GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models

The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite advancements, a lack of evaluation framework makes it difficult to ensure equitable assessment due to experimental settings, model intricacy, benchmark datasets, and reproducibility challenges. In the absence of standardization, comparative analyses risk becoming biased and unreliable. To surmount this impasse, we introduce GenBench, a comprehensive benchmarking suite specifically tailored for evaluating the efficacy of Genomic Foundation Models. GenBench offers a modular and expandable framework that encapsulates a variety of state-of-the-art methodologies. Through systematic evaluations of datasets spanning diverse biological domains with a particular emphasis on both short-range and long-range genomic tasks, firstly including the three most important DNA tasks covering Coding Region, Non-Coding Region, Genome Structure, etc. Moreover, We provide a nuanced analysis of the interplay between model architecture and dataset characteristics on task-specific performance. Our findings reveal an interesting observation: independent of the number of parameters, the discernible difference in preference between the attention-based and convolution-based models on short- and long-range tasks may provide insights into the future design of GFM.

FSC: Few-point Shape Completion

While previous studies have demonstrated successful 3D object shape completion with a sufficient number of points, they often fail in scenarios when a few points, e.g. tens of points, are observed. Surprisingly, via entropy analysis, we find that even a few points, e.g. 64 points, could retain substantial information to help recover the 3D shape of the object. To address the challenge of shape completion with very sparse point clouds, we then propose Few-point Shape Completion (FSC) model, which contains a novel dual-branch feature extractor for handling extremely sparse inputs, coupled with an extensive branch for maximal point utilization with a saliency branch for dynamic importance assignment. This model is further bolstered by a two-stage revision network that refines both the extracted features and the decoder output, enhancing the detail and authenticity of the completed point cloud. Our experiments demonstrate the feasibility of recovering 3D shapes from a few points. The proposed Few-point Shape Completion (FSC) model outperforms previous methods on both few-point inputs and many-point inputs, and shows good generalizability to different object categories.