computationally expensive]. ] --- count: false ## Machine learning in the loop .context35[The traditional scientific discovery loop is too slow for certain applications.] .right-column-66[<br>.center[]] .left-column-33[ <br> A .highlight1[machine learning model] can be: * trained with data from _real-world_ experiments and ] --- count: false ## Machine learning in the loop .context35[The traditional scientific discovery loop is too slow for certain applications.] .right-column-66[<br>.center[]] .left-column-33[ <br> A .highlight1[machine learning model] can be: * trained with data from _real-world_ experiments and * used to quickly and cheaply evaluate queries ] --- count: false ## Machine learning in the loop .context35[The traditional scientific discovery loop is too slow for certain applications.] .right-column-66[<br>.center[]] .left-column-33[ <br> A .highlight1[machine learning model] can be: * trained with data from _real-world_ experiments and * used to quickly and cheaply evaluate queries .conclusion[There are infinitely many conceivable materials, $10^{180}$ potentially stable and $10^{60}$ drug molecules. Are predictive models enough?] ] --- count: false ## _Generative_ machine learning in the loop .right-column-66[<br>.center[]] .left-column-33[ <br> .highlight1[Generative machine learning] can: * .highlight1[learn structure] from the available data, * .highlight1[generalise] to unexplored regions of the search space and * .highlight1[build better queries] ] --- count: false ## _Generative_ machine learning in the loop .right-column-66[<br>.center[]] .left-column-33[ <br> .highlight1[Generative machine learning] can: * .highlight1[learn structure] from the available data, * .highlight1[generalise] to unexplored regions of the search space and * .highlight1[build better queries] .conclusion[Active learning with generative machine learning can in theory more efficiently explore the candidate space.] ] --- count: false name: title class: title, middle ### The challenges of scientific discoveries .center[] .center[] --- ## An intuitive trivial problem .highlight1[Problem]: find one arrangement of Tetris pieces on the board that minimise the empty space. .left-column-33[ .center[] ] .right-column-66[ .center[] ] -- .full-width[.center[ <figure> <img src="../assets/images/slides/tetris/mode1.png" alt="Score 12" style="width: 3%"> <figcaption>Score: 12</figcaption> </figure> ]] --- count: false ## An intuitive ~~trivial~~ easy problem .highlight1[Problem]: find .highlight2[all] the arrangements of Tetris pieces on the board that minimise the empty space. .left-column-33[ .center[] ] .right-column-66[ .center[] ] -- .full-width[.center[ <div style="display: flex"> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/mode1.png" alt="Score 12" style="width: 20%"> <figcaption>12</figcaption> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/mode2.png" alt="Score 12" style="width: 20%"> <figcaption>12</figcaption> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/mode3.png" alt="Score 12" style="width: 20%"> <figcaption>12</figcaption> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/mode4.png" alt="Score 12" style="width: 20%"> <figcaption>12</figcaption> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/mode5.png" alt="Score 12" style="width: 20%"> <figcaption>12</figcaption> </figure> </div> </div> ]] --- count: false ## An intuitive ~~easy~~ hard problem .highlight1[Problem]: find .highlight2[all] the arrangements of Tetris pieces on the board that minimise the empty space. .left-column-33[ .center[] ] .right-column-66[ .center[] ] -- .full-width[.center[ <div style="display: flex"> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/mode1.png" alt="Random board" style="width: 40%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/mode2.png" alt="Random board" style="width: 40%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/mode3.png" alt="Random board" style="width: 40%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/mode4.png" alt="Random board" style="width: 40%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/mode5.png" alt="Random board" style="width: 40%"> </figure> </div> </div> ]] --- count: false ## An incredibly ~~intuitive easy~~ hard problem .highlight1[Problem]: find .highlight2[all] the arrangements of Tetris pieces on the board that .highlight2[optimise an unknown function]. .left-column-33[ .center[] ] .right-column-66[ .center[] ] -- .full-width[.center[ <div style="display: flex"> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_434.png" alt="Random board" style="width: 40%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_800.png" alt="Random board" style="width: 40%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_815.png" alt="Random board" style="width: 40%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_849.png" alt="Random board" style="width: 40%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_905.png" alt="Random board" style="width: 40%"> </figure> </div> </div> ]] --- count: false ## An incredibly ~~intuitive easy~~ hard problem .highlight1[Problem]: find .highlight2[all] the arrangements of Tetris pieces on the board that .highlight2[optimise an unknown function]. .left-column-33[ .center[] ] .right-column-66[ .center[] ] .full-width[.conclusion[Materials and drug discovery involve finding candidates with rare properties from combinatorially or infinitely many options.]] --- ## Why Tetris for scientific discovery? .context35[The "Tetris problem" involves .highlight1[sampling from an unknown distribution] in a .highlight1[discrete, high-dimensional, combinatorially large space].] --- count: false ## Why Tetris for scientific discovery? ### Biological sequence design <br> Proteins, antimicrobial peptides (AMP) and DNA can be represented as sequences of amino acids or nucleobases. There are $22^{100} \approx 10^{134}$ protein sequences with 100 amino acids. .context35[The "Tetris problem" involves sampling from an unknown distribution in a discrete, high-dimensional, combinatorially large space] .center[] -- .left-column-66[ .dnag[`G`].dnaa[`A`].dnag[`G`].dnag[`G`].dnag[`G`].dnac[`C`].dnag[`G`].dnaa[`A`].dnac[`C`].dnag[`G`].dnag[`G`].dnat[`T`].dnaa[`A`].dnac[`C`].dnag[`G`].dnag[`G`].dnaa[`A`].dnag[`G`].dnac[`C`].dnat[`T`].dnac[`C`].dnat[`T`].dnag[`G`].dnac[`C`].dnat[`T`].dnac[`C`].dnac[`C`].dnag[`G`].dnat[`T`].dnat[`T`].dnaa[`A`]<br> .dnat[`T`].dnac[`C`].dnaa[`A`].dnac[`C`].dnac[`C`].dnat[`T`].dnac[`C`].dnac[`C`].dnac[`C`].dnag[`G`].dnaa[`A`].dnag[`G`].dnac[`C`].dnaa[`A`].dnaa[`A`].dnat[`T`].dnaa[`A`].dnag[`G`].dnat[`T`].dnat[`T`].dnag[`G`].dnat[`T`].dnaa[`A`].dnag[`G`].dnag[`G`].dnac[`C`].dnaa[`A`].dnag[`G`].dnac[`C`].dnag[`G`].dnat[`T`].dnac[`C`].dnac[`C`].dnat[`T`].dnaa[`A`].dnac[`C`].dnac[`C`].dnag[`G`].dnat[`T`].dnat[`T`].dnac[`C`].dnag[`G`]<br> .dnac[`C`].dnat[`T`].dnaa[`A`].dnac[`C`].dnag[`G`].dnac[`C`].dnag[`G`].dnat[`T`].dnac[`C`].dnat[`T`].dnac[`C`].dnat[`T`].dnat[`T`].dnat[`T`].dnac[`C`].dnag[`G`].dnag[`G`].dnag[`G`].dnag[`G`].dnag[`G`].dnat[`T`].dnat[`T`].dnaa[`A`]<br> .dnat[`T`].dnat[`T`].dnag[`G`].dnac[`C`].dnaa[`A`].dnag[`G`].dnaa[`A`].dnag[`G`].dnag[`G`].dnat[`T`].dnat[`T`].dnaa[`A`].dnaa[`A`].dnac[`C`].dnag[`G`].dnac[`C`].dnag[`G`].dnac[`C`].dnaa[`A`].dnat[`T`].dnag[`G`].dnac[`C`].dnag[`G`].dnaa[`A`].dnac[`C`].dnat[`T`].dnag[`G`].dnag[`G`].dnag[`G`].dnag[`G`].dnat[`T`].dnat[`T`].dnaa[`A`].dnag[`G`].dnat[`T`].dnaa[`A`].dnag[`G`].dnat[`T`].dnac[`C`].dnag[`G`].dnaa[`A`].dnaa[`A`].dnac[`C`].dnaa[`A`].dnat[`T`].dnaa[`A`].dnat[`T`].dnaa[`A`].dnat[`T`].dnat[`T`].dnag[`G`].dnaa[`A`].dnat[`T`].dnaa[`A`].dnaa[`A`].dnaa[`A`].dnac[`C`].dnaa[`A`]<br> .dnag[`G`].dnac[`C`].dnat[`T`].dnac[`C`].dnag[`G`].dnac[`C`].dnat[`T`].dnat[`T`].dnaa[`A`].dnag[`G`].dnag[`G`].dnag[`G`].dnac[`C`].dnac[`C`].dnat[`T`].dnac[`C`].dnag[`G`].dnaa[`A`].dnac[`C`].dnat[`T`].dnac[`C`].dnac[`C`].dnat[`T`].dnac[`C`].dnat[`T`].dnag[`G`].dnaa[`A`].dnaa[`A`].dnat[`T`].dnag[`G`].dnag[`G`].dnaa[`A`].dnag[`G`].dnat[`T`].dnag[`G`].dnat[`T`].dnat[`T`].dnac[`C`].dnaa[`A`].dnat[`T`].dnac[`C`].dnag[`G`].dnaa[`A`].dnaa[`A`].dnat[`T`].dnag[`G`].dnag[`G`].dnaa[`A`].dnag[`G`].dnat[`T`].dnag[`G`]<br> ] --- ## Why Tetris for scientific discovery? ### Molecular generation .context35[The "Tetris problem" involves sampling from an unknown distribution in a discrete, high-dimensional, combinatorially large space] <br> Small molecules can also be represented as sequences or by a combination of of higher-level fragments. There may be about $10^{60}$ drug-like molecules. -- .columns-3-left[ .center[  `CC(=O)NCCC1=CNc2c1cc(OC)cc2 CC(=O)NCCc1c[nH]c2ccc(OC)cc12` ]] .columns-3-center[ .center[  `OCCc1c(C)[n+](cs1)Cc2cnc(C)nc2N` ]] .columns-3-right[ .center[  `CN1CCC[C@H]1c2cccnc2` ]] --- ## Machine learning for scientific discovery ### Challenges and limitations of existing methods -- .highlight1[Challenge]: very large and high-dimensional search spaces. -- → Need for .highlight2[efficient search and generalisation] of underlying structure. -- .highlight1[Challenge]: underspecification of objective functions or metrics. -- → Need for .highlight2[diverse] candidates. -- .highlight1[Limitation]: Reinforcement learning excels at optimisation in complex spaces but tends to lack diversity. -- .highlight1[Limitation]: Markov chain Monte Carlo (MCMC) can _sample_ from a distribution (diversity) but struggles at mode mixing in high dimensions. -- → Need to .highlight2[combine all of the above]: sampling from complex, high-dimensional distributions. -- .conclusion[Generative flow networks (GFlowNets) address these challenges.] --- count: false name: gflownets class: title, middle ### A gentle introduction to GFlowNets .center[] --- ## GFlowNets for science ### 3 key ingredients .context[Materials and drug discovery involve .highlight1[sampling from unknown distributions] in .highlight1[discrete or mixed, high-dimensional, combinatorially large spaces.]] -- <br><br> 1. .highlight1[Diversity] as an objective. -- - Given a score or reward function $R(x)$, learn to _sample proportionally to the reward_. -- 2. .highlight1[Compositionality] in the sample generation. -- - A meaningful decomposition of samples $x$ into multiple sub-states $s_0\rightarrow s_1 \rightarrow \dots \rightarrow x$ can yield generalisable patterns. -- 3. .highlight1[Deep learning] to learn from the generated samples. -- - A machine learning model can learn the transition function $F(s\rightarrow s')$ and generalise the patterns. --- ## 1. Diversity as an objective .context[Many existing approaches treat scientific discovery as an _optimisation_ problem.] <br> Given a reward or objective function $R(x)$, GFlowNet can be seen a generative model trained to sample objects $x \in \cal X$ according to .highlight1[a sampling policy $\pi(x)$ proportional to the reward $R(x)$]: -- .left-column[ $$\pi(x) = \frac{R(x)}{Z} \propto R(x)$$ ] -- .right-column[ $$Z = \sum_{x' \in \cal X} R(x')$$ ] -- .full-width[ .center[                                     ]] --- count: false ## 1. Diversity as an objective .context[Many existing approaches treat scientific discovery as an _optimisation_ problem.] <br> Given a reward or objective function $R(x)$, GFlowNet can be seen a generative model trained to sample objects $x \in \cal X$ according to .highlight1[a sampling policy $\pi(x)$ proportional to the reward $R(x)$]: .left-column[ $$\pi(x) = \frac{R(x)}{Z} \propto R(x)$$ ] .right-column[ $$Z = \sum_{x' \in \cal X} R(x')$$ ] .full-width[ → Sampling proportionally to the reward function enables finding .highlight1[multiple modes], hence .highlight1[diversity]. .center[] ] --- ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] The principle of compositionality is fundamental in semantics, linguistics, mathematical logic and is thought to be a cornerstone of human reasoning. --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. -- .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] .right-column[ <br><br> .conclusion[The decomposition of the sampling process into meaningful steps yields patterns that may be correlated with the reward function and facilitates learning complex distributions.] ] --- count: false ## 2. Compositionality ### Sample generation process .context35[Sampling _directly_ from a complex, high-dimensional distribution is difficult.] For the Tetris problem, a meaningful decomposition of the samples is .highlight1[adding one piece to the board at a time]. .left-column[.center[]] .right-column[ Objects $x \in \cal X$ are constructed through a sequence of actions from an .highlight1[action space $\cal A$]. ] .right-column[ At each step of the .highlight1[trajectory $\tau=(s_0\rightarrow s_1 \rightarrow \dots \rightarrow s_f)$], we get a partially constructed object $s$ in .highlight1[state space $\cal S$]. ] -- .right-column[ .conclusion[These ideas and terminology is reminiscent of reinforcement learning (RL).] ] --- ## 3. Deep learning policy .context35[GFlowNets learn a sampling policy $\pi\_{\theta}(x)$ proportional to the reward $R(x)$.] -- .left-column[ .center[] ] --- count: false ## 3. Deep learning policy .context35[GFlowNets learn a sampling policy $\pi\_{\theta}(x)$ proportional to the reward $R(x)$.] .left-column[ .center[] ] .right-column[ <br> Deep neural networks are trained to learn the transitions (flows) policy: $F\_{\theta}(s\_t\rightarrow s\_{t+1})$. ] -- .right-column[ Consistent flow theorem (informal): if the sum of the flows into state $s$ is equal to the sum of the flows out, then $\pi(x) \propto R(x)$. ] .references[ Bengio et al. [Flow network based generative models for non-iterative diverse candidate generation](https://arxiv.org/abs/2106.04399), NeurIPS, 2021. (_not_ co-authored) ] -- .right-column[ .conclusion[GFlowNets can be trained with deep learning methods to learn a sampling policy $\pi\_{\theta}$ proportional to a reward $R(x)$.] ] --- ## To know more - Jain et al. [GFlowNets for AI-Driven Scientific Discovery](https://pubs.rsc.org/en/content/articlelanding/2023/dd/d3dd00002h). Digital Discovery, 2023. - Jain et al. [Biological Sequence Design with GFlowNets](https://arxiv.org/abs/2203.04115), ICML, 2022. - Volokhova, Koziarski et al. [Towards equilibrium molecular conformation generation with GFlowNets](https://arxiv.org/abs/2310.14782), Digital Discovery, 2024. - Lahlou et al. [A Theory of Continuous Generative Flow Networks](https://arxiv.org/abs/2301.12594), ICML, 2023. - Jain et al. [Multi-Objective GFlowNets](https://arxiv.org/abs/2210.12765), ICML, 2023. -- Open source implementation, developed together with Mila collaborators: Nikita Saxena, Alexandra Volokhova, Michał Koziarski, Divya Sharma, Pierre Luc Carrier, Victor Schmidt, Joseph Viviano. .center[.highlight2[[github.com/alexhernandezgarcia/gflownet](https://github.com/alexhernandezgarcia/gflownet)]] -- * A key design principle is the simplicity to create new environments (tasks). * Discrete and continuous environments, multiple loss functions, etc. * Visualisation of results on WandDB --- count: false name: mfal class: title, middle ## Multi-fidelity active learning Nikita Saxena, Moksh Jain, Cheng-Hao Liu, Yoshua Bengio .smaller[[Multi-fidelity active learning with GFlowNets](https://arxiv.org/abs/2306.11715). RealML, NeurIPS 2023 / under review.] .center[] --- ## Why multi-fidelity? .context35[We had described the scientific discovery loop as a cycle with one single oracle.] <br><br> .right-column[ .center[] ] -- .left-column[ Example: "incredibly hard" Tetris problem: find arrangements of Tetris pieces that optimise an .highlight2[unknown function $f$]. - $f$: Oracle, cost per evaluation 1000 CAD. .center[ <div style="display: flex"> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_434.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_800.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_815.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_849.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_905.png" alt="Random board" style="width: 200%"> </figure> </div> </div> ] ] --- count: false ## Why multi-fidelity? .context35[However, in practice, multiple oracles (models) of different fidelity and cost are available in scientific applications.] <br><br> .right-column[ .center[] ] .left-column[ Example: "incredibly hard" Tetris problem: find arrangements of Tetris pieces that optimise an .highlight2[unknown function $f$]. - $f$: Oracle, cost per evaluation 1000 CAD. .center[ <div style="display: flex"> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_434.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_800.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_815.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_849.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_905.png" alt="Random board" style="width: 200%"> </figure> </div> </div> ] ] --- count: false ## Why multi-fidelity? .context35[However, in practice, multiple oracles (models) of different fidelity and cost are available in scientific applications.] <br><br> .right-column[ .center[] ] .left-column[ Example: "incredibly hard" Tetris problem: find arrangements of Tetris pieces that optimise an .highlight2[unknown function $f$]. - $f$: Oracle, cost per evaluation 1000 CAD. - $f\_1$: Slightly inaccurate oracle, cost 100 CAD. - $f\_2$: Noisy but informative oracle, cost 1 CAD. .center[ <div style="display: flex"> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_434.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_800.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_815.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_849.png" alt="Random board" style="width: 200%"> </figure> </div> <div style="flex: 20%;"> <figure> <img src="../assets/images/slides/tetris/10x20/random_905.png" alt="Random board" style="width: 200%"> </figure> </div> </div> ] ] --- count: false ## Why multi-fidelity? .context[In many scientific applications we have access to multiple approximations of the objective function.] .left-column[ For example, in .highlight1[material discovery]: * .highlight1[Synthesis] of a material and characterisation of a property in the lab * Quantum mechanic .highlight1[simulations] to estimate the property * .highlight1[Machine learning] models trained to predict the property ] .right-column[ .center[] ] -- .conclusion[However, current machine learning methods cannot efficiently leverage the availability of multiple oracles and multi-fidelity data. Especially with .highlight1[structured, large, high-dimensional search spaces].] --- ## Contribution - An .highlight1[active learning] algorithm to leverage the availability of .highlight1[multiple oracles at different fidelities and costs]. -- - The goal is two-fold: 1. Find high-scoring candidates 2. Candidates must be diverse -- - Experimental evaluation with .highlight1[biological sequences and molecules]: - DNA - Antimicrobial peptides - Small molecules - Classical multi-fidelity toy functions (Branin and Hartmann) -- .conclusion[Likely the first multi-fidelity active learning method for biological sequences and molecules.] --- ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- count: false ## Our multi-fidelity active learning algorithm .center[] --- ## Experiments ### Baselines .context[This is the .highlight1[first multi-fidelity active learning algorithm tested on biological sequence design and molecular design problems]. There did not exist baselines from the literature.] -- <br> * .highlight1[SF-GFN]: GFlowNet with highest fidelity oracle to establish a benchmark for performance without considering the cost-accuracy trade-offs. -- * .highlight1[Random]: Quasi-random approach where the candidates and fidelities are picked randomly and the top $(x, m)$ pairs scored by the acquisition function are queried. -- * .highlight1[Random fid. GFN]: GFlowNet with random fidelities, to investigate the benefit of deciding the fidelity with GFlowNets. -- * .highlight1[MF-PPO]: Replacement of MF-GFN with a reinforcement learning algorithm to _optimise_ the acquisition function. --- ## Small molecules - Realistic experiments with experimental oracles and costs that reflect the computational demands (1, 3, 7). - GFlowNet adds one SELFIES token (out of 26) at a time with variable length up to 64 ($|\mathcal{X}| > 26^{64}$). - Property: Adiabatic electron affinity (EA). Relevant in organic semiconductors, photoredox catalysis and organometallic synthesis. -- .center[] --- count: false ## Small molecules - Realistic experiments with experimental oracles and costs that reflect the computational demands (1, 3, 7). - GFlowNet adds one SELFIES token (out of 26) at a time with variable length up to 64 ($|\mathcal{X}| > 26^{64}$). - Property: Adiabatic electron affinity (EA). Relevant in organic semiconductors, photoredox catalysis and organometallic synthesis. .center[] --- count: false ## Small molecules - Realistic experiments with experimental oracles and costs that reflect the computational demands (1, 3, 7). - GFlowNet adds one SELFIES token (out of 26) at a time with variable length up to 64 ($|\mathcal{X}| > 26^{64}$). - Property: Adiabatic electron affinity (EA). Relevant in organic semiconductors, photoredox catalysis and organometallic synthesis. .center[] --- count: false ## Small molecules - Realistic experiments with experimental oracles and costs that reflect the computational demands (1, 3, 7). - GFlowNet adds one SELFIES token (out of 26) at a time with variable length up to 64 ($|\mathcal{X}| > 26^{64}$). - Property: Adiabatic electron affinity (EA). Relevant in organic semiconductors, photoredox catalysis and organometallic synthesis. .center[] --- count: false ## Small molecules - Realistic experiments with experimental oracles and costs that reflect the computational demands (1, 3, 7). - GFlowNet adds one SELFIES token (out of 26) at a time with variable length up to 64 ($|\mathcal{X}| > 26^{64}$). - Property: Adiabatic electron affinity (EA). Relevant in organic semiconductors, photoredox catalysis and organometallic synthesis. .center[] --- count: false ## Small molecules - Realistic experiments with experimental oracles and costs that reflect the computational demands (1, 3, 7). - GFlowNet adds one SELFIES token (out of 26) at a time with variable length up to 64 ($|\mathcal{X}| > 26^{64}$). - Property: Adiabatic electron affinity (EA). Relevant in organic semiconductors, photoredox catalysis and organometallic synthesis. .center[] --- count: false ## Small molecules - Realistic experiments with experimental oracles and costs that reflect the computational demands (1, 3, 7). - GFlowNet adds one SELFIES token (out of 26) at a time with variable length up to 64 ($|\mathcal{X}| > 26^{64}$). - Property: Adiabatic electron affinity (EA). Relevant in organic semiconductors, photoredox catalysis and organometallic synthesis. .center[] --- count: false ## Small molecules - Realistic experiments with experimental oracles and costs that reflect the computational demands (1, 3, 7). - GFlowNet adds one SELFIES token (out of 26) at a time with variable length up to 64 ($|\mathcal{X}| > 26^{64}$). - Property: Adiabatic .highlight1[ionisation potential (IP)]. Relevant in organic semiconductors, photoredox catalysis and organometallic synthesis. .center[] --- ## DNA aptamers - GFlowNet adds one nucleobase (`A`, `T`, `C`, `G`) at a time up to length 30. This yields a design space of size $|\mathcal{X}| = 4^{30}$. - The objective function is the free energy estimated by a bioinformatics tool. - The (simulated) lower fidelity oracle is a transformer trained with 1 million sequences. -- .center[] --- count: false ## Antimicrobial peptides (AMP) - Protein sequences (20 amino acids) with variable length (max. 50). - The oracles are 3 ML models trained with different subsets of data. -- .center[] --- ## How does multi-fidelity help? .context[Visualisation on the synthetic 2D Branin function task.] .center[] --- count: false ## How does multi-fidelity help? .context[Visualisation on the synthetic 2D Branin function task.] .center[] --- count: false ## How does multi-fidelity help? .context[Visualisation on the synthetic 2D Branin function task.] .center[] --- count: false ## How does multi-fidelity help? .context[Visualisation on the synthetic 2D Branin function task.] .center[] --- ## Multi-fidelity active learning with GFlowNets ### Summary and conclusions .references[ * Hernandez-Garcia, Saxena et al. [Multi-fidelity active learning with GFlowNets](https://arxiv.org/abs/2306.11715). RealML, NeurIPS 2023. ] * Current ML for science methods do not utilise all the information and resources at our disposal. -- * AI-driven scientific discovery demands learning methods that can .highlight1[efficiently discover diverse candidates in combinatorially large, high-dimensional search spaces]. -- * .highlight1[Multi-fidelity active learning with GFlowNets] enables .highlight1[cost-effective exploration] of large, high-dimensional and structured spaces, and discovers multiple, diverse modes of black-box score functions. -- * This is to our knowledge the first algorithm capable of effectively leveraging multi-fidelity oracles to discover diverse biological sequences and molecules. --- ## Acknowledgements .columns-3-left[ Victor Schmidt<br> Mélisande Teng<br> Alexandre Duval<br> Yasmine Benabed<br> Pierre Luc Carrier<br> Divya Sharma<br> Yoshua Bengio<br> Lena Simine<br> Michael Kilgour<br> ... ] .columns-3-center[ Alexandra Volokhova<br> Michał Koziarski<br> Paula Harder<br> David Rolnick<br> Qidong Yang<br> Santiago Miret<br> Sasha Luccioni<br> Alexia Reynaud<br> Tianyu Zhang<br> ... ] .columns-3-right[ Nikita Saxena<br> Moksh Jain<br> Cheng-Hao Liu<br> Kolya Malkin<br> Tristan Deleu<br> Salem Lahlou<br> Alvaro Carbonero<br> José González-Abad<br> Emmanuel Bengio<br> ... ] .conclusion[Science is a lot more fun when shared with bright and interesting people!] --- name: mlforscience-mar24 class: title, middle  Alex Hernández-García (he/il/él) .center[ <a href="https://mila.quebec/"><img src="../assets/images/slides/logos/mila-beige.png" alt="Mila" style="height: 4em"></a> <a href="https://www.umontreal.ca/"><img src="../assets/images/slides/logos/udem-white.png" alt="UdeM" style="height: 4em"></a> ] .footer[[alexhernandezgarcia.github.io](https://alexhernandezgarcia.github.io/) | [alex.hernandez-garcia@mila.quebec](mailto:alex.hernandez-garcia@mila.quebec)]<br> .footer[[@alexhg@scholar.social](https://scholar.social/@alexhg) [](https://scholar.social/@alexhg) | [@alexhdezgcia](https://twitter.com/alexhdezgcia) [](https://twitter.com/alexhdezgcia)] .smaller[.footer[ Slides: [alexhernandezgarcia.github.io/slides/{{ name }}](https://alexhernandezgarcia.github.io/slides/{{ name }}) ]]