ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about the true capabilities of such agents. In this work, we argue that for an agent to fully automate scientific discovery, it must be able to complete all essential tasks in the workflow. Thus, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To this end, we present ScienceAgentBench, a new benchmark for evaluating language agents for data-driven scientific discovery. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. These results underscore the limited capacities of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

Fine-Tuning is Fine, if Calibrated

Fine-tuning is arguably the most straightforward way to tailor a pre-trained model (e.g., a foundation model) to downstream applications, but it also comes with the risk of losing valuable knowledge the model had learned in pre-training. For example, fine-tuning a pre-trained classifier capable of recognizing a large number of classes to master a subset of classes at hand is shown to drastically degrade the model's accuracy in the other classes it had previously learned. As such, it is hard to further use the fine-tuned model when it encounters classes beyond the fine-tuning data. In this paper, we systematically dissect the issue, aiming to answer the fundamental question, ''What has been damaged in the fine-tuned model?'' To our surprise, we find that the fine-tuned model neither forgets the relationship among the other classes nor degrades the features to recognize these classes. Instead, the fine-tuned model often produces more discriminative features for these other classes, even if they were missing during fine-tuning! {What really hurts the accuracy is the discrepant logit scales between the fine-tuning classes and the other classes}, implying that a simple post-processing calibration would bring back the pre-trained model's capability and at the same time unveil the feature improvement over all classes. We conduct an extensive empirical study to demonstrate the robustness of our findings and provide preliminary explanations underlying them, suggesting new directions for future theoretical analysis. Our code is available at https://github.com/OSU-MLB/Fine-Tuning-Is-Fine-If-Calibrated.

Context-aware knowledge graph framework for traffic speed forecasting using graph neural network

Human mobility is intricately influenced by urban contexts spatially and temporally, constituting essential domain knowledge in understanding traffic systems. While existing traffic forecasting models primarily rely on raw traffic data and advanced deep learning techniques, incorporating contextual information remains underexplored due to the lack of effective integration frameworks and the complexity of urban contexts. This study proposes a novel context-aware knowledge graph (CKG) framework to enhance traffic speed forecasting by effectively modeling spatial and temporal contexts. Employing a relation-dependent integration strategy, the framework generates context-aware representations from the spatial and temporal units of CKG to capture spatio-temporal dependencies of urban contexts. A CKG-GNN model, combining the CKG, dual-view multi-head self-attention (MHSA), and graph neural network (GNN), is then designed to predict traffic speed using these context-aware representations. Our experiments demonstrate that CKG's configuration significantly influences embedding performance, with ComplEx and KG2E emerging as optimal for embedding spatial and temporal units, respectively. The CKG-GNN model surpasses benchmark models, achieving an average MAE of $3.46\pm0.01$ and a MAPE of $14.76\pm0.09\%$ for traffic speed predictions from 10 to 120 minutes. The dual-view MHSA analysis reveals the crucial role of relation-dependent features from the context-based view and the model's ability to prioritize recent time slots in prediction from the sequence-based view. The CKG framework's model-agnostic nature suggests its potential applicability in various applications of intelligent transportation systems. Overall, this study underscores the importance of incorporating domain-specific contexts into traffic forecasting and merging context-aware knowledge graphs with neural networks to enhance accuracy.

Bringing Back the Context: Camera Trap Species Identification as Link Prediction on Multimodal Knowledge Graphs

Camera traps are valuable tools in animal ecology for biodiversity monitoring and conservation. However, challenges like poor generalization to deployment at new unseen locations limit their practical application. Images are naturally associated with heterogeneous forms of context possibly in different modalities. In this work, we leverage the structured context associated with the camera trap images to improve out-of-distribution generalization for the task of species identification in camera traps. For example, a photo of a wild animal may be associated with information about where and when it was taken, as well as structured biology knowledge about the animal species. While typically overlooked by existing work, bringing back such context offers several potential benefits for better image understanding, such as addressing data scarcity and enhancing generalization. However, effectively integrating such heterogeneous context into the visual domain is a challenging problem. To address this, we propose a novel framework that reformulates species classification as link prediction in a multimodal knowledge graph (KG). This framework seamlessly integrates various forms of multimodal context for visual recognition. We apply this framework for out-of-distribution species classification on the iWildCam2020-WILDS and Snapshot Mountain Zebra datasets and achieve competitive performance with state-of-the-art approaches. Furthermore, our framework successfully incorporates biological taxonomy for improved generalization and enhances sample efficiency for recognizing under-represented species.

Artificial Intelligence and Human Geography

This paper examines the recent advances and applications of AI in human geography especially the use of machine (deep) learning, including place representation and modeling, spatial analysis and predictive mapping, and urban planning and design. AI technologies have enabled deeper insights into complex human-environment interactions, contributing to more effective scientific exploration, understanding of social dynamics, and spatial decision-making. Furthermore, human geography offers crucial contributions to AI, particularly in context-aware model development, human-centered design, biases and ethical considerations, and data privacy. The synergy beween AI and human geography is essential for addressing global challenges like disaster resilience, poverty, and equitable resource access. This interdisciplinary collaboration between AI and geography will help advance the development of GeoAI and promise a better and sustainable world for all.

Artificial Intelligence Studies in Cartography: A Review and Synthesis of Methods, Applications, and Ethics

The past decade has witnessed the rapid development of geospatial artificial intelligence (GeoAI) primarily due to the ground-breaking achievements in deep learning and machine learning. A growing number of scholars from cartography have demonstrated successfully that GeoAI can accelerate previously complex cartographic design tasks and even enable cartographic creativity in new ways. Despite the promise of GeoAI, researchers and practitioners have growing concerns about the ethical issues of GeoAI for cartography. In this paper, we conducted a systematic content analysis and narrative synthesis of research studies integrating GeoAI and cartography to summarize current research and development trends regarding the usage of GeoAI for cartographic design. Based on this review and synthesis, we first identify dimensions of GeoAI methods for cartography such as data sources, data formats, map evaluations, and six contemporary GeoAI models, each of which serves a variety of cartographic tasks. These models include decision trees, knowledge graph and semantic web technologies, deep convolutional neural networks, generative adversarial networks, graph neural networks, and reinforcement learning. Further, we summarize seven cartographic design applications where GeoAI have been effectively employed: generalization, symbolization, typography, map reading, map interpretation, map analysis, and map production. We also raise five potential ethical challenges that need to be addressed in the integration of GeoAI for cartography: commodification, responsibility, privacy, bias, and (together) transparency, explainability, and provenance. We conclude by identifying four potential research directions for future cartographic research with GeoAI: GeoAI-enabled active cartographic symbolism, human-in-the-loop GeoAI for cartography, GeoAI-based mapping-as-a-service, and generative GeoAI for cartography.

DTA: Distribution Transform-based Attack for Query-Limited Scenario

In generating adversarial examples, the conventional black-box attack methods rely on sufficient feedback from the to-be-attacked models by repeatedly querying until the attack is successful, which usually results in thousands of trials during an attack. This may be unacceptable in real applications since Machine Learning as a Service Platform (MLaaS) usually only returns the final result (i.e., hard-label) to the client and a system equipped with certain defense mechanisms could easily detect malicious queries. By contrast, a feasible way is a hard-label attack that simulates an attacked action being permitted to conduct a limited number of queries. To implement this idea, in this paper, we bypass the dependency on the to-be-attacked model and benefit from the characteristics of the distributions of adversarial examples to reformulate the attack problem in a distribution transform manner and propose a distribution transform-based attack (DTA). DTA builds a statistical mapping from the benign example to its adversarial counterparts by tackling the conditional likelihood under the hard-label black-box settings. In this way, it is no longer necessary to query the target model frequently. A well-trained DTA model can directly and efficiently generate a batch of adversarial examples for a certain input, which can be used to attack un-seen models based on the assumed transferability. Furthermore, we surprisingly find that the well-trained DTA model is not sensitive to the semantic spaces of the training dataset, meaning that the model yields acceptable attack performance on other datasets. Extensive experiments validate the effectiveness of the proposed idea and the superiority of DTA over the state-of-the-art.

Here Is Not There: Measuring Entailment-Based Trajectory Similarity for Location-Privacy Protection and Beyond

While the paths humans take play out in social as well as physical space, measures to describe and compare their trajectories are carried out in abstract, typically Euclidean, space. When these measures are applied to trajectories of actual individuals in an application area, alterations that are inconsequential in abstract space may suddenly become problematic once overlaid with geographic reality. In this work, we present a different view on trajectory similarity by introducing a measure that utilizes logical entailment. This is an inferential perspective that considers facts as triple statements deduced from the social and environmental context in which the travel takes place, and their practical implications. We suggest a formalization of entailment-based trajectory similarity, measured as the overlapping proportion of facts, which are spatial relation statements in our case study. With the proposed measure, we evaluate LSTM-TrajGAN, a privacy-preserving trajectory-generation model. The entailment-based model evaluation reveals potential consequences of disregarding the rich structure of geographic space (e.g., miscalculated insurance risk due to regional shifts in our toy example). Our work highlights the advantage of applying logical entailment to trajectory-similarity reasoning for location-privacy protection and beyond.

Holistic Transfer: Towards Non-Disruptive Fine-Tuning with Partial Target Data

We propose a learning problem involving adapting a pre-trained source model to the target domain for classifying all classes that appeared in the source data, using target data that covers only a partial label space. This problem is practical, as it is unrealistic for the target end-users to collect data for all classes prior to adaptation. However, it has received limited attention in the literature. To shed light on this issue, we construct benchmark datasets and conduct extensive experiments to uncover the inherent challenges. We found a dilemma -- on the one hand, adapting to the new target domain is important to claim better performance; on the other hand, we observe that preserving the classification accuracy of classes missing in the target adaptation data is highly challenging, let alone improving them. To tackle this, we identify two key directions: 1) disentangling domain gradients from classification gradients, and 2) preserving class relationships. We present several effective solutions that maintain the accuracy of the missing classes and enhance the overall performance, establishing solid baselines for holistic transfer of pre-trained models with partial target data.

FLEE-GNN: A Federated Learning System for Edge-Enhanced Graph Neural Network in Analyzing Geospatial Resilience of Multicommodity Food Flows

Understanding and measuring the resilience of food supply networks is a global imperative to tackle increasing food insecurity. However, the complexity of these networks, with their multidimensional interactions and decisions, presents significant challenges. This paper proposes FLEE-GNN, a novel Federated Learning System for Edge-Enhanced Graph Neural Network, designed to overcome these challenges and enhance the analysis of geospatial resilience of multicommodity food flow network, which is one type of spatial networks. FLEE-GNN addresses the limitations of current methodologies, such as entropy-based methods, in terms of generalizability, scalability, and data privacy. It combines the robustness and adaptability of graph neural networks with the privacy-conscious and decentralized aspects of federated learning on food supply network resilience analysis across geographical regions. This paper also discusses FLEE-GNN's innovative data generation techniques, experimental designs, and future directions for improvement. The results show the advancements of this approach to quantifying the resilience of multicommodity food flow networks, contributing to efforts towards ensuring global food security using AI methods. The developed FLEE-GNN has the potential to be applied in other spatial networks with spatially heterogeneous sub-network distributions.