UCell: rethinking generalizability and scaling of bio-medical vision models

The modern deep learning field is a scale-centric one. Larger models have been shown to consistently perform better than smaller models of similar architecture. In many sub-domains of biomedical research, however, the model scaling is bottlenecked by the amount of available training data, and the high cost associated with generating and validating additional high quality data. Despite the practical hurdle, the majority of the ongoing research still focuses on building bigger foundation models, whereas the alternative of improving the ability of small models has been under-explored. Here we experiment with building models with 10-30M parameters, tiny by modern standards, to perform the single-cell segmentation task. An important design choice is the incorporation of a recursive structure into the model's forward computation graph, leading to a more parameter-efficient architecture. We found that for the single-cell segmentation, on multiple benchmarks, our small model, UCell, matches the performance of models 10-20 times its size, and with a similar generalizability to unseen out-of-domain data. More importantly, we found that ucell can be trained from scratch using only a set of microscopy imaging data, without relying on massive pretraining on natural images, and therefore decouples the model building from any external commercial interests. Finally, we examined and confirmed the adaptability of ucell by performing a wide range of one-shot and few-shot fine tuning experiments on a diverse set of small datasets. Implementation is available at https://github.com/jiyuuchc/ucell

ACMID: Automatic Curation of Musical Instrument Dataset for 7-Stem Music Source Separation

Most current music source separation (MSS) methods rely on supervised learning, limited by training data quan- tity and quality. Though web-crawling can bring abundant data, platform-level track labeling often causes metadata mismatches, impeding accurate "audio-label" pair acquisi- tion. To address this, we present ACMID: a dataset for MSS generated through web crawling of extensive raw data, fol- lowed by automatic cleaning via an instrument classifier built on a pre-trained audio encoder that filters and aggregates clean segments of target instruments from the crawled tracks, resulting in the refined ACMID-Cleaned dataset. Leverag- ing abundant data, we expand the conventional classifica- tion from 4-stem (Vocal/Bass/Drums/Others) to 7-stem (Pi- ano/Drums/Bass/Acoustic Guitar/Electric Guitar/Strings/Wind- Brass), enabling high granularity MSS systems. Experiments on SOTA MSS model demonstrates two key results: (i) MSS model trained with ACMID-Cleaned achieved a 2.39dB improvement in SDR performance compared to that with ACMID-Uncleaned, demostrating the effectiveness of our data cleaning procedure; (ii) incorporating ACMID-Cleaned to training enhances MSS model's average performance by 1.16dB, confirming the value of our dataset. Our data crawl- ing code, cleaning model code and weights are available at: https://github.com/scottishfold0621/ACMID.

Point-supervised Single-cell Segmentation via Collaborative Knowledge Sharing

Despite their superior performance, deep-learning methods often suffer from the disadvantage of needing large-scale well-annotated training data. In response, recent literature has seen a proliferation of efforts aimed at reducing the annotation burden. This paper focuses on a weakly-supervised training setting for single-cell segmentation models, where the only available training label is the rough locations of individual cells. The specific problem is of practical interest due to the widely available nuclei counter-stain data in biomedical literature, from which the cell locations can be derived programmatically. Of more general interest is a proposed self-learning method called collaborative knowledge sharing, which is related to but distinct from the more well-known consistency learning methods. This strategy achieves self-learning by sharing knowledge between a principal model and a very light-weight collaborator model. Importantly, the two models are entirely different in their architectures, capacities, and model outputs: In our case, the principal model approaches the segmentation problem from an object-detection perspective, whereas the collaborator model a sematic segmentation perspective. We assessed the effectiveness of this strategy by conducting experiments on LIVECell, a large single-cell segmentation dataset of bright-field images, and on A431 dataset, a fluorescence image dataset in which the location labels are generated automatically from nuclei counter-stain data. Implementing code is available at https://github.com/jiyuuchc/lacss_jax