Yujia Guo

Yujia Guo, Mikhail Kabeshov, Tat Hong Duong Le et al.

Selecting efficient multi-step synthetic routes is a central challenge in organic synthesis, particularly in medicinal and process chemistry, where route choice directly impacts feasibility, cost, and development efficiency. Data-driven assessment systems often oversimplify the multi-objective nature of synthesis design and rely on proxy datasets, such as patent routes, rather than universally grounded criteria. To address this, we introduce an expert-augmented, data-driven scoring framework that integrates machine learning with chemists' domain knowledge for both numerical and explainable route assessment. A DeepSets-based model is trained using tree edit distance between reference and machine-generated routes, and then fine-tuned with expert evaluations to produce both quantitative scores and interpretable qualitative categories: Good, Plausible, and Bad. The resulting system achieves a Spearman correlation coefficient of 0.78 and a Pearson correlation of 0.77 for category assessment prediction, and 60.2% top-1 ranking accuracy for score prediction, substantially outperforming the previous baseline of 17.5%.

Yujia Guo, Daolang Huang, Xinyu Zhang et al.

Bayesian experimental design (BED) is a principled framework for data-efficient design of sequential experiments. However, existing BED methods are unable to adapt to dynamic constraints inherent in real-world tasks due to budget limitations, varying costs, or physical constraints that restrict how designs evolve over time. In this paper, we introduce a novel approach to BED that enables constrained optimization of experimental designs by combining offline pre-training of an amortized policy and a posterior network with online multi-step lookahead planning using scenario trees. We empirically demonstrate that our method yields substantially more informative design sequences than existing methods across a range of constrained BED tasks, while incurring only a modest additional computational overhead.

Daolang Huang, Yujia Guo, Luigi Acerbi et al.

Many critical decisions, such as personalized medical diagnoses and product pricing, are made based on insights gained from designing, observing, and analyzing a series of experiments. This highlights the crucial role of experimental design, which goes beyond merely collecting information on system parameters as in traditional Bayesian experimental design (BED), but also plays a key part in facilitating downstream decision-making. Most recent BED methods use an amortized policy network to rapidly design experiments. However, the information gathered through these methods is suboptimal for down-the-line decision-making, as the experiments are not inherently designed with downstream objectives in mind. In this paper, we present an amortized decision-aware BED framework that prioritizes maximizing downstream decision utility. We introduce a novel architecture, the Transformer Neural Decision Process (TNDP), capable of instantly proposing the next experimental design, whilst inferring the downstream decision, thus effectively amortizing both tasks within a unified workflow. We demonstrate the performance of our method across several tasks, showing that it can deliver informative designs and facilitate accurate decision-making.

Tommi Gröndahl, Yujia Guo, N. Asokan

To improve the explainability of leading Transformer networks used in NLP, it is important to tease apart genuine symbolic rules from merely associative input-output patterns. However, we identify several inconsistencies in how ``symbolicity'' has been construed in recent NLP literature. To mitigate this problem, we propose two criteria to be the most relevant, one pertaining to a system's internal architecture and the other to the dissociation between abstract rules and specific input identities. From this perspective, we critically examine prior work on the symbolic capacities of Transformers, and deem the results to be fundamentally inconclusive for reasons inherent in experiment design. We further maintain that there is no simple fix to this problem, since it arises -- to an extent -- in all end-to-end settings. Nonetheless, we emphasize the need for more robust evaluation of whether non-symbolic explanations exist for success in seemingly symbolic tasks. To facilitate this, we experiment on four sequence modelling tasks on the T5 Transformer in two experiment settings: zero-shot generalization, and generalization across class-specific vocabularies flipped between the training and test set. We observe that T5's generalization is markedly stronger in sequence-to-sequence tasks than in comparable classification tasks. Based on this, we propose a thus far overlooked analysis, where the Transformer itself does not need to be symbolic to be part of a symbolic architecture as the processor, operating on the input and output as external memory components.