Graph-based Molecular In-context Learning Grounded on Morgan Fingerprints

In-context learning (ICL) effectively conditions large language models (LLMs) for molecular tasks, such as property prediction and molecule captioning, by embedding carefully selected demonstration examples into the input prompt. This approach avoids the computational overhead of extensive pertaining and fine-tuning. However, current prompt retrieval methods for molecular tasks have relied on molecule feature similarity, such as Morgan fingerprints, which do not adequately capture the global molecular and atom-binding relationships. As a result, these methods fail to represent the full complexity of molecular structures during inference. Moreover, small-to-medium-sized LLMs, which offer simpler deployment requirements in specialized systems, have remained largely unexplored in the molecular ICL literature. To address these gaps, we propose a self-supervised learning technique, GAMIC (Graph-Aligned Molecular In-Context learning, which aligns global molecular structures, represented by graph neural networks (GNNs), with textual captions (descriptions) while leveraging local feature similarity through Morgan fingerprints. In addition, we introduce a Maximum Marginal Relevance (MMR) based diversity heuristic during retrieval to optimize input prompt demonstration samples. Our experimental findings using diverse benchmark datasets show GAMIC outperforms simple Morgan-based ICL retrieval methods across all tasks by up to 45%.

Semantic Captioning: Benchmark Dataset and Graph-Aware Few-Shot In-Context Learning for SQL2Text

Large Language Models (LLMs) have demonstrated remarkable performance in various NLP tasks, including semantic parsing, which trans lates natural language into formal code representations. However, the reverse process, translating code into natural language, termed semantic captioning, has received less attention. This task is becoming increasingly important as LLMs are integrated into platforms for code generation, security analysis, and educational purposes. In this paper, we focus on the captioning of SQL query (SQL2Text) to address the critical need for understanding and explaining SQL queries in an era where LLM-generated code poses potential security risks. We repurpose Text2SQL datasets for SQL2Text by introducing an iterative ICL prompt using GPT-4o to generate multiple additional utterances, which enhances the robustness of the datasets for the reverse task. We conduct our experiments using in-context learning (ICL) based on different sample selection methods, emphasizing smaller, more computationally efficient LLMs. Our findings demonstrate that leveraging the inherent graph properties of SQL for ICL sample selection significantly outperforms random selection by up to 39% on BLEU score and provides better results than alternative methods. Dataset and codes are published: \url{https://github.com/aliwister/ast-icl}.

WildGraph: Realistic Graph-based Trajectory Generation for Wildlife

Trajectory generation is an important task in movement studies; it circumvents the privacy, ethical, and technical challenges of collecting real trajectories from the target population. In particular, real trajectories in the wildlife domain are scarce as a result of ethical and environmental constraints of the collection process. In this paper, we consider the problem of generating long-horizon trajectories, akin to wildlife migration, based on a small set of real samples. We propose a hierarchical approach to learn the global movement characteristics of the real dataset and recursively refine localized regions. Our solution, WildGraph, discretizes the geographic path into a prototype network of H3 (https://www.uber.com/blog/h3/) regions and leverages a recurrent variational auto-encoder to probabilistically generate paths over the regions, based on occupancy. WildGraph successfully generates realistic months-long trajectories using a sample size as small as 60. Experiments performed on two wildlife migration datasets demonstrate that our proposed method improves the generalization of the generated trajectories in comparison to existing work while achieving superior or comparable performance in several benchmark metrics. Our code is published on the following repository: \url{https://github.com/aliwister/wildgraph}.

WildGEN: Long-horizon Trajectory Generation for Wildlife

Trajectory generation is an important concern in pedestrian, vehicle, and wildlife movement studies. Generated trajectories help enrich the training corpus in relation to deep learning applications, and may be used to facilitate simulation tasks. This is especially significant in the wildlife domain, where the cost of obtaining additional real data can be prohibitively expensive, time-consuming, and bear ethical considerations. In this paper, we introduce WildGEN: a conceptual framework that addresses this challenge by employing a Variational Auto-encoders (VAEs) based method for the acquisition of movement characteristics exhibited by wild geese over a long horizon using a sparse set of truth samples. A subsequent post-processing step of the generated trajectories is performed based on smoothing filters to reduce excessive wandering. Our evaluation is conducted through visual inspection and the computation of the Hausdorff distance between the generated and real trajectories. In addition, we utilize the Pearson Correlation Coefficient as a way to measure how realistic the trajectories are based on the similarity of clusters evaluated on the generated and real trajectories.