In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-1M 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.

Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences or structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein.

An important line of research in the field of explainability is to extract a small subset of crucial rationales from the full input. The most widely used criterion for rationale extraction is the maximum mutual information (MMI) criterion. However, in certain datasets, there are spurious features non-causally correlated with the label and also get high mutual information, complicating the loss landscape of MMI. Although some penalty-based methods have been developed to penalize the spurious features (e.g., invariance penalty, intervention penalty, etc) to help MMI work better, these are merely remedial measures. In the optimization objectives of these methods, spurious features are still distinguished from plain noise, which hinders the discovery of causal rationales.

Large language models produce human-like text that drives a growing number of applications. However, recent literature and, increasingly, real world observations, have demonstrated that these models can generate language that is toxic, biased, untruthful or otherwise harmful. Though work to evaluate language model harms is under way, translating foresight about which harms may arise into rigorous benchmarks is not straightforward. To facilitate this translation, we outline six ways of characterizing harmful text which merit explicit consideration when designing new benchmarks. We then use these characteristics as a lens to identify trends and gaps in existing benchmarks. Finally, we apply them in a case study of the Perspective API, a toxicity classifier that is widely used in harm benchmarks. Our characteristics provide one piece of the bridge that translates between foresight and effective evaluation.

This paper introduces AutoSurvey, a speedy and well-organized methodology for automating the creation of comprehensive literature surveys in rapidly evolving fields like artificial intelligence. Traditional survey paper creation faces challenges due to the vast volume and complexity of information, prompting the need for efficient survey methods. While large language models (LLMs) offer promise in automating this process, challenges such as context window limitations, parametric knowledge constraints, and the lack of evaluation benchmarks remain. AutoSurvey addresses these challenges through a systematic approach that involves initial retrieval and outline generation, subsection drafting by specialized LLMs, integration and refinement, and rigorous evaluation and iteration. Our contributions include a comprehensive solution to the survey problem, a reliable evaluation method, and experimental validation demonstrating AutoSurvey's effectiveness.