Learning Chemical Reaction Representation with Reactant-Product Alignment

Organic synthesis stands as a cornerstone of chemical industry. The development of robust machine learning models to support tasks associated with organic reactions is of significant interest. However, current methods rely on hand-crafted features or direct adaptations of model architectures from other domains, which lacks feasibility as data scales increase or overlook the rich chemical information inherent in reactions. To address these issues, this paper introduces {\modelname}, a novel chemical reaction representation learning model tailored for a variety of organic-reaction-related tasks. By integrating atomic correspondence between reactants and products, our model discerns the molecular transformations that occur during the reaction, thereby enhancing the comprehension of the reaction mechanism. We have designed an adapter structure to incorporate reaction conditions into the chemical reaction representation, allowing the model to handle diverse reaction conditions and adapt to various datasets and downstream tasks, e.g., reaction performance prediction. Additionally, we introduce a reaction-center aware attention mechanism that enables the model to concentrate on key functional groups, thereby generating potent representations for chemical reactions. Our model has been evaluated on a range of downstream tasks, including reaction condition prediction, reaction yield prediction, and reaction selectivity prediction. Experimental results indicate that our model markedly outperforms existing chemical reaction representation learning architectures across all tasks. Notably, our model significantly outperforms all the baselines with up to 25\% (top-1) and 16\% (top-10) increased accuracy over the strongest baseline on USPTO\_CONDITION dataset for reaction condition prediction. We plan to open-source the code contingent upon the acceptance of the paper.

Alignment Between the Decision-Making Logic of LLMs and Human Cognition: A Case Study on Legal LLMs

This paper presents a method to evaluate the alignment between the decision-making logic of Large Language Models (LLMs) and human cognition in a case study on legal LLMs. Unlike traditional evaluations on language generation results, we propose to evaluate the correctness of the detailed decision-making logic of an LLM behind its seemingly correct outputs, which represents the core challenge for an LLM to earn human trust. To this end, we quantify the interactions encoded by the LLM as primitive decision-making logic, because recent theoretical achievements have proven several mathematical guarantees of the faithfulness of the interaction-based explanation. We design a set of metrics to evaluate the detailed decision-making logic of LLMs. Experiments show that even when the language generation results appear correct, a significant portion of the internal inference logic contains notable issues.

Text-Augmented Multimodal LLMs for Chemical Reaction Condition Recommendation

High-throughput reaction condition (RC) screening is fundamental to chemical synthesis. However, current RC screening suffers from laborious and costly trial-and-error workflows. Traditional computer-aided synthesis planning (CASP) tools fail to find suitable RCs due to data sparsity and inadequate reaction representations. Nowadays, large language models (LLMs) are capable of tackling chemistry-related problems, such as molecule design, and chemical logic Q\&A tasks. However, LLMs have not yet achieved accurate predictions of chemical reaction conditions. Here, we present MM-RCR, a text-augmented multimodal LLM that learns a unified reaction representation from SMILES, reaction graphs, and textual corpus for chemical reaction recommendation (RCR). To train MM-RCR, we construct 1.2 million pair-wised Q\&A instruction datasets. Our experimental results demonstrate that MM-RCR achieves state-of-the-art performance on two open benchmark datasets and exhibits strong generalization capabilities on out-of-domain (OOD) and High-Throughput Experimentation (HTE) datasets. MM-RCR has the potential to accelerate high-throughput condition screening in chemical synthesis.

Hypothesis Testing Prompting Improves Deductive Reasoning in Large Language Models

Combining different forms of prompts with pre-trained large language models has yielded remarkable results on reasoning tasks (e.g. Chain-of-Thought prompting). However, along with testing on more complex reasoning, these methods also expose problems such as invalid reasoning and fictional reasoning paths. In this paper, we develop \textit{Hypothesis Testing Prompting}, which adds conclusion assumptions, backward reasoning, and fact verification during intermediate reasoning steps. \textit{Hypothesis Testing prompting} involves multiple assumptions and reverses validation of conclusions leading to its unique correct answer. Experiments on two challenging deductive reasoning datasets ProofWriter and RuleTaker show that hypothesis testing prompting not only significantly improves the effect, but also generates a more reasonable and standardized reasoning process.

Logical Negation Augmenting and Debiasing for Prompt-based Methods

Prompt-based methods have gained increasing attention on NLP and shown validity on many downstream tasks. Many works have focused on mining these methods' potential for knowledge extraction, but few explore their ability to make logical reasoning. In this work, we focus on the effectiveness of the prompt-based methods on first-order logical reasoning and find that the bottleneck lies in logical negation. Based on our analysis, logical negation tends to result in spurious correlations to negative answers, while propositions without logical negation correlate to positive answers. To solve the problem, we propose a simple but effective method, Negation Augmenting and Negation Debiasing (NAND), which introduces negative propositions to prompt-based methods without updating parameters. Specifically, these negative propositions can counteract spurious correlations by providing "not" for all instances so that models cannot make decisions only by whether expressions contain a logical negation. Experiments on three datasets show that NAND not only solves the problem of calibrating logical negation but also significantly enhances prompt-based methods of logical reasoning without model retraining.

UAlign: Pushing the Limit of Template-free Retrosynthesis Prediction with Unsupervised SMILES Alignment

Retrosynthesis planning poses a formidable challenge in the organic chemical industry, particularly in pharmaceuticals. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, Our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.

Look Before You Leap: Problem Elaboration Prompting Improves Mathematical Reasoning in Large Language Models

Large language models~(LLMs) have exhibited impressive performance across NLP tasks. So far they still face challenges in complex reasoning tasks and can be sensitive to input context. Despite significant efforts have been invested in enhancing reasoning process and improving prefix-prompts robustness, the crucial role of problem context has been overlooked. In this study, we propose a new approach to improve the mathematical capacities of LLMs, named Problem Elaboration Prompting~(PEP). Specifically, PEP decomposes and elucidates the problem context before reasoning, thus enhancing the global context modeling and reducing the parsing difficulties. Experiments on datasets demonstrate promising performances on complex reasoning and indicate the beneficial impact for ill-formed problems. For instance, with the GPT-3.5 model~(\texttt{text-davinci-003}), we observed a 9.93\% improvement with greedy decoding and 8.80\% improvement with self-consistency on GSM8k compared to the standard CoT. With ChatGPT~(\texttt{turbo}) and PEP, we achieve SOTA performances on SVAMP with 86.2\% and GSM8k with 90.98\%.

AgentBoard: An Analytical Evaluation Board of Multi-turn LLM Agents

Evaluating large language models (LLMs) as general-purpose agents is essential for understanding their capabilities and facilitating their integration into practical applications. However, the evaluation process presents substantial challenges. A primary obstacle is the benchmarking of agent performance across diverse scenarios within a unified framework, especially in maintaining partially-observable environments and ensuring multi-round interactions. Moreover, current evaluation frameworks mostly focus on the final success rate, revealing few insights during the process and failing to provide a deep understanding of the model abilities. To address these challenges, we introduce AgentBoard, a pioneering comprehensive benchmark and accompanied open-source evaluation framework tailored to analytical evaluation of LLM agents. AgentBoard offers a fine-grained progress rate metric that captures incremental advancements as well as a comprehensive evaluation toolkit that features easy assessment of agents for multi-faceted analysis through interactive visualization. This not only sheds light on the capabilities and limitations of LLM agents but also propels the interpretability of their performance to the forefront. Ultimately, AgentBoard serves as a significant step towards demystifying agent behaviors and accelerating the development of stronger LLM agents.

Swap-based Deep Reinforcement Learning for Facility Location Problems in Networks

Facility location problems on graphs are ubiquitous in real world and hold significant importance, yet their resolution is often impeded by NP-hardness. Recently, machine learning methods have been proposed to tackle such classical problems, but they are limited to the myopic constructive pattern and only consider the problems in Euclidean space. To overcome these limitations, we propose a general swap-based framework that addresses the p-median problem and the facility relocation problem on graphs and a novel reinforcement learning model demonstrating a keen awareness of complex graph structures. Striking a harmonious balance between solution quality and running time, our method surpasses handcrafted heuristics on intricate graph datasets. Additionally, we introduce a graph generation process to simulate real-world urban road networks with demand, facilitating the construction of large datasets for the classic problem. For the initialization of the locations of facilities, we introduce a physics-inspired strategy for the p-median problem, reaching more stable solutions than the random strategy. The proposed pipeline coupling the classic swap-based method with deep reinforcement learning marks a significant step forward in addressing the practical challenges associated with facility location on graphs.

Modeling Complex Mathematical Reasoning via Large Language Model based MathAgent

Large language models (LLMs) face challenges in solving complex mathematical problems that require comprehensive capacities to parse the statements, associate domain knowledge, perform compound logical reasoning, and integrate the intermediate rationales. Tackling all these problems once could be arduous for LLMs, thus leading to confusion in generation. In this work, we explore the potential of enhancing LLMs with agents by meticulous decomposition and modeling of mathematical reasoning process. Specifically, we propose a formal description of the mathematical solving and extend LLMs with an agent-based zero-shot framework named $\bf{P}$lanner-$\bf{R}$easoner-$\bf{E}$xecutor-$\bf{R}$eflector (PRER). We further provide and implement two MathAgents that define the logical forms and inherent relations via a pool of actions in different grains and orientations: MathAgent-M adapts its actions to LLMs, while MathAgent-H aligns with humankind. Experiments on miniF2F and MATH have demonstrated the effectiveness of PRER and proposed MathAgents, achieving an increase of $12.3\%$($53.9\%\xrightarrow{}66.2\%$) on the MiniF2F, $9.2\%$ ($49.8\%\xrightarrow{}59.0\%$) on MATH, and $13.2\%$($23.2\%\xrightarrow{}35.4\%$) for level-5 problems of MATH against GPT-4. Further analytical results provide more insightful perspectives on exploiting the behaviors of LLMs as agents.