Austin T. Wang

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, 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.

Hou In Ivan Tam, Hou In Derek Pun, Austin T. Wang et al.

Despite recent advances in text-conditioned 3D indoor scene generation, there remain gaps in the evaluation of these methods. Existing metrics primarily assess the realism of generated scenes by comparing them to a set of ground-truth scenes, often overlooking alignment with the input text - a critical factor in determining how effectively a method meets user requirements. We present SceneEval, an evaluation framework designed to address this limitation. SceneEval includes metrics for both explicit user requirements, such as the presence of specific objects and their attributes described in the input text, and implicit expectations, like the absence of object collisions, providing a comprehensive assessment of scene quality. To facilitate evaluation, we introduce SceneEval-500, a dataset of scene descriptions with annotated ground-truth scene properties. We evaluate recent scene generation methods using SceneEval and demonstrate its ability to provide detailed assessments of the generated scenes, highlighting strengths and areas for improvement across multiple dimensions. Our results show that current methods struggle at generating scenes that meet user requirements, underscoring the need for further research in this direction.

Hou In Derek Pun, Hou In Ivan Tam, Austin T. Wang et al.

Despite advances in indoor 3D scene layout generation, synthesizing scenes with dense object arrangements remains challenging. Existing methods focus on large furniture while neglecting smaller objects, resulting in unrealistically empty scenes. Those that place small objects typically do not honor arrangement specifications, resulting in largely random placement not following the text description. We present Hierarchical Scene Motifs (HSM): a hierarchical framework for indoor scene generation with dense object arrangements across spatial scales. Indoor scenes are inherently hierarchical, with surfaces supporting objects at different scales, from large furniture on floors to smaller objects on tables and shelves. HSM embraces this hierarchy and exploits recurring cross-scale spatial patterns to generate complex and realistic scenes in a unified manner. Our experiments show that HSM outperforms existing methods by generating scenes that better conform to user input across room types and spatial configurations. Project website is available at https://3dlg-hcvc.github.io/hsm .

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.