Solvent-Aware 2D NMR Prediction: Leveraging Multi-Tasking Training and Iterative Self-Training Strategies

Nuclear magnetic resonance (NMR) spectroscopy plays a pivotal role in various scientific fields, offering insights into structural information, electronic properties and dynamic behaviors of molecules. Accurate NMR spectrum prediction efficiently produces candidate molecules, enabling chemists to compare them with actual experimental spectra. This process aids in confirming molecular structures or pinpointing discrepancies, guiding further investigation. Machine Learning (ML) has then emerged as a promising alternative approach for predicting atomic NMR chemical shits of molecules given their structures. Although significant progresses have been made in predicting one-dimensional (1D) NMR, two-dimensional (2D) NMR prediction via ML remains a challenge due to the lack of annotated NMR training datasets. To address this gap, we propose an iterative self-training (IST) approach to train a deep learning model for predicting atomic 2DNMR shifts and assigning peaks in experimental spectra. Our model undergoes an initial pre-training phase employing a Multi-Task Training (MTT) approach, which simultaneously leverages annotated 1D NMR datasets of both $^{1}\text{H}$ and $^{13}\text{C}$ spectra to enhance its understanding of NMR spectra. Subsequently, the pre-trained model is utilized to generate pseudo-annotations for unlabelled 2D NMR spectra, which are subsequently used to refine the 2D NMR prediction model. Our approach iterates between annotated unlabelled 2D NMR data and refining our 2D NMR prediction model until convergence. Finally, our model is able to not only accurately predict 2D NMR but also annotate peaks in experimental 2D NMR spectra. Experimental results show that our model is capable of accurately handling medium-sized and large molecules, including polysaccharides, underscoring its effectiveness.

Graph Multi-Similarity Learning for Molecular Property Prediction

Enhancing accurate molecular property prediction relies on effective and proficient representation learning. It is crucial to incorporate diverse molecular relationships characterized by multi-similarity (self-similarity and relative similarities) between molecules. However, current molecular representation learning methods fall short in exploring multi-similarity and often underestimate the complexity of relationships between molecules. Additionally, previous multi-similarity approaches require the specification of positive and negative pairs to attribute distinct predefined weights to different relative similarities, which can introduce potential bias. In this work, we introduce Graph Multi-Similarity Learning for Molecular Property Prediction (GraphMSL) framework, along with a novel approach to formulate a generalized multi-similarity metric without the need to define positive and negative pairs. In each of the chemical modality spaces (e.g.,molecular depiction image, fingerprint, NMR, and SMILES) under consideration, we first define a self-similarity metric (i.e., similarity between an anchor molecule and another molecule), and then transform it into a generalized multi-similarity metric for the anchor through a pair weighting function. GraphMSL validates the efficacy of the multi-similarity metric across MoleculeNet datasets. Furthermore, these metrics of all modalities are integrated into a multimodal multi-similarity metric, which showcases the potential to improve the performance. Moreover, the focus of the model can be redirected or customized by altering the fusion function. Last but not least, GraphMSL proves effective in drug discovery evaluations through post-hoc analyses of the learnt representations.

GlycoNMR: Dataset and benchmarks for NMR chemical shift prediction of carbohydrates with graph neural networks

Molecular representation learning (MRL) is a powerful tool for bridging the gap between machine learning and chemical sciences, as it converts molecules into numerical representations while preserving their chemical features. These encoded representations serve as a foundation for various downstream biochemical studies, including property prediction and drug design. MRL has had great success with proteins and general biomolecule datasets. Yet, in the growing sub-field of glycoscience (the study of carbohydrates, where longer carbohydrates are also called glycans), MRL methods have been barely explored. This under-exploration can be primarily attributed to the limited availability of comprehensive and well-curated carbohydrate-specific datasets and a lack of Machine learning (ML) pipelines specifically tailored to meet the unique problems presented by carbohydrate data. Since interpreting and annotating carbohydrate-specific data is generally more complicated than protein data, domain experts are usually required to get involved. The existing MRL methods, predominately optimized for proteins and small biomolecules, also cannot be directly used in carbohydrate applications without special modifications. To address this challenge, accelerate progress in glycoscience, and enrich the data resources of the MRL community, we introduce GlycoNMR. GlycoNMR contains two laboriously curated datasets with 2,609 carbohydrate structures and 211,543 annotated nuclear magnetic resonance (NMR) chemical shifts for precise atomic-level prediction. We tailored carbohydrate-specific features and adapted existing MRL models to tackle this problem effectively. For illustration, we benchmark four modified MRL models on our new datasets.

Molecular Identification and Peak Assignment: Leveraging Multi-Level Multimodal Alignment on NMR

Nuclear magnetic resonance (NMR) spectroscopy plays an essential role across various scientific disciplines, providing valuable insights into molecular dynamics and interactions. Despite the promise of AI-enhanced NMR prediction models, challenges persist in the interpretation of spectra for tasks such as molecular retrieval, isomer recognition, and peak assignment. In response, this paper introduces Multi-Level Multimodal Alignment with Knowledge-Guided Instance-Wise Discrimination (K-M3AID) to establish meaningful correspondences between two heterogeneous modalities: molecular graphs (structures) and NMR spectra. In particular, K-M3AID employs a dual-coordinated contrastive learning architecture, and incorporates a graph-level alignment module, a node-level alignment module, and a communication channel. Notably, the framework introduces knowledge-guided instance-wise discrimination into contrastive learning within the node-level alignment module, significantly enhancing accuracy in cross-modal alignment. Additionally, K-M3AID showcases its capability of meta-learning by demonstrating that skills acquired during node-level alignment positively impact graph-level alignment. Empirical validation underscores K-M3AID's effectiveness in addressing multiple zero-shot tasks, offering a promising solution to bridge the gap between structural information and spectral data in complex NMR scenarios.

Asymmetric Contrastive Multimodal Learning for Advancing Chemical Understanding

The versatility of multimodal deep learning holds tremendous promise for advancing scientific research and practical applications. As this field continues to evolve, the collective power of cross-modal analysis promises to drive transformative innovations, leading us to new frontiers in chemical understanding and discovery. Hence, we introduce Asymmetric Contrastive Multimodal Learning (ACML) as a novel approach tailored for molecules, showcasing its potential to advance the field of chemistry. ACML harnesses the power of effective asymmetric contrastive learning to seamlessly transfer information from various chemical modalities to molecular graph representations. By combining pre-trained chemical unimodal encoders and a shallow-designed graph encoder, ACML facilitates the assimilation of coordinated chemical semantics from different modalities, leading to comprehensive representation learning with efficient training. This innovative framework enhances the interpretability of learned representations and bolsters the expressive power of graph neural networks. Through practical tasks such as isomer discrimination and uncovering crucial chemical properties for drug discovery, ACML exhibits its capability to revolutionize chemical research and applications, providing a deeper understanding of chemical semantics of different modalities.

Counterpart Fairness -- Addressing Systematic between-group Differences in Fairness Evaluation

When using machine learning (ML) to aid decision-making, it is critical to ensure that an algorithmic decision is fair, i.e., it does not discriminate against specific individuals/groups, particularly those from underprivileged populations. Existing group fairness methods require equal group-wise measures, which however fails to consider systematic between-group differences. The confounding factors, which are non-sensitive variables but manifest systematic differences, can significantly affect fairness evaluation. To mitigate this problem, we believe that a fairness measurement should be based on the comparison between counterparts (i.e., individuals who are similar to each other with respect to the task of interest) from different groups, whose group identities cannot be distinguished algorithmically by exploring confounding factors. We have developed a propensity-score-based method for identifying counterparts, which prevents fairness evaluation from comparing "oranges" with "apples". In addition, we propose a counterpart-based statistical fairness index, termed Counterpart-Fairness (CFair), to assess fairness of ML models. Empirical studies on the Medical Information Mart for Intensive Care (MIMIC)-IV database were conducted to validate the effectiveness of CFair. We publish our code at \url{https://github.com/zhengyjo/CFair}.

Characterizing the Influence of Graph Elements

Influence function, a method from robust statistics, measures the changes of model parameters or some functions about model parameters concerning the removal or modification of training instances. It is an efficient and useful post-hoc method for studying the interpretability of machine learning models without the need for expensive model re-training. Recently, graph convolution networks (GCNs), which operate on graph data, have attracted a great deal of attention. However, there is no preceding research on the influence functions of GCNs to shed light on the effects of removing training nodes/edges from an input graph. Since the nodes/edges in a graph are interdependent in GCNs, it is challenging to derive influence functions for GCNs. To fill this gap, we started with the simple graph convolution (SGC) model that operates on an attributed graph and formulated an influence function to approximate the changes in model parameters when a node or an edge is removed from an attributed graph. Moreover, we theoretically analyzed the error bound of the estimated influence of removing an edge. We experimentally validated the accuracy and effectiveness of our influence estimation function. In addition, we showed that the influence function of an SGC model could be used to estimate the impact of removing training nodes/edges on the test performance of the SGC without re-training the model. Finally, we demonstrated how to use influence functions to guide the adversarial attacks on GCNs effectively.

Motif-based Graph Representation Learning with Application to Chemical Molecules

This work considers the task of representation learning on the attributed relational graph (ARG). Both the nodes and edges in an ARG are associated with attributes/features allowing ARGs to encode rich structural information widely observed in real applications. Existing graph neural networks offer limited ability to capture complex interactions within local structural contexts, which hinders them from taking advantage of the expression power of ARGs. We propose Motif Convolution Module (MCM), a new motif-based graph representation learning technique to better utilize local structural information. The ability to handle continuous edge and node features is one of MCM's advantages over existing motif-based models. MCM builds a motif vocabulary in an unsupervised way and deploys a novel motif convolution operation to extract the local structural context of individual nodes, which is then used to learn higher-level node representations via multilayer perceptron and/or message passing in graph neural networks. When compared with other graph learning approaches to classifying synthetic graphs, our approach is substantially better in capturing structural context. We also demonstrate the performance and explainability advantages of our approach by applying it to several molecular benchmarks.

Knowledgebra: An Algebraic Learning Framework for Knowledge Graph

Knowledge graph (KG) representation learning aims to encode entities and relations into dense continuous vector spaces such that knowledge contained in a dataset could be consistently represented. Dense embeddings trained from KG datasets benefit a variety of downstream tasks such as KG completion and link prediction. However, existing KG embedding methods fell short to provide a systematic solution for the global consistency of knowledge representation. We developed a mathematical language for KG based on an observation of their inherent algebraic structure, which we termed as Knowledgebra. By analyzing five distinct algebraic properties, we proved that the semigroup is the most reasonable algebraic structure for the relation embedding of a general knowledge graph. We implemented an instantiation model, SemE, using simple matrix semigroups, which exhibits state-of-the-art performance on standard datasets. Moreover, we proposed a regularization-based method to integrate chain-like logic rules derived from human knowledge into embedding training, which further demonstrates the power of the developed language. As far as we know, by applying abstract algebra in statistical learning, this work develops the first formal language for general knowledge graphs, and also sheds light on the problem of neural-symbolic integration from an algebraic perspective.