ZeMing Gong

Yiming Zhang, ZeMing Gong, Angel X. Chang

We introduce the task of localizing a flexible number of objects in real-world 3D scenes using natural language descriptions. Existing 3D visual grounding tasks focus on localizing a unique object given a text description. However, such a strict setting is unnatural as localizing potentially multiple objects is a common need in real-world scenarios and robotic tasks (e.g., visual navigation and object rearrangement). To address this setting we propose Multi3DRefer, generalizing the ScanRefer dataset and task. Our dataset contains 61926 descriptions of 11609 objects, where zero, single or multiple target objects are referenced by each description. We also introduce a new evaluation metric and benchmark methods from prior work to enable further investigation of multi-modal 3D scene understanding. Furthermore, we develop a better baseline leveraging 2D features from CLIP by rendering object proposals online with contrastive learning, which outperforms the state of the art on the ScanRefer benchmark.

Pablo Millan Arias, Niousha Sadjadi, Monireh Safari et al.

In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of life. Although machine learning algorithms specifically designed for the analysis of DNA barcodes are becoming more popular, most existing methodologies rely on generic supervised training algorithms. We introduce BarcodeBERT, a family of models tailored to biodiversity analysis and trained exclusively on data from a reference library of 1.5M invertebrate DNA barcodes. We compared the performance of BarcodeBERT on taxonomic identification tasks against a spectrum of machine learning approaches including supervised training of classical neural architectures and fine-tuning of general DNA foundation models. Our self-supervised pretraining strategies on domain-specific data outperform fine-tuned foundation models, especially in identification tasks involving lower taxa such as genera and species. We also compared BarcodeBERT with BLAST, one of the most widely used bioinformatics tools for sequence searching, and found that our method matched BLAST's performance in species-level classification while being 55 times faster. Our analysis of masking and tokenization strategies also provides practical guidance for building customized DNA language models, emphasizing the importance of aligning model training strategies with dataset characteristics and domain knowledge. The code repository is available at https://github.com/bioscan-ml/BarcodeBERT.

Zahra Gharaee, ZeMing Gong, Nicholas Pellegrino et al.

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

Zahra Gharaee, Scott C. Lowe, ZeMing Gong et al.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, geographical, and size information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at https://github.com/bioscan-ml/BIOSCAN-5M.

Austin T. Wang, ZeMing Gong, Angel X. Chang

3D visual grounding (3DVG) involves localizing entities in a 3D scene referred to by natural language text. Such models are useful for embodied AI and scene retrieval applications, which involve searching for objects or patterns using natural language descriptions. While recent works have focused on LLM-based scaling of 3DVG datasets, these datasets do not capture the full range of potential prompts which could be specified in the English language. To ensure that we are scaling up and testing against a useful and representative set of prompts, we propose a framework for linguistically analyzing 3DVG prompts and introduce Visual Grounding with Diverse Language in 3D (ViGiL3D), a diagnostic dataset for evaluating visual grounding methods against a diverse set of language patterns. We evaluate existing open-vocabulary 3DVG methods to demonstrate that these methods are not yet proficient in understanding and identifying the targets of more challenging, out-of-distribution prompts, toward real-world applications.

ZeMing Gong, Chuanqi Tang, Xiaoliang Huo et al.

Taxonomic classification in biodiversity research involves organizing biological specimens into structured hierarchies based on evidence, which can come from multiple modalities such as images and genetic information. We investigate whether hyperbolic networks can provide a better embedding space for such hierarchical models. Our method embeds multimodal inputs into a shared hyperbolic space using contrastive and a novel stacked entailment-based objective. Experiments on the BIOSCAN-1M dataset show that hyperbolic embedding achieves competitive performance with Euclidean baselines, and outperforms all other models on unseen species classification using DNA barcodes. However, fine-grained classification and open-world generalization remain challenging. Our framework offers a structure-aware foundation for biodiversity modelling, with potential applications to species discovery, ecological monitoring, and conservation efforts.