A Self-feedback Knowledge Elicitation Approach for Chemical Reaction Predictions

The task of chemical reaction predictions (CRPs) plays a pivotal role in advancing drug discovery and material science. However, its effectiveness is constrained by the vast and uncertain chemical reaction space and challenges in capturing reaction selectivity, particularly due to existing methods' limitations in exploiting the data's inherent knowledge. To address these challenges, we introduce a data-curated self-feedback knowledge elicitation approach. This method starts from iterative optimization of molecular representations and facilitates the extraction of knowledge on chemical reaction types (RTs). Then, we employ adaptive prompt learning to infuse the prior knowledge into the large language model (LLM). As a result, we achieve significant enhancements: a 14.2% increase in retrosynthesis prediction accuracy, a 74.2% rise in reagent prediction accuracy, and an expansion in the model's capability for handling multi-task chemical reactions. This research offers a novel paradigm for knowledge elicitation in scientific research and showcases the untapped potential of LLMs in CRPs.

Scientific Language Modeling: A Quantitative Review of Large Language Models in Molecular Science

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

FlowHON: Representing Flow Fields Using Higher-Order Networks

Flow fields are often partitioned into data blocks for massively parallel computation and analysis based on blockwise relationships. However, most of the previous techniques only consider the first-order dependencies among blocks, which is insufficient in describing complex flow patterns. In this work, we present FlowHON, an approach to construct higher-order networks (HONs) from flow fields. FlowHON captures the inherent higher-order dependencies in flow fields as nodes and estimates the transitions among them as edges. We formulate the HON construction as an optimization problem with three linear transformations. The first two layers correspond to the node generation and the third one corresponds to edge estimation. Our formulation allows the node generation and edge estimation to be solved in a unified framework. With FlowHON, the rich set of traditional graph algorithms can be applied without any modification to analyze flow fields, while leveraging the higher-order information to understand the inherent structure and manage flow data for efficiency. We demonstrate the effectiveness of FlowHON using a series of downstream tasks, including estimating the density of particles during tracing, partitioning flow fields for data management, and understanding flow fields using the node-link diagram representation of networks.

A Graphical Point Process Framework for Understanding Removal Effects in Multi-Touch Attribution

Marketers employ various online advertising channels to reach customers, and they are particularly interested in attribution for measuring the degree to which individual touchpoints contribute to an eventual conversion. The availability of individual customer-level path-to-purchase data and the increasing number of online marketing channels and types of touchpoints bring new challenges to this fundamental problem. We aim to tackle the attribution problem with finer granularity by conducting attribution at the path level. To this end, we develop a novel graphical point process framework to study the direct conversion effects and the full relational structure among numerous types of touchpoints simultaneously. Utilizing the temporal point process of conversion and the graphical structure, we further propose graphical attribution methods to allocate proper path-level conversion credit, called the attribution score, to individual touchpoints or corresponding channels for each customer's path to purchase. Our proposed attribution methods consider the attribution score as the removal effect, and we use the rigorous probabilistic definition to derive two types of removal effects. We examine the performance of our proposed methods in extensive simulation studies and compare their performance with commonly used attribution models. We also demonstrate the performance of the proposed methods in a real-world attribution application.

Vector Approximate Message Passing based Channel Estimation for MIMO-OFDM Underwater Acoustic Communications

Accurate channel estimation is critical to the performance of orthogonal frequency-division multiplexing (OFDM) underwater acoustic (UWA) communications, especially under multiple-input multiple-output (MIMO) scenarios. In this paper, we explore Vector Approximate Message Passing (VAMP) coupled with Expected Maximum (EM) to obtain channel estimation (CE) for MIMO OFDM UWA communications. The EM-VAMP-CE scheme is developed by employing a Bernoulli-Gaussian (BG) prior distribution for the channel impulse response, and hyperparameters of the BG prior distribution are learned via the EM algorithm. Performance of the EM-VAMP-CE is evaluated through both synthesized data and real data collected in two at-sea UWA communication experiments. It is shown the EM-VAMP-CE achieves better performance-complexity tradeoff compared with existing channel estimation methods.

An additive graphical model for discrete data

We introduce a nonparametric graphical model for discrete node variables based on additive conditional independence. Additive conditional independence is a three way statistical relation that shares similar properties with conditional independence by satisfying the semi-graphoid axioms. Based on this relation we build an additive graphical model for discrete variables that does not suffer from the restriction of a parametric model such as the Ising model. We develop an estimator of the new graphical model via the penalized estimation of the discrete version of the additive precision operator and establish the consistency of the estimator under the ultrahigh-dimensional setting. Along with these methodological developments, we also exploit the properties of discrete random variables to uncover a deeper relation between additive conditional independence and conditional independence than previously known. The new graphical model reduces to a conditional independence graphical model under certain sparsity conditions. We conduct simulation experiments and analysis of an HIV antiretroviral therapy data set to compare the new method with existing ones.

A Unified Model for the Two-stage Offline-then-Online Resource Allocation

With the popularity of the Internet, traditional offline resource allocation has evolved into a new form, called online resource allocation. It features the online arrivals of agents in the system and the real-time decision-making requirement upon the arrival of each online agent. Both offline and online resource allocation have wide applications in various real-world matching markets ranging from ridesharing to crowdsourcing. There are some emerging applications such as rebalancing in bike sharing and trip-vehicle dispatching in ridesharing, which involve a two-stage resource allocation process. The process consists of an offline phase and another sequential online phase, and both phases compete for the same set of resources. In this paper, we propose a unified model which incorporates both offline and online resource allocation into a single framework. Our model assumes non-uniform and known arrival distributions for online agents in the second online phase, which can be learned from historical data. We propose a parameterized linear programming (LP)-based algorithm, which is shown to be at most a constant factor of $1/4$ from the optimal. Experimental results on the real dataset show that our LP-based approaches outperform the LP-agnostic heuristics in terms of robustness and effectiveness.

Projection based Active Gaussian Process Regression for Pareto Front Modeling

Pareto Front (PF) modeling is essential in decision making problems across all domains such as economics, medicine or engineering. In Operation Research literature, this task has been addressed based on multi-objective optimization algorithms. However, without learning models for PF, these methods cannot examine whether a new provided point locates on PF or not. In this paper, we reconsider the task from Data Mining perspective. A novel projection based active Gaussian process regression (P- aGPR) method is proposed for efficient PF modeling. First, P- aGPR chooses a series of projection spaces with dimensionalities ranking from low to high. Next, in each projection space, a Gaussian process regression (GPR) model is trained to represent the constraint that PF should satisfy in that space. Moreover, in order to improve modeling efficacy and stability, an active learning framework has been developed by exploiting the uncertainty information obtained in the GPR models. Different from all existing methods, our proposed P-aGPR method can not only provide a generative PF model, but also fast examine whether a provided point locates on PF or not. The numerical results demonstrate that compared to state-of-the-art passive learning methods the proposed P-aGPR method can achieve higher modeling accuracy and stability.