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.

Evaluating Mathematical Reasoning Beyond Accuracy

The leaderboard of Large Language Models (LLMs) in mathematical tasks has been continuously updated. However, the majority of evaluations focus solely on the final results, neglecting the quality of the intermediate steps. This oversight can mask underlying problems, such as logical errors or unnecessary steps in the reasoning process. To measure reasoning beyond final-answer accuracy, we introduce ReasonEval, a new methodology for evaluating the quality of reasoning steps. ReasonEval employs $\textit{validity}$ and $\textit{redundancy}$ to characterize the reasoning quality, as well as accompanying LLMs to assess them automatically. Instantiated by base models that possess strong mathematical knowledge and trained with high-quality labeled data, ReasonEval achieves state-of-the-art performance on human-labeled datasets and can accurately detect different types of errors generated by perturbation. When applied to evaluate LLMs specialized in math, we find that an increase in final-answer accuracy does not necessarily guarantee an improvement in the overall quality of the reasoning steps for challenging mathematical problems. Additionally, we observe that ReasonEval can play a significant role in data selection. We release the best-performing model, meta-evaluation script, and all evaluation results at https://github.com/GAIR-NLP/ReasonEval.

CodeBenchGen: Creating Scalable Execution-based Code Generation Benchmarks

To facilitate evaluation of code generation systems across diverse scenarios, we present CodeBenchGen, a framework to create scalable execution-based benchmarks that only requires light guidance from humans. Specifically, we leverage a large language model (LLM) to convert an arbitrary piece of code into an evaluation example, including test cases for execution-based evaluation. We illustrate the usefulness of our framework by creating a dataset, Exec-CSN, which includes 1,931 examples involving 293 libraries revised from code in 367 GitHub repositories taken from the CodeSearchNet dataset. To demonstrate the complexity and solvability of examples in Exec-CSN, we present a human study demonstrating that 81.3% of the examples can be solved by humans and 61% are rated as ``requires effort to solve''. We conduct code generation experiments on open-source and proprietary models and analyze the performance of both humans and models. We will release the code of both the framework and the dataset upon acceptance.

LLMCRIT: Teaching Large Language Models to Use Criteria

Humans follow criteria when they execute tasks, and these criteria are directly used to assess the quality of task completion. Therefore, having models learn to use criteria to provide feedback can help humans or models to perform tasks better. However, existing research in this field tends to consider only a limited set of criteria or quality assessment aspects. To fill this gap, we propose a general framework that enables large language models (LLMs) to use comprehensive criteria for a task in delivering natural language feedback on task execution. In particular, we present a model-in-the-loop framework that semi-automatically derives criteria from collected guidelines for different writing tasks and constructs in-context demonstrations for each criterion. We choose three tasks from real-world scenarios to operationalize this idea: paper introduction writing, Python code writing, and Reddit post writing, and evaluate our feedback generation framework using different LLMs. The results reveal the fine-grained effects of incorporating criteria and demonstrations and provide valuable insights on how to teach LLMs to use criteria more effectively.

Reformatted Alignment

The quality of finetuning data is crucial for aligning large language models (LLMs) with human values. Current methods to improve data quality are either labor-intensive or prone to factual errors caused by LLM hallucinations. This paper explores elevating the quality of existing instruction data to better align with human values, introducing a simple and effective approach named ReAlign, which reformats the responses of instruction data into a format that better aligns with pre-established criteria and the collated evidence. This approach minimizes human annotation, hallucination, and the difficulty in scaling, remaining orthogonal to existing alignment techniques. Experimentally, ReAlign significantly boosts the general alignment ability, math reasoning, factuality, and readability of the LLMs. Encouragingly, without introducing any additional data or advanced training techniques, and merely by reformatting the response, LLaMA-2-13B's mathematical reasoning ability on GSM8K can be improved from 46.77% to 56.63% in accuracy. Additionally, a mere 5% of ReAlign data yields a 67% boost in general alignment ability measured by the Alpaca dataset. This work highlights the need for further research into the science and mechanistic interpretability of LLMs. We have made the associated code and data publicly accessible to support future studies at https://github.com/GAIR-NLP/ReAlign.

The Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey

The precise prediction of molecular properties is essential for advancements in drug development, particularly in virtual screening and compound optimization. The recent introduction of numerous deep learning-based methods has shown remarkable potential in enhancing molecular property prediction (MPP), especially improving accuracy and insights into molecular structures. Yet, two critical questions arise: does the integration of domain knowledge augment the accuracy of molecular property prediction and does employing multi-modal data fusion yield more precise results than unique data source methods? To explore these matters, we comprehensively review and quantitatively analyze recent deep learning methods based on various benchmarks. We discover that integrating molecular information will improve both MPP regression and classification tasks by upto 3.98% and 1.72%, respectively. We also discover that the utilizing 3-dimensional information with 1-dimensional and 2-dimensional information simultaneously can substantially enhance MPP upto 4.2%. The two consolidated insights offer crucial guidance for future advancements in drug discovery.

Dissecting Human and LLM Preferences

As a relative quality comparison of model responses, human and Large Language Model (LLM) preferences serve as common alignment goals in model fine-tuning and criteria in evaluation. Yet, these preferences merely reflect broad tendencies, resulting in less explainable and controllable models with potential safety risks. In this work, we dissect the preferences of human and 32 different LLMs to understand their quantitative composition, using annotations from real-world user-model conversations for a fine-grained, scenario-wise analysis. We find that humans are less sensitive to errors, favor responses that support their stances, and show clear dislike when models admit their limits. On the contrary, advanced LLMs like GPT-4-Turbo emphasize correctness, clarity, and harmlessness more. Additionally, LLMs of similar sizes tend to exhibit similar preferences, regardless of their training methods, and fine-tuning for alignment does not significantly alter the preferences of pretrained-only LLMs. Finally, we show that preference-based evaluation can be intentionally manipulated. In both training-free and training-based settings, aligning a model with the preferences of judges boosts scores, while injecting the least preferred properties lowers them. This results in notable score shifts: up to 0.59 on MT-Bench (1-10 scale) and 31.94 on AlpacaEval 2.0 (0-100 scale), highlighting the significant impact of this strategic adaptation. Interactive Demo: https://huggingface.co/spaces/GAIR/Preference-Dissection-Visualization Dataset: https://huggingface.co/datasets/GAIR/preference-dissection Code: https://github.com/GAIR-NLP/Preference-Dissection

Deep Rib Fracture Instance Segmentation and Classification from CT on the RibFrac Challenge

Rib fractures are a common and potentially severe injury that can be challenging and labor-intensive to detect in CT scans. While there have been efforts to address this field, the lack of large-scale annotated datasets and evaluation benchmarks has hindered the development and validation of deep learning algorithms. To address this issue, the RibFrac Challenge was introduced, providing a benchmark dataset of over 5,000 rib fractures from 660 CT scans, with voxel-level instance mask annotations and diagnosis labels for four clinical categories (buckle, nondisplaced, displaced, or segmental). The challenge includes two tracks: a detection (instance segmentation) track evaluated by an FROC-style metric and a classification track evaluated by an F1-style metric. During the MICCAI 2020 challenge period, 243 results were evaluated, and seven teams were invited to participate in the challenge summary. The analysis revealed that several top rib fracture detection solutions achieved performance comparable or even better than human experts. Nevertheless, the current rib fracture classification solutions are hardly clinically applicable, which can be an interesting area in the future. As an active benchmark and research resource, the data and online evaluation of the RibFrac Challenge are available at the challenge website. As an independent contribution, we have also extended our previous internal baseline by incorporating recent advancements in large-scale pretrained networks and point-based rib segmentation techniques. The resulting FracNet+ demonstrates competitive performance in rib fracture detection, which lays a foundation for further research and development in AI-assisted rib fracture detection and diagnosis.

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.