EvoLlama: Enhancing LLMs' Understanding of Proteins via Multimodal Structure and Sequence Representations

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from the universe of natural protein sequences. Furthermore, structure-based encoders like ProteinMPNN learn the structural information of proteins through Graph Neural Networks. However, whether the incorporation of protein encoders can enhance the protein understanding of LLMs has not been explored. To bridge this gap, we propose EvoLlama, a multimodal framework that connects a structure-based encoder, a sequence-based protein encoder and an LLM for protein understanding. EvoLlama consists of a ProteinMPNN structure encoder, an ESM-2 protein sequence encoder, a multimodal projector to align protein and text representations and a Llama-3 text decoder. To train EvoLlama, we fine-tune it on protein-oriented instructions and protein property prediction datasets verbalized via natural language instruction templates. Our experiments show that EvoLlama's protein understanding capabilities have been significantly enhanced, outperforming other fine-tuned protein-oriented LLMs in zero-shot settings by an average of 1%-8% and surpassing the state-of-the-art baseline with supervised fine-tuning by an average of 6%. On protein property prediction datasets, our approach achieves promising results that are competitive with state-of-the-art task-specific baselines. We will release our code in a future version.

CERD: A Comprehensive Chinese Rhetoric Dataset for Rhetorical Understanding and Generation in Essays

Existing rhetorical understanding and generation datasets or corpora primarily focus on single coarse-grained categories or fine-grained categories, neglecting the common interrelations between different rhetorical devices by treating them as independent sub-tasks. In this paper, we propose the Chinese Essay Rhetoric Dataset (CERD), consisting of 4 commonly used coarse-grained categories including metaphor, personification, hyperbole and parallelism and 23 fine-grained categories across both form and content levels. CERD is a manually annotated and comprehensive Chinese rhetoric dataset with five interrelated sub-tasks. Unlike previous work, our dataset aids in understanding various rhetorical devices, recognizing corresponding rhetorical components, and generating rhetorical sentences under given conditions, thereby improving the author's writing proficiency and language usage skills. Extensive experiments are conducted to demonstrate the interrelations between multiple tasks in CERD, as well as to establish a benchmark for future research on rhetoric. The experimental results indicate that Large Language Models achieve the best performance across most tasks, and jointly fine-tuning with multiple tasks further enhances performance.

Cause-Aware Empathetic Response Generation via Chain-of-Thought Fine-Tuning

Empathetic response generation endows agents with the capability to comprehend dialogue contexts and react to expressed emotions. Previous works predominantly focus on leveraging the speaker's emotional labels, but ignore the importance of emotion cause reasoning in empathetic response generation, which hinders the model's capacity for further affective understanding and cognitive inference. In this paper, we propose a cause-aware empathetic generation approach by integrating emotions and causes through a well-designed Chain-of-Thought (CoT) prompt on Large Language Models (LLMs). Our approach can greatly promote LLMs' performance of empathy by instruction tuning and enhancing the role awareness of an empathetic listener in the prompt. Additionally, we propose to incorporate cause-oriented external knowledge from COMET into the prompt, which improves the diversity of generation and alleviates conflicts between internal and external knowledge at the same time. Experimental results on the benchmark dataset demonstrate that our approach on LLaMA-7b achieves state-of-the-art performance in both automatic and human evaluations.

Enhancing Language Model Rationality with Bi-Directional Deliberation Reasoning

This paper introduces BI-Directional DEliberation Reasoning (BIDDER), a novel reasoning approach to enhance the decision rationality of language models. Traditional reasoning methods typically rely on historical information and employ uni-directional (left-to-right) reasoning strategy. This lack of bi-directional deliberation reasoning results in limited awareness of potential future outcomes and insufficient integration of historical context, leading to suboptimal decisions. BIDDER addresses this gap by incorporating principles of rational decision-making, specifically managing uncertainty and predicting expected utility. Our approach involves three key processes: Inferring hidden states to represent uncertain information in the decision-making process from historical data; Using these hidden states to predict future potential states and potential outcomes; Integrating historical information (past contexts) and long-term outcomes (future contexts) to inform reasoning. By leveraging bi-directional reasoning, BIDDER ensures thorough exploration of both past and future contexts, leading to more informed and rational decisions. We tested BIDDER's effectiveness in two well-defined scenarios: Poker (Limit Texas Hold'em) and Negotiation. Our experiments demonstrate that BIDDER significantly improves the decision-making capabilities of LLMs and LLM agents.

LLM as a Mastermind: A Survey of Strategic Reasoning with Large Language Models

This paper presents a comprehensive survey of the current status and opportunities for Large Language Models (LLMs) in strategic reasoning, a sophisticated form of reasoning that necessitates understanding and predicting adversary actions in multi-agent settings while adjusting strategies accordingly. Strategic reasoning is distinguished by its focus on the dynamic and uncertain nature of interactions among multi-agents, where comprehending the environment and anticipating the behavior of others is crucial. We explore the scopes, applications, methodologies, and evaluation metrics related to strategic reasoning with LLMs, highlighting the burgeoning development in this area and the interdisciplinary approaches enhancing their decision-making performance. It aims to systematize and clarify the scattered literature on this subject, providing a systematic review that underscores the importance of strategic reasoning as a critical cognitive capability and offers insights into future research directions and potential improvements.

Temporal Knowledge Graph Completion with Time-sensitive Relations in Hypercomplex Space

Temporal knowledge graph completion (TKGC) aims to fill in missing facts within a given temporal knowledge graph at a specific time. Existing methods, operating in real or complex spaces, have demonstrated promising performance in this task. This paper advances beyond conventional approaches by introducing more expressive quaternion representations for TKGC within hypercomplex space. Unlike existing quaternion-based methods, our study focuses on capturing time-sensitive relations rather than time-aware entities. Specifically, we model time-sensitive relations through time-aware rotation and periodic time translation, effectively capturing complex temporal variability. Furthermore, we theoretically demonstrate our method's capability to model symmetric, asymmetric, inverse, compositional, and evolutionary relation patterns. Comprehensive experiments on public datasets validate that our proposed approach achieves state-of-the-art performance in the field of TKGC.

A Survey on Temporal Knowledge Graph: Representation Learning and Applications

Knowledge graphs have garnered significant research attention and are widely used to enhance downstream applications. However, most current studies mainly focus on static knowledge graphs, whose facts do not change with time, and disregard their dynamic evolution over time. As a result, temporal knowledge graphs have attracted more attention because a large amount of structured knowledge exists only within a specific period. Knowledge graph representation learning aims to learn low-dimensional vector embeddings for entities and relations in a knowledge graph. The representation learning of temporal knowledge graphs incorporates time information into the standard knowledge graph framework and can model the dynamics of entities and relations over time. In this paper, we conduct a comprehensive survey of temporal knowledge graph representation learning and its applications. We begin with an introduction to the definitions, datasets, and evaluation metrics for temporal knowledge graph representation learning. Next, we propose a taxonomy based on the core technologies of temporal knowledge graph representation learning methods, and provide an in-depth analysis of different methods in each category. Finally, we present various downstream applications related to the temporal knowledge graphs. In the end, we conclude the paper and have an outlook on the future research directions in this area.

K-Level Reasoning with Large Language Models

While Large Language Models (LLMs) have demonstrated their proficiency in complex reasoning tasks, their performance in dynamic, interactive, and competitive scenarios - such as business strategy and stock market analysis - remains underexplored. To bridge this gap, we formally explore the dynamic reasoning capabilities of LLMs for decision-making in rapidly evolving environments. We introduce two game theory-based pilot challenges that mirror the complexities of real-world dynamic decision-making. These challenges are well-defined, enabling clear, controllable, and precise evaluation of LLMs' dynamic reasoning abilities. Through extensive experiments, we find that existing reasoning methods tend to falter in dynamic settings that require k-level thinking - a key concept not tackled by previous works. To address this, we propose a novel reasoning approach for LLMs, named "K-Level Reasoning". This approach adopts the perspective of rivals to recursively employ k-level thinking based on available historical information, which significantly improves the prediction accuracy of rivals' subsequent moves and informs more strategic decision-making. This research not only sets a robust quantitative benchmark for the assessment of dynamic reasoning but also markedly enhances the proficiency of LLMs in dynamic contexts.

BIBench: Benchmarking Data Analysis Knowledge of Large Language Models

Large Language Models (LLMs) have demonstrated impressive capabilities across a wide range of tasks. However, their proficiency and reliability in the specialized domain of Data Analysis, particularly with a focus on data-driven thinking, remain uncertain. To bridge this gap, we introduce BIBench, a comprehensive benchmark designed to evaluate the data analysis capabilities of LLMs within the context of Business Intelligence (BI). BIBench assesses LLMs across three dimensions: 1) BI foundational knowledge, evaluating the models' numerical reasoning and familiarity with financial concepts; 2) BI knowledge application, determining the models' ability to quickly comprehend textual information and generate analysis questions from multiple views; and 3) BI technical skills, examining the models' use of technical knowledge to address real-world data analysis challenges. BIBench comprises 11 sub-tasks, spanning three categories of task types: classification, extraction, and generation. Additionally, we've developed BIChat, a domain-specific dataset with over a million data points, to fine-tune LLMs. We will release BIBenchmark, BIChat, and the evaluation scripts at \url{https://github.com/cubenlp/BIBench}. This benchmark aims to provide a measure for in-depth analysis of LLM abilities and foster the advancement of LLMs in the field of data analysis.

An Effective and Efficient Time-aware Entity Alignment Framework via Two-aspect Three-view Label Propagation

Entity alignment (EA) aims to find the equivalent entity pairs between different knowledge graphs (KGs), which is crucial to promote knowledge fusion. With the wide use of temporal knowledge graphs (TKGs), time-aware EA (TEA) methods appear to enhance EA. Existing TEA models are based on Graph Neural Networks (GNN) and achieve state-of-the-art (SOTA) performance, but it is difficult to transfer them to large-scale TKGs due to the scalability issue of GNN. In this paper, we propose an effective and efficient non-neural EA framework between TKGs, namely LightTEA, which consists of four essential components: (1) Two-aspect Three-view Label Propagation, (2) Sparse Similarity with Temporal Constraints, (3) Sinkhorn Operator, and (4) Temporal Iterative Learning. All of these modules work together to improve the performance of EA while reducing the time consumption of the model. Extensive experiments on public datasets indicate that our proposed model significantly outperforms the SOTA methods for EA between TKGs, and the time consumed by LightTEA is only dozens of seconds at most, no more than 10% of the most efficient TEA method.