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.
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Retrieval-augmented large language models (LLMs) have been remarkably competent in various NLP tasks. However, it was observed by previous works that retrieval is not always helpful, especially when the LLM is already knowledgeable on the query to answer. Motivated by this, Adaptive Retrieval-Augmented Generation (ARAG) studies retrieving only when the knowledge asked by the query is absent in the LLM. Previous works of ARAG either require accessing the pre-training corpus or prompting with additional model inferences. Aiming to avoid such drawbacks, we propose to determine whether the model is knowledgeable on a query via inspecting the (contextualized) pre-trained token embeddings of LLMs. We hypothesize that such embeddings capture rich information on the model's intrinsic knowledge base, which enables an efficient way of judging the necessity to retrieve from an external corpus. Extensive experiments demonstrate our ARAG approach's superior performance across various benchmarks.
Large language models (LLMs) have exhibited remarkable few-shot learning capabilities and unified the paradigm of NLP tasks through the in-context learning (ICL) technique. Despite the success of ICL, the quality of the exemplar demonstrations can significantly influence the LLM's performance. Existing exemplar selection methods mainly focus on the semantic similarity between queries and candidate exemplars. On the other hand, the logical connections between reasoning steps can be beneficial to depict the problem-solving process as well. In this paper, we proposes a novel method named Reasoning Graph-enhanced Exemplar Retrieval (RGER). RGER first quires LLM to generate an initial response, then expresses intermediate problem-solving steps to a graph structure. After that, it employs graph kernel to select exemplars with semantic and structural similarity. Extensive experiments demonstrate the structural relationship is helpful to the alignment of queries and candidate exemplars. The efficacy of RGER on math and logit reasoning tasks showcases its superiority over state-of-the-art retrieval-based approaches. Our code is released at //github.com/Yukang-Lin/RGER.
In-context learning (ICL) is a new paradigm for natural language processing (NLP), where a large language model (LLM) observes a small number of demonstrations and a test instance as its input, and directly makes predictions without updating model parameters. Previous studies have revealed that ICL is sensitive to the selection and the ordering of demonstrations. However, there are few studies regarding the impact of the demonstration number on the ICL performance within a limited input length of LLM, because it is commonly believed that the number of demonstrations is positively correlated with model performance. In this paper, we found this conclusion does not always hold true. Through pilot experiments, we discover that increasing the number of demonstrations does not necessarily lead to improved performance. Building upon this insight, we propose a Dynamic Demonstrations Controller (D$^2$Controller), which can improve the ICL performance by adjusting the number of demonstrations dynamically. The experimental results show that D$^2$Controller yields a 4.6% relative improvement on ten different sizes of LLMs across ten datasets. Moreover, we also extend our method to previous ICL models and achieve competitive results.
Recent advanced large language models (LLMs) have showcased their emergent capability of in-context learning, facilitating intelligent decision-making through natural language prompts without retraining. This new machine learning paradigm has shown promise in various fields, including general control and optimization problems. Inspired by these advancements, we explore the potential of LLMs for a specific and essential engineering task: parametric shape optimization (PSO). We develop an optimization framework, LLM-PSO, that leverages an LLM to determine the optimal shape of parameterized engineering designs in the spirit of evolutionary strategies. Utilizing the ``Claude 3.5 Sonnet'' LLM, we evaluate LLM-PSO on two benchmark flow optimization problems, specifically aiming to identify drag-minimizing profiles for 1) a two-dimensional airfoil in laminar flow, and 2) a three-dimensional axisymmetric body in Stokes flow. In both cases, LLM-PSO successfully identifies optimal shapes in agreement with benchmark solutions. Besides, it generally converges faster than other classical optimization algorithms. Our preliminary exploration may inspire further investigations into harnessing LLMs for shape optimization and engineering design more broadly.
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.
Approaches based on deep neural networks have achieved striking performance when testing data and training data share similar distribution, but can significantly fail otherwise. Therefore, eliminating the impact of distribution shifts between training and testing data is crucial for building performance-promising deep models. Conventional methods assume either the known heterogeneity of training data (e.g. domain labels) or the approximately equal capacities of different domains. In this paper, we consider a more challenging case where neither of the above assumptions holds. We propose to address this problem by removing the dependencies between features via learning weights for training samples, which helps deep models get rid of spurious correlations and, in turn, concentrate more on the true connection between discriminative features and labels. Extensive experiments clearly demonstrate the effectiveness of our method on multiple distribution generalization benchmarks compared with state-of-the-art counterparts. Through extensive experiments on distribution generalization benchmarks including PACS, VLCS, MNIST-M, and NICO, we show the effectiveness of our method compared with state-of-the-art counterparts.
External knowledge is often useful for natural language understanding tasks. We introduce a contextual text representation model called Conceptual-Contextual (CC) embeddings, which incorporates structured knowledge into text representations. Unlike entity embedding methods, our approach encodes a knowledge graph into a context model. CC embeddings can be easily reused for a wide range of tasks just like pre-trained language models. Our model effectively encodes the huge UMLS database by leveraging semantic generalizability. Experiments on electronic health records (EHRs) and medical text processing benchmarks showed our model gives a major boost to the performance of supervised medical NLP tasks.
External knowledge is often useful for natural language understanding tasks. We introduce a contextual text representation model called Conceptual-Contextual (CC) embeddings, which incorporates structured knowledge into text representations. Unlike entity embedding methods, our approach encodes a knowledge graph into a context model. CC embeddings can be easily reused for a wide range of tasks just like pre-trained language models. Our model effectively encodes the huge UMLS database by leveraging semantic generalizability. Experiments on electronic health records (EHRs) and medical text processing benchmarks showed our model gives a major boost to the performance of supervised medical NLP tasks.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
Deep learning has yielded state-of-the-art performance on many natural language processing tasks including named entity recognition (NER). However, this typically requires large amounts of labeled data. In this work, we demonstrate that the amount of labeled training data can be drastically reduced when deep learning is combined with active learning. While active learning is sample-efficient, it can be computationally expensive since it requires iterative retraining. To speed this up, we introduce a lightweight architecture for NER, viz., the CNN-CNN-LSTM model consisting of convolutional character and word encoders and a long short term memory (LSTM) tag decoder. The model achieves nearly state-of-the-art performance on standard datasets for the task while being computationally much more efficient than best performing models. We carry out incremental active learning, during the training process, and are able to nearly match state-of-the-art performance with just 25\% of the original training data.
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