chemical domain
The Importance of Being Scalable: Improving the Speed and Accuracy of Neural Network Interatomic Potentials Across Chemical Domains
Scaling has been a critical factor in improving model performance and generalization across various fields of machine learning.It involves how a model's performance changes with increases in model size or input data, as well as how efficiently computational resources are utilized to support this growth. Despite successes in scaling other types of machine learning models, the study of scaling in Neural Network Interatomic Potentials (NNIPs) remains limited. NNIPs act as surrogate models for ab initio quantum mechanical calculations, predicting the energy and forces between atoms in molecules and materials based on atomic configurations. The dominant paradigm in this field is to incorporate numerous physical domain constraints into the model, such as symmetry constraints like rotational equivariance. We contend that these increasingly complex domain constraints inhibit the scaling ability of NNIPs, and such strategies are likely to cause model performance to plateau in the long run.
Integrating knowledge bases to improve coreference and bridging resolution for the chemical domain
Lu, Pengcheng, Poesio, Massimo
Resolving coreference and bridging relations in chemical patents is important for better understanding the precise chemical process, where chemical domain knowledge is very critical. We proposed an approach incorporating external knowledge into a multi-task learning model for both coreference and bridging resolution in the chemical domain. The results show that integrating external knowledge can benefit both chemical coreference and bridging resolution.
Name Tagging Under Domain Shift via Metric Learning for Life Sciences
Liu, Hongyi, Wang, Qingyun, Karisani, Payam, Ji, Heng
Name tagging is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a name tagging model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments we observed that such a model is prone to mis-labeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, however, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mis-labeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We carry out our extensive experiments across three source and three target datasets, and demonstrate that our method outperforms the baselines, in some scenarios by 5\% absolute value.
Unifying Molecular and Textual Representations via Multi-task Language Modelling
Christofidellis, Dimitrios, Giannone, Giorgio, Born, Jannis, Winther, Ole, Laino, Teodoro, Manica, Matteo
The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose the first multi-domain, multi-task language model that can solve a wide range of tasks in both the chemical and natural language domains. Our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.