Predicting enzymatic reactions is crucial for applications in biocatalysis, metabolic engineering, and drug discovery, yet it remains a complex and resource-intensive task. Large Language Models (LLMs) have recently demonstrated remarkable success in various scientific domains, e.g., through their ability to generalize knowledge, reason over complex structures, and leverage in-context learning strategies. In this study, we systematically evaluate the capability of LLMs, particularly the Llama-3.1 family (8B and 70B), across three core biochemical tasks: Enzyme Commission number prediction, forward synthesis, and retrosynthesis. We compare single-task and multitask learning strategies, employing parameter-efficient fine-tuning via LoRA adapters. Additionally, we assess performance across different data regimes to explore their adaptability in low-data settings. Our results demonstrate that fine-tuned LLMs capture biochemical knowledge, with multitask learning enhancing forward- and retrosynthesis predictions by leveraging shared enzymatic information. We also identify key limitations, for example challenges in hierarchical EC classification schemes, highlighting areas for further improvement in LLM-driven biochemical modeling.
Large language models (LLMs) perform remarkably well on tabular datasets in zero- and few-shot settings, since they can extract meaning from natural language column headers that describe features and labels. Similarly, TabPFN, a recent non-LLM transformer pretrained on numerous tables for in-context learning, has demonstrated excellent performance for dataset sizes up to a thousand samples. In contrast, gradient-boosted decision trees (GBDTs) are typically trained from scratch on each dataset without benefiting from pretraining data and must learn the relationships between columns from their entries alone since they lack natural language understanding. LLMs and TabPFN excel on small tabular datasets where a strong prior is essential, yet they are not competitive with GBDTs on medium or large datasets, since their context lengths are limited. In this paper, we propose a simple and lightweight approach for fusing large language models and TabPFN with gradient-boosted decision trees, which allows scalable GBDTs to benefit from the natural language capabilities and pretraining of transformers. We name our fusion methods LLM-Boost and PFN-Boost, respectively. While matching or surpassing the performance of the transformer at sufficiently small dataset sizes and GBDTs at sufficiently large sizes, LLM-Boost and PFN-Boost outperform both standalone components on a wide range of dataset sizes in between. We demonstrate state-of-the-art performance against numerous baselines and ensembling algorithms. We find that PFN-Boost achieves the best average performance among all methods we test for all but very small dataset sizes. We release our code at http://github.com/MayukaJ/LLM-Boost .
Large-scale models trained on extensive datasets have become the standard due to their strong generalizability across diverse tasks. In-context learning (ICL), widely used in natural language processing, leverages these models by providing task-specific prompts without modifying their parameters. This paradigm is increasingly being adapted for computer vision, where models receive an input-output image pair, known as an in-context pair, alongside a query image to illustrate the desired output. However, the success of visual ICL largely hinges on the quality of these prompts. To address this, we propose Enhanced Instruct Me More (E-InMeMo), a novel approach that incorporates learnable perturbations into in-context pairs to optimize prompting. Through extensive experiments on standard vision tasks, E-InMeMo demonstrates superior performance over existing state-of-the-art methods. Notably, it improves mIoU scores by 7.99 for foreground segmentation and by 17.04 for single object detection when compared to the baseline without learnable prompts. These results highlight E-InMeMo as a lightweight yet effective strategy for enhancing visual ICL. Code is publicly available at: https://github.com/Jackieam/E-InMeMo
One of the primary aspirations in reinforcement learning research is developing general-purpose agents capable of rapidly adapting to and mastering novel tasks. While RL gaming agents have mastered many Atari games, they remain slow and costly to train for each game. In this work, we demonstrate that latest reasoning LLMs with out-of-domain RL post-training can play a challenging Atari game called Frogger under a zero-shot setting. We then investigate the effect of in-context learning and the amount of reasoning effort on LLM performance. Lastly, we demonstrate a way to bootstrap traditional RL method with LLM demonstrations, which significantly improves their performance and sample efficiency. Our implementation is open sourced at https://github.com/AlienKevin/frogger.
In-Context Learning (ICL) has gained prominence due to its ability to perform tasks without requiring extensive training data and its robustness to noisy labels. A typical ICL workflow involves selecting localized examples relevant to a given input using sparse or dense embedding-based similarity functions. However, relying solely on similarity-based selection may introduce topical biases in the retrieved contexts, potentially leading to suboptimal downstream performance. We posit that reranking the retrieved context to enhance topical diversity can improve downstream task performance. To achieve this, we leverage maximum marginal relevance (MMR) which balances topical similarity with inter-example diversity. Our experimental results demonstrate that diversifying the selected examples leads to consistent improvements in downstream performance across various context sizes and similarity functions. The implementation of our approach is made available at https://github.com/janak11111/Diverse-ICL.
In-context learning (ICL) has emerged as a powerful capability of large language models (LLMs), enabling them to perform new tasks based on a few provided examples without explicit fine-tuning. Despite their impressive adaptability, these models remain vulnerable to subtle adversarial perturbations and exhibit unpredictable behavior when faced with linguistic variations. Inspired by software testing principles, we introduce a software testing-inspired framework, called MMT4NL, for evaluating the trustworthiness of in-context learning by utilizing adversarial perturbations and software testing techniques. It includes diverse evaluation aspects of linguistic capabilities for testing the ICL capabilities of LLMs. MMT4NL is built around the idea of crafting metamorphic adversarial examples from a test set in order to quantify and pinpoint bugs in the designed prompts of ICL. Our philosophy is to treat any LLM as software and validate its functionalities just like testing the software. Finally, we demonstrate applications of MMT4NL on the sentiment analysis and question-answering tasks. Our experiments could reveal various linguistic bugs in state-of-the-art LLMs.
We present an embodied robotic system with an LLM-driven agent-orchestration architecture for autonomous household object management. The system integrates memory-augmented task planning, enabling robots to execute high-level user commands while tracking past actions. It employs three specialized agents: a routing agent, a task planning agent, and a knowledge base agent, each powered by task-specific LLMs. By leveraging in-context learning, our system avoids the need for explicit model training. RAG enables the system to retrieve context from past interactions, enhancing long-term object tracking. A combination of Grounded SAM and LLaMa3.2-Vision provides robust object detection, facilitating semantic scene understanding for task planning. Evaluation across three household scenarios demonstrates high task planning accuracy and an improvement in memory recall due to RAG. Specifically, Qwen2.5 yields best performance for specialized agents, while LLaMA3.1 excels in routing tasks. The source code is available at: https://github.com/marc1198/chat-hsr.
Recent improvements in large language model (LLM) performance on academic benchmarks, such as MATH and GSM8K, have emboldened their use as standalone tutors and as simulations of human learning. However, these new applications require more than evaluations of final solution generation. We introduce TutorGym to evaluate these applications more directly. TutorGym is a standard interface for testing artificial intelligence (AI) agents within existing intelligent tutoring systems (ITS) that have been tested and refined in classroom studies, including Cognitive Tutors (CTAT), Apprentice Tutors, and OATutors. TutorGym is more than a simple problem-solution benchmark, it situates AI agents within the interactive interfaces of existing ITSs. At each step of problem-solving, AI agents are asked what they would do as a tutor or as a learner. As tutors, AI agents are prompted to provide tutoring support -- such as generating examples, hints, and step-level correctness feedback -- which can be evaluated directly against the adaptive step-by-step support provided by existing ITSs. As students, agents directly learn from ITS instruction, and their mistakes and learning trajectories can be compared to student data. TutorGym establishes a common framework for training and evaluating diverse AI agents, including LLMs, computational models of learning, and reinforcement learning agents, within a growing suite of learning environments. Currently, TutorGym includes 223 different tutor domains. In an initial evaluation, we find that current LLMs are poor at tutoring -- none did better than chance at labeling incorrect actions, and next-step actions were correct only ~52-70% of the time -- but they could produce remarkably human-like learning curves when trained as students with in-context learning.
Graph In-Context Learning, with the ability to adapt pre-trained graph models to novel and diverse downstream graphs without updating any parameters, has gained much attention in the community. The key to graph in-context learning is to perform downstream graphs conditioned on chosen prompt examples. Existing methods randomly select subgraphs or edges as prompts, leading to noisy graph prompts and inferior model performance. Additionally, due to the gap between pre-training and testing graphs, when the number of classes in the testing graphs is much greater than that in the training, the in-context learning ability will also significantly deteriorate. To tackle the aforementioned challenges, we develop a multi-stage adaptive prompt optimization method GraphPrompter, which optimizes the entire process of generating, selecting, and using graph prompts for better in-context learning capabilities. Firstly, Prompt Generator introduces a reconstruction layer to highlight the most informative edges and reduce irrelevant noise for graph prompt construction. Furthermore, in the selection stage, Prompt Selector employs the $k$-nearest neighbors algorithm and pre-trained selection layers to dynamically choose appropriate samples and minimize the influence of irrelevant prompts. Finally, we leverage a Prompt Augmenter with a cache replacement strategy to enhance the generalization capability of the pre-trained model on new datasets. Extensive experiments show that GraphPrompter effectively enhances the in-context learning ability of graph models. On average across all the settings, our approach surpasses the state-of-the-art baselines by over 8%. Our code is released at https://github.com/karin0018/GraphPrompter.
Visual In-Context Learning (VICL) enables adaptively solving vision tasks by leveraging pixel demonstrations, mimicking human-like task completion through analogy. Prompt selection is critical in VICL, but current methods assume the existence of a single "ideal" prompt in a pool of candidates, which in practice may not hold true. Multiple suitable prompts may exist, but individually they often fall short, leading to difficulties in selection and the exclusion of useful context. To address this, we propose a new perspective: prompt condensation. Rather than relying on a single prompt, candidate prompts collaborate to efficiently integrate informative contexts without sacrificing resolution. We devise Condenser, a lightweight external plugin that compresses relevant fine-grained context across multiple prompts. Optimized end-to-end with the backbone, Condenser ensures accurate integration of contextual cues. Experiments demonstrate Condenser outperforms state-of-the-arts across benchmark tasks, showing superior context compression, scalability with more prompts, and enhanced computational efficiency compared to ensemble methods, positioning it as a highly competitive solution for VICL. Code is open-sourced at https://github.com/gimpong/CVPR25-Condenser.
Chain-of-Thought (CoT) prompting has emerged as a powerful technique to improve in-context learning (ICL) in large language models (LLMs) by breaking complex reasoning into intermediate steps. However, the ability of CoT to generalize under distribution shift remains poorly understood. In this work, we extend a latent-variable framework for CoT prompting and study its behavior on two prototypical out-of-distribution (OOD) scenarios: (i) the latent variables for CoT steps are permuted into novel combinations, and (ii) the latent variables uniformly scaled by a factor. Our experiments demonstrate that CoT inference generalizes effectively to OOD samples whose latent variables closely resemble those seen during training, but its performance degrades as this similarity decreases. These findings provide foundational insights into the strengths and limitations of CoT prompting under OOD conditions and suggest directions for developing more resilient reasoning strategies in future LLMs.
Language models rely on semantic priors to perform in-context learning, which leads to poor performance on tasks involving inductive reasoning. Instruction-tuning methods based on imitation learning can superficially enhance the in-context learning performance of language models, but they often fail to improve the model's understanding of the underlying rules that connect inputs and outputs in few-shot demonstrations. We propose ReDis, a reasoning distillation technique designed to improve the inductive reasoning capabilities of language models. Through a careful combination of data augmentation, filtering, supervised fine-tuning, and alignment, ReDis achieves significant performance improvements across a diverse range of tasks, including 1D-ARC, List Function, ACRE, and MiniSCAN. Experiments on three language model backbones show that ReDis outperforms equivalent few-shot prompting baselines across all tasks and even surpasses the teacher model, GPT-4o, in some cases. ReDis, based on the LLaMA-3 backbone, achieves relative improvements of 23.2%, 2.8%, and 66.6% over GPT-4o on 1D-ARC, ACRE, and MiniSCAN, respectively, within a similar hypothesis search space. The code, dataset, and model checkpoints will be made available at https://github.com/NafisSadeq/reasoning-distillation.git.
Mixture-of-Experts (MoE) Large Language Models (LLMs) suffer from severely sub-optimal expert pathways-our study reveals that naive expert selection learned from pretraining leaves a surprising 10-20% accuracy gap for improvement. Motivated by this observation, we develop a novel class of test-time optimization methods to re-weight or "re-mixing" the experts in different layers jointly for each test sample. Since the test sample's ground truth is unknown, we propose to optimize a surrogate objective defined by the sample's "successful neighbors" from a reference set of samples. We introduce three surrogates and algorithms based on mode-finding, kernel regression, and the average loss of similar reference samples/tasks. To reduce the cost of optimizing whole pathways, we apply our algorithms merely to the core experts' mixing weights in critical layers, which enjoy similar performance but save significant computation. This leads to "Critical-Layer, Core-Expert, Collaborative Pathway Optimization (C3PO)". We apply C3PO to two recent MoE LLMs and examine it on six widely-used benchmarks. It consistently improves the base model by 7-15% in accuracy and outperforms widely used test-time learning baselines, e.g., in-context learning and prompt/prefix tuning, by a large margin. Moreover, C3PO enables MoE LLMs with 1-3B active parameters to outperform LLMs of 7-9B parameters, hence improving MoE's advantages on efficiency. Our thorough ablation study further sheds novel insights on achieving test-time improvement on MoE.
Recent advances in large language and vision-language models have enabled zero-shot inference, allowing models to solve new tasks without task-specific training. Various adaptation techniques such as prompt engineering, In-Context Learning (ICL), and supervised fine-tuning can further enhance the model's performance on a downstream task, but they require substantial manual effort to construct effective prompts or labeled examples. In this work, we introduce a joint inference framework for fully unsupervised adaptation, eliminating the need for manual prompt engineering and labeled examples. Unlike zero-shot inference, which makes independent predictions, the joint inference makes predictions simultaneously for all inputs in a given task. Since direct joint inference involves computationally expensive optimization, we develop efficient approximation techniques, leading to two unsupervised adaptation methods: unsupervised fine-tuning and unsupervised ICL. We demonstrate the effectiveness of our methods across diverse tasks and models, including language-only Llama-3.1 on natural language processing tasks, reasoning-oriented Qwen2.5-Math on grade school math problems, vision-language OpenFlamingo on vision tasks, and the API-only access GPT-4o model on massive multi-discipline tasks. Our experiments demonstrate substantial improvements over the standard zero-shot approach, including 39% absolute improvement on the challenging GSM8K math reasoning dataset. Remarkably, despite being fully unsupervised, our framework often performs on par with supervised approaches that rely on ground truth labels.
Accurate speed estimation in sensorless brushless DC motors is essential for high-performance control and monitoring, yet conventional model-based approaches struggle with system nonlinearities and parameter uncertainties. In this work, we propose an in-context learning framework leveraging transformer-based models to perform zero-shot speed estimation using only electrical measurements. By training the filter offline on simulated motor trajectories, we enable real-time inference on unseen real motors without retraining, eliminating the need for explicit system identification while retaining adaptability to varying operating conditions. Experimental results demonstrate that our method outperforms traditional Kalman filter-based estimators, especially in low-speed regimes that are crucial during motor startup.
This study evaluates the baseline capabilities of Large Language Models (LLMs) like ChatGPT, Claude, and Gemini to learn concepts in music theory through in-context learning and chain-of-thought prompting. Using carefully designed prompts (in-context learning) and step-by-step worked examples (chain-of-thought prompting), we explore how LLMs can be taught increasingly complex material and how pedagogical strategies for human learners translate to educating machines. Performance is evaluated using questions from an official Canadian Royal Conservatory of Music (RCM) Level 6 examination, which covers a comprehensive range of topics, including interval and chord identification, key detection, cadence classification, and metrical analysis. Additionally, we evaluate the suitability of various music encoding formats for these tasks (ABC, Humdrum, MEI, MusicXML). All experiments were run both with and without contextual prompts. Results indicate that without context, ChatGPT with MEI performs the best at 52%, while with context, Claude with MEI performs the best at 75%. Future work will further refine prompts and expand to cover more advanced music theory concepts. This research contributes to the broader understanding of teaching LLMs and has applications for educators, students, and developers of AI music tools alike.
Biomedical ontologies, which comprehensively define concepts and relations for biomedical entities, are crucial for structuring and formalizing domain-specific information representations. Biomedical code mapping identifies similarity or equivalence between concepts from different ontologies. Obtaining high-quality mapping usually relies on automatic generation of unrefined mapping with ontology domain fine-tuned language models (LMs), followed by manual selections or corrections by coding experts who have extensive domain expertise and familiarity with ontology schemas. The LMs usually provide unrefined code mapping suggestions as a list of candidates without reasoning or supporting evidence, hence coding experts still need to verify each suggested candidate against ontology sources to pick the best matches. This is also a recurring task as ontology sources are updated regularly to incorporate new research findings. Consequently, the need of regular LM retraining and manual refinement make code mapping time-consuming and labour intensive. In this work, we created OntologyRAG, an ontology-enhanced retrieval-augmented generation (RAG) method that leverages the inductive biases from ontological knowledge graphs for in-context-learning (ICL) in large language models (LLMs). Our solution grounds LLMs to knowledge graphs with unrefined mappings between ontologies and processes questions by generating an interpretable set of results that include prediction rational with mapping proximity assessment. Our solution doesn't require re-training LMs, as all ontology updates could be reflected by updating the knowledge graphs with a standard process. Evaluation results on a self-curated gold dataset show promises of using our method to enable coding experts to achieve better and faster code mapping. The code is available at https://github.com/iqvianlp/ontologyRAG.
We study how multi-head softmax attention models are trained to perform in-context learning on linear data. Through extensive empirical experiments and rigorous theoretical analysis, we demystify the emergence of elegant attention patterns: a diagonal and homogeneous pattern in the key-query (KQ) weights, and a last-entry-only and zero-sum pattern in the output-value (OV) weights. Remarkably, these patterns consistently appear from gradient-based training starting from random initialization. Our analysis reveals that such emergent structures enable multi-head attention to approximately implement a debiased gradient descent predictor -- one that outperforms single-head attention and nearly achieves Bayesian optimality up to proportional factor. Furthermore, compared to linear transformers, the softmax attention readily generalizes to sequences longer than those seen during training. We also extend our study to scenarios with non-isotropic covariates and multi-task linear regression. In the former, multi-head attention learns to implement a form of pre-conditioned gradient descent. In the latter, we uncover an intriguing regime where the interplay between head number and task number triggers a superposition phenomenon that efficiently resolves multi-task in-context learning. Our results reveal that in-context learning ability emerges from the trained transformer as an aggregated effect of its architecture and the underlying data distribution, paving the way for deeper understanding and broader applications of in-context learning.
Visual in-context learning (VICL), as a new paradigm in computer vision, allows the model to rapidly adapt to various tasks with only a handful of prompts and examples. While effective, the existing VICL paradigm exhibits poor generalizability under distribution shifts. In this work, we propose test-time Visual In-Context Tuning (VICT), a method that can adapt VICL models on the fly with a single test sample. Specifically, we flip the role between the task prompts and the test sample and use a cycle consistency loss to reconstruct the original task prompt output. Our key insight is that a model should be aware of a new test distribution if it can successfully recover the original task prompts. Extensive experiments on six representative vision tasks ranging from high-level visual understanding to low-level image processing, with 15 common corruptions, demonstrate that our VICT can improve the generalizability of VICL to unseen new domains. In addition, we show the potential of applying VICT for unseen tasks at test time. Code: https://github.com/Jiahao000/VICT.
Modern transportation systems face pressing challenges due to increasing demand, dynamic environments, and heterogeneous information integration. The rapid evolution of Large Language Models (LLMs) offers transformative potential to address these challenges. Extensive knowledge and high-level capabilities derived from pretraining evolve the default role of LLMs as text generators to become versatile, knowledge-driven task solvers for intelligent transportation systems. This survey first presents LLM4TR, a novel conceptual framework that systematically categorizes the roles of LLMs in transportation into four synergetic dimensions: information processors, knowledge encoders, component generators, and decision facilitators. Through a unified taxonomy, we systematically elucidate how LLMs bridge fragmented data pipelines, enhance predictive analytics, simulate human-like reasoning, and enable closed-loop interactions across sensing, learning, modeling, and managing tasks in transportation systems. For each role, our review spans diverse applications, from traffic prediction and autonomous driving to safety analytics and urban mobility optimization, highlighting how emergent capabilities of LLMs such as in-context learning and step-by-step reasoning can enhance the operation and management of transportation systems. We further curate practical guidance, including available resources and computational guidelines, to support real-world deployment. By identifying challenges in existing LLM-based solutions, this survey charts a roadmap for advancing LLM-driven transportation research, positioning LLMs as central actors in the next generation of cyber-physical-social mobility ecosystems. Online resources can be found in the project page: https://github.com/tongnie/awesome-llm4tr.