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Large language models (LLMs) have recently shown significant potential in various biological tasks such as protein engineering and molecule design. These tasks typically involve black-box discrete sequence optimization, where the challenge lies in generating sequences that are not only biologically feasible but also adhere to hard fine-grained constraints. However, LLMs often struggle with such constraints, especially in biological contexts where verifying candidate solutions is costly and time-consuming. In this study, we explore the possibility of employing LLMs as highly-constrained bilevel optimizers through a methodology we refer to as Language Model Optimization with Margin Expectation (LLOME). This approach combines both offline and online optimization, utilizing limited oracle evaluations to iteratively enhance the sequences generated by the LLM. We additionally propose a novel training objective -- Margin-Aligned Expectation (MargE) -- that trains the LLM to smoothly interpolate between the reward and reference distributions. Lastly, we introduce a synthetic test suite that bears strong geometric similarity to real biophysical problems and enables rapid evaluation of LLM optimizers without time-consuming lab validation. Our findings reveal that, in comparison to genetic algorithm baselines, LLMs achieve significantly lower regret solutions while requiring fewer test function evaluations. However, we also observe that LLMs exhibit moderate miscalibration, are susceptible to generator collapse, and have difficulty finding the optimal solution when no explicit ground truth rewards are available.

Large language models (LLMs) have demonstrated impressive capabilities in various tasks using the in-context learning (ICL) paradigm. However, their effectiveness is often compromised by inherent bias, leading to prompt brittleness, i.e., sensitivity to design settings such as example selection, order, and prompt formatting. Previous studies have addressed LLM bias through external adjustment of model outputs, but the internal mechanisms that lead to such bias remain unexplored. Our work delves into these mechanisms, particularly investigating how feedforward neural networks (FFNs) and attention heads result in the bias of LLMs. By Interpreting the contribution of individual FFN vectors and attention heads, we identify the biased LLM components that skew LLMs' prediction toward specific labels. To mitigate these biases, we introduce UniBias, an inference-only method that effectively identifies and eliminates biased FFN vectors and attention heads. Extensive experiments across 12 NLP datasets demonstrate that UniBias significantly enhances ICL performance and alleviates prompt brittleness of LLMs.

The emergence of Large Language Models (LLMs) has revolutionized many fields, not only traditional natural language processing (NLP) tasks. Recently, research on applying LLMs to the database field has been booming, and as a typical non-relational database, the use of LLMs in graph database research has naturally gained significant attention. Recent efforts have increasingly focused on leveraging LLMs to translate natural language into graph query language (NL2GQL). Although some progress has been made, these methods have clear limitations, such as their reliance on streamlined processes that often overlook the potential of LLMs to autonomously plan and collaborate with other LLMs in tackling complex NL2GQL challenges. To address this gap, we propose NAT-NL2GQL, a novel multi-agent framework for translating natural language to graph query language. Specifically, our framework consists of three synergistic agents: the Preprocessor agent, the Generator agent, and the Refiner agent. The Preprocessor agent manages data processing as context, including tasks such as name entity recognition, query rewriting, path linking, and the extraction of query-related schemas. The Generator agent is a fine-tuned LLM trained on NL-GQL data, responsible for generating corresponding GQL statements based on queries and their related schemas. The Refiner agent is tasked with refining the GQL or context using error information obtained from the GQL execution results. Given the scarcity of high-quality open-source NL2GQL datasets based on nGQL syntax, we developed StockGQL, a dataset constructed from a financial market graph database. It is available at: //github.com/leonyuancode/StockGQL. Experimental results on the StockGQL and SpCQL datasets reveal that our method significantly outperforms baseline approaches, highlighting its potential for advancing NL2GQL research.

Large language models (LLMs) have achieved superior performance in powering text-based AI agents, endowing them with decision-making and reasoning abilities akin to humans. Concurrently, there is an emerging research trend focused on extending these LLM-powered AI agents into the multimodal domain. This extension enables AI agents to interpret and respond to diverse multimodal user queries, thereby handling more intricate and nuanced tasks. In this paper, we conduct a systematic review of LLM-driven multimodal agents, which we refer to as large multimodal agents ( LMAs for short). First, we introduce the essential components involved in developing LMAs and categorize the current body of research into four distinct types. Subsequently, we review the collaborative frameworks integrating multiple LMAs , enhancing collective efficacy. One of the critical challenges in this field is the diverse evaluation methods used across existing studies, hindering effective comparison among different LMAs . Therefore, we compile these evaluation methodologies and establish a comprehensive framework to bridge the gaps. This framework aims to standardize evaluations, facilitating more meaningful comparisons. Concluding our review, we highlight the extensive applications of LMAs and propose possible future research directions. Our discussion aims to provide valuable insights and guidelines for future research in this rapidly evolving field. An up-to-date resource list is available at //github.com/jun0wanan/awesome-large-multimodal-agents.

Large language models (LLMs) have demonstrated impressive capabilities in natural language processing. However, their internal mechanisms are still unclear and this lack of transparency poses unwanted risks for downstream applications. Therefore, understanding and explaining these models is crucial for elucidating their behaviors, limitations, and social impacts. In this paper, we introduce a taxonomy of explainability techniques and provide a structured overview of methods for explaining Transformer-based language models. We categorize techniques based on the training paradigms of LLMs: traditional fine-tuning-based paradigm and prompting-based paradigm. For each paradigm, we summarize the goals and dominant approaches for generating local explanations of individual predictions and global explanations of overall model knowledge. We also discuss metrics for evaluating generated explanations, and discuss how explanations can be leveraged to debug models and improve performance. Lastly, we examine key challenges and emerging opportunities for explanation techniques in the era of LLMs in comparison to conventional machine learning models.

The emergence of large language models (LLMs) has substantially influenced natural language processing, demonstrating exceptional results across various tasks. In this study, we employ ``Introspective Tips" to facilitate LLMs in self-optimizing their decision-making. By introspectively examining trajectories, LLM refines its policy by generating succinct and valuable tips. Our method enhances the agent's performance in both few-shot and zero-shot learning situations by considering three essential scenarios: learning from the agent's past experiences, integrating expert demonstrations, and generalizing across diverse games. Importantly, we accomplish these improvements without fine-tuning the LLM parameters; rather, we adjust the prompt to generalize insights from the three aforementioned situations. Our framework not only supports but also emphasizes the advantage of employing LLM in in-contxt decision-making. Experiments involving over 100 games in TextWorld illustrate the superior performance of our approach.

Pre-trained language representation models, such as BERT, capture a general language representation from large-scale corpora, but lack domain-specific knowledge. When reading a domain text, experts make inferences with relevant knowledge. For machines to achieve this capability, we propose a knowledge-enabled language representation model (K-BERT) with knowledge graphs (KGs), in which triples are injected into the sentences as domain knowledge. However, too much knowledge incorporation may divert the sentence from its correct meaning, which is called knowledge noise (KN) issue. To overcome KN, K-BERT introduces soft-position and visible matrix to limit the impact of knowledge. K-BERT can easily inject domain knowledge into the models by equipped with a KG without pre-training by-self because it is capable of loading model parameters from the pre-trained BERT. Our investigation reveals promising results in twelve NLP tasks. Especially in domain-specific tasks (including finance, law, and medicine), K-BERT significantly outperforms BERT, which demonstrates that K-BERT is an excellent choice for solving the knowledge-driven problems that require experts.

Contextual word representations derived from pre-trained bidirectional language models (biLMs) have recently been shown to provide significant improvements to the state of the art for a wide range of NLP tasks. However, many questions remain as to how and why these models are so effective. In this paper, we present a detailed empirical study of how the choice of neural architecture (e.g. LSTM, CNN, or self attention) influences both end task accuracy and qualitative properties of the representations that are learned. We show there is a tradeoff between speed and accuracy, but all architectures learn high quality contextual representations that outperform word embeddings for four challenging NLP tasks. Additionally, all architectures learn representations that vary with network depth, from exclusively morphological based at the word embedding layer through local syntax based in the lower contextual layers to longer range semantics such coreference at the upper layers. Together, these results suggest that unsupervised biLMs, independent of architecture, are learning much more about the structure of language than previously appreciated.

Recurrent neural nets (RNN) and convolutional neural nets (CNN) are widely used on NLP tasks to capture the long-term and local dependencies, respectively. Attention mechanisms have recently attracted enormous interest due to their highly parallelizable computation, significantly less training time, and flexibility in modeling dependencies. We propose a novel attention mechanism in which the attention between elements from input sequence(s) is directional and multi-dimensional (i.e., feature-wise). A light-weight neural net, "Directional Self-Attention Network (DiSAN)", is then proposed to learn sentence embedding, based solely on the proposed attention without any RNN/CNN structure. DiSAN is only composed of a directional self-attention with temporal order encoded, followed by a multi-dimensional attention that compresses the sequence into a vector representation. Despite its simple form, DiSAN outperforms complicated RNN models on both prediction quality and time efficiency. It achieves the best test accuracy among all sentence encoding methods and improves the most recent best result by 1.02% on the Stanford Natural Language Inference (SNLI) dataset, and shows state-of-the-art test accuracy on the Stanford Sentiment Treebank (SST), Multi-Genre natural language inference (MultiNLI), Sentences Involving Compositional Knowledge (SICK), Customer Review, MPQA, TREC question-type classification and Subjectivity (SUBJ) datasets.