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Dec 26

GreenHyperSpectra: A multi-source hyperspectral dataset for global vegetation trait prediction

Plant traits such as leaf carbon content and leaf mass are essential variables in the study of biodiversity and climate change. However, conventional field sampling cannot feasibly cover trait variation at ecologically meaningful spatial scales. Machine learning represents a valuable solution for plant trait prediction across ecosystems, leveraging hyperspectral data from remote sensing. Nevertheless, trait prediction from hyperspectral data is challenged by label scarcity and substantial domain shifts (\eg across sensors, ecological distributions), requiring robust cross-domain methods. Here, we present GreenHyperSpectra, a pretraining dataset encompassing real-world cross-sensor and cross-ecosystem samples designed to benchmark trait prediction with semi- and self-supervised methods. We adopt an evaluation framework encompassing in-distribution and out-of-distribution scenarios. We successfully leverage GreenHyperSpectra to pretrain label-efficient multi-output regression models that outperform the state-of-the-art supervised baseline. Our empirical analyses demonstrate substantial improvements in learning spectral representations for trait prediction, establishing a comprehensive methodological framework to catalyze research at the intersection of representation learning and plant functional traits assessment. All code and data are available at: https://github.com/echerif18/HyspectraSSL.

  • 10 authors
·
Jul 9

FAIR Jupyter: a knowledge graph approach to semantic sharing and granular exploration of a computational notebook reproducibility dataset

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

  • 2 authors
·
Apr 19, 2024

Discovering Failure Modes of Text-guided Diffusion Models via Adversarial Search

Text-guided diffusion models (TDMs) are widely applied but can fail unexpectedly. Common failures include: (i) natural-looking text prompts generating images with the wrong content, or (ii) different random samples of the latent variables that generate vastly different, and even unrelated, outputs despite being conditioned on the same text prompt. In this work, we aim to study and understand the failure modes of TDMs in more detail. To achieve this, we propose SAGE, the first adversarial search method on TDMs that systematically explores the discrete prompt space and the high-dimensional latent space, to automatically discover undesirable behaviors and failure cases in image generation. We use image classifiers as surrogate loss functions during searching, and employ human inspections to validate the identified failures. For the first time, our method enables efficient exploration of both the discrete and intricate human language space and the challenging latent space, overcoming the gradient vanishing problem. Then, we demonstrate the effectiveness of SAGE on five widely used generative models and reveal four typical failure modes: (1) We find a variety of natural text prompts that generate images failing to capture the semantics of input texts. We further discuss the underlying causes and potential solutions based on the results. (2) We find regions in the latent space that lead to distorted images independent of the text prompt, suggesting that parts of the latent space are not well-structured. (3) We also find latent samples that result in natural-looking images unrelated to the text prompt, implying a possible misalignment between the latent and prompt spaces. (4) By appending a single adversarial token embedding to any input prompts, we can generate a variety of specified target objects. Project page: https://sage-diffusion.github.io/

  • 5 authors
·
Jun 1, 2023

AssistedDS: Benchmarking How External Domain Knowledge Assists LLMs in Automated Data Science

Large language models (LLMs) have advanced the automation of data science workflows. Yet it remains unclear whether they can critically leverage external domain knowledge as human data scientists do in practice. To answer this question, we introduce AssistedDS (Assisted Data Science), a benchmark designed to systematically evaluate how LLMs handle domain knowledge in tabular prediction tasks. AssistedDS features both synthetic datasets with explicitly known generative mechanisms and real-world Kaggle competitions, each accompanied by curated bundles of helpful and adversarial documents. These documents provide domain-specific insights into data cleaning, feature engineering, and model selection. We assess state-of-the-art LLMs on their ability to discern and apply beneficial versus harmful domain knowledge, evaluating submission validity, information recall, and predictive performance. Our results demonstrate three key findings: (1) LLMs frequently exhibit an uncritical adoption of provided information, significantly impairing their predictive performance when adversarial content is introduced, (2) helpful guidance is often insufficient to counteract the negative influence of adversarial information, and (3) in Kaggle datasets, LLMs often make errors in handling time-series data, applying consistent feature engineering across different folds, and interpreting categorical variables correctly. These findings highlight a substantial gap in current models' ability to critically evaluate and leverage expert knowledge, underscoring an essential research direction for developing more robust, knowledge-aware automated data science systems.

  • 15 authors
·
May 25

PAK-UCB Contextual Bandit: An Online Learning Approach to Prompt-Aware Selection of Generative Models and LLMs

Selecting a sample generation scheme from multiple prompt-based generative models, including large language models (LLMs) and prompt-guided image and video generation models, is typically addressed by choosing the model that maximizes an averaged evaluation score. However, this score-based selection overlooks the possibility that different models achieve the best generation performance for different types of text prompts. An online identification of the best generation model for various input prompts can reduce the costs associated with querying sub-optimal models. In this work, we explore the possibility of varying rankings of text-based generative models for different text prompts and propose an online learning framework to predict the best data generation model for a given input prompt. The proposed PAK-UCB algorithm addresses a contextual bandit (CB) setting with shared context variables across the arms, utilizing the generated data to update kernel-based functions that predict the score of each model available for unseen text prompts. Additionally, we leverage random Fourier features (RFF) to accelerate the online learning process of PAK-UCB. Our numerical experiments on real and simulated text-to-image and image-to-text generative models show that RFF-UCB performs successfully in identifying the best generation model across different sample types. The code is available at: github.com/yannxiaoyanhu/dgm-online-select.

  • 3 authors
·
Oct 17, 2024

Privacy-Preserving Biometric Verification with Handwritten Random Digit String

Handwriting verification has stood as a steadfast identity authentication method for decades. However, this technique risks potential privacy breaches due to the inclusion of personal information in handwritten biometrics such as signatures. To address this concern, we propose using the Random Digit String (RDS) for privacy-preserving handwriting verification. This approach allows users to authenticate themselves by writing an arbitrary digit sequence, effectively ensuring privacy protection. To evaluate the effectiveness of RDS, we construct a new HRDS4BV dataset composed of online naturally handwritten RDS. Unlike conventional handwriting, RDS encompasses unconstrained and variable content, posing significant challenges for modeling consistent personal writing style. To surmount this, we propose the Pattern Attentive VErification Network (PAVENet), along with a Discriminative Pattern Mining (DPM) module. DPM adaptively enhances the recognition of consistent and discriminative writing patterns, thus refining handwriting style representation. Through comprehensive evaluations, we scrutinize the applicability of online RDS verification and showcase a pronounced outperformance of our model over existing methods. Furthermore, we discover a noteworthy forgery phenomenon that deviates from prior findings and discuss its positive impact in countering malicious impostor attacks. Substantially, our work underscores the feasibility of privacy-preserving biometric verification and propels the prospects of its broader acceptance and application.

  • 5 authors
·
Mar 16