University of Toronto, Department of Electrical and Computer Engineering Graph neural networks (GNNs) have emerged as powerful tools to accurately predict materials and molecular properties in computational discovery pipelines. In this article, we exploit the invertible nature of these neural networks to directly generate molecular structures with desired electronic properties. Starting from a random graph or an existing molecule, we perform a gradient ascent while holding the GNN weights fixed in order to optimize its input, the molecular graph, towards the target property. Valence rules are enforced strictly through a judicious graph construction. The method relies entirely on the property predictor; no additional training is required on molecular structures. We demonstrate the application of this method by generating molecules with specific DFT-verified energy gaps and octanol-water partition coefficients (logP). Our approach hits target properties with rates comparable to or better than state-of-the-art generative models while consistently generating more diverse molecules.

Generations from large language models (LLMs) can be improved by sampling and scoring multiple solutions to select a final answer. Current "sample and select" methods such as self-consistency (SC) rely on majority voting to score answers. However, when tasks have many distinct and valid answers, selection by voting requires a large number of samples. This makes SC prohibitively expensive for interactive tasks that involve generating multiple actions (answers) sequentially. After establishing that majority voting fails to provide consistent gains on such tasks, we demonstrate how to increase success rates by softening the scoring criterion. We introduce Soft Self-Consistency (SOFT-SC), which replaces SC's discontinuous scoring with a continuous score computed from model likelihoods, allowing for selection even when actions are sparsely distributed. SOFT-SC improves both performance and efficiency on long-horizon interactive tasks, requiring half as many samples as SC for comparable or better performance. For a fixed number of samples, SOFT-SC leads to a 1.3% increase over SC in absolute success rate on writing bash programs, a 6.6% increase on online shopping (WebShop), and a 4.7% increase for an interactive household game (ALFWorld). Finally, we show that SOFT-SC can be applied to both open-source and black-box models.

Molecule synthesis through machine learning is one of the fundamental problems in drug discovery. Current data-driven strategies employ one-step retrosynthesis models and search algorithms to predict synthetic routes in a top-bottom manner. Despite their effective performance, these strategies face limitations in the molecule synthetic route generation due to a greedy selection of the next molecule set without any lookahead. Furthermore, existing strategies cannot control the generation of synthetic routes based on possible criteria such as material costs, yields, and step count. In this work, we propose a general and principled framework via conditional residual energy-based models (EBMs), that focus on the quality of the entire synthetic route based on the specific criteria. By incorporating an additional energy-based function into our probabilistic model, our proposed algorithm can enhance the quality of the most probable synthetic routes (with higher probabilities) generated by various strategies in a plug-and-play fashion. Extensive experiments demonstrate that our framework can consistently boost performance across various strategies and outperforms previous state-of-the-art top-1 accuracy by a margin of 2.5%. Code is available at https://github.com/SongtaoLiu0823/CREBM.

Density-functional theory with extended Hubbard functionals (DFT+$U$+$V$) provides a robust framework to accurately describe complex materials containing transition-metal or rare-earth elements. It does so by mitigating self-interaction errors inherent to semi-local functionals which are particularly pronounced in systems with partially-filled $d$ and $f$ electronic states. However, achieving accuracy in this approach hinges upon the accurate determination of the on-site $U$ and inter-site $V$ Hubbard parameters. In practice, these are obtained either by semi-empirical tuning, requiring prior knowledge, or, more correctly, by using predictive but expensive first-principles calculations. Here, we present a machine learning model based on equivariant neural networks which uses atomic occupation matrices as descriptors, directly capturing the electronic structure, local chemical environment, and oxidation states of the system at hand. We target here the prediction of Hubbard parameters computed self-consistently with iterative linear-response calculations, as implemented in density-functional perturbation theory (DFPT), and structural relaxations. Remarkably, when trained on data from 11 materials spanning various crystal structures and compositions, our model achieves mean absolute relative errors of 3% and 5% for Hubbard $U$ and $V$ parameters, respectively. By circumventing computationally expensive DFT or DFPT self-consistent protocols, our model significantly expedites the prediction of Hubbard parameters with negligible computational overhead, while approaching the accuracy of DFPT. Moreover, owing to its robust transferability, the model facilitates accelerated materials discovery and design via high-throughput calculations, with relevance for various technological applications.

We consider the problem of optimizing initial conditions and timing in dynamical systems governed by unknown ordinary differential equations (ODEs), where evaluating different initial conditions is costly and there are constraints on observation times. To identify the optimal conditions within several trials, we introduce a few-shot Bayesian Optimization (BO) framework based on the system's prior information. At the core of our approach is the System-Aware Neural ODE Processes (SANODEP), an extension of Neural ODE Processes (NODEP) designed to meta-learn ODE systems from multiple trajectories using a novel context embedding block. Additionally, we propose a multi-scenario loss function specifically for optimization purposes. Our two-stage BO framework effectively incorporates search space constraints, enabling efficient optimization of both initial conditions and observation timings. We conduct extensive experiments showcasing SANODEP's potential for few-shot BO. We also explore SANODEP's adaptability to varying levels of prior information, highlighting the trade-off between prior flexibility and model fitting accuracy.

In this paper, an improved method for VR user experience prediction is investigated by introducing a sparrow search algorithm and a random forest algorithm improved by an iterative local search-optimised sparrow search algorithm. The study firstly conducted a statistical analysis of the data, and then trained and tested using the traditional random forest model, the random forest model improved by the sparrow search algorithm, and the random forest algorithm improved based on the iterative local search-sparrow search algorithm, respectively. The results show that the traditional random forest model has a prediction accuracy of 93% on the training set but only 73.3% on the test set, which is poor in generalisation; whereas the model improved by the sparrow search algorithm has a prediction accuracy of 94% on the test set, which is improved compared with the traditional model. What is more noteworthy is that the improved model based on the iterative local search-sparrow search algorithm achieves 100% accuracy on both the training and test sets, which is significantly better than the other two methods. These research results provide new ideas and methods for VR user experience prediction, especially the improved model based on the iterative local search-sparrow search algorithm performs well and is able to more accurately predict and classify the user's VR experience. In the future, the application of this method in other fields can be further explored, and its effectiveness can be verified through real cases to promote the development of AI technology in the field of user experience.

In recent years, as machine learning, particularly for vision and language understanding, has been improved, research in embedded AI has also evolved. VOYAGER is a well-known LLM-based embodied AI that enables autonomous exploration in the Minecraft world, but it has issues such as underutilization of visual data and insufficient functionality as a world model. In this research, the possibility of utilizing visual data and the function of LLM as a world model were investigated with the aim of improving the performance of embodied AI. The experimental results revealed that LLM can extract necessary information from visual data, and the utilization of the information improves its performance as a world model. It was also suggested that devised prompts could bring out the LLM's function as a world model.

Generative models hold great promise for small molecule discovery, significantly increasing the size of search space compared to traditional in silico screening libraries. However, most existing machine learning methods for small molecule generation suffer from poor synthesizability of candidate compounds, making experimental validation difficult. In this paper we propose Reaction-GFlowNet (RGFN), an extension of the GFlowNet framework that operates directly in the space of chemical reactions, thereby allowing out-of-the-box synthesizability while maintaining comparable quality of generated candidates. We demonstrate that with the proposed set of reactions and building blocks, it is possible to obtain a search space of molecules orders of magnitude larger than existing screening libraries coupled with low cost of synthesis. We also show that the approach scales to very large fragment libraries, further increasing the number of potential molecules. We demonstrate the effectiveness of the proposed approach across a range of oracle models, including pretrained proxy models and GPU-accelerated docking.

Recent SO(3)-equivariant models embedded a molecule as a set of single atoms fixed in the three-dimensional space, which is analogous to a ball-and-stick view. This perspective provides a concise view of atom arrangements, however, the surrounding electron density cannot be represented and its polarization effects may be underestimated. To overcome this limitation, we propose \textit{Neural Polarization}, a novel method extending equivariant network by embedding each atom as a pair of fixed and moving points. Motivated by density functional theory, Neural Polarization represents molecules as a space-filling view which includes an electron density, in contrast with a ball-and-stick view. Neural Polarization can flexibly be applied to most type of existing equivariant models. We showed that Neural Polarization can improve prediction performances of existing models over a wide range of targets. Finally, we verified that our method can improve the expressiveness and equivariance in terms of mathematical aspects.

Creation of nanomaterials with specific morphology remains a complex experimental process, even though there is a growing demand for these materials in various industry sectors. This study explores the potential of AI to predict the morphology of nanoparticles within the data availability constraints. For that, we first generated a new multi-modal dataset that is double the size of analogous studies. Then, we systematically evaluated performance of classical machine learning and large language models in prediction of nanomaterial shapes and sizes. Finally, we prototyped a text-to-image system, discussed the obtained empirical results, as well as the limitations and promises of existing approaches.