arXiv subjects

Xiao Gan

Publications and source records attributed to Xiao Gan.

4 recordsLinked to original sources

arXiv2024

Pathological Primitive Segmentation Based on Visual Foundation Model with Zero-Shot Mask Generation

Medical image processing usually requires a model trained with carefully crafted datasets due to unique image characteristics and domain-specific challenges, especially in pathology. Primitive detection and segmentation in digitized tissue samples are essential for objective and automated diagnosis and prognosis of cancer. SAM (Segment Anything Model) has recently been developed to segment general objects from natural images with high accuracy, but it requires human prompts to generate masks. In this work, we present a novel approach that adapts pre-trained natural image encoders of SAM for detection-based region proposals. Regions proposed by a pre-trained encoder are sent to cascaded feature propagation layers for projection. Then, local semantic and global context is aggregated from multi-scale for bounding box localization and classification. Finally, the SAM decoder uses the identified bounding boxes as essential prompts to generate a comprehensive primitive segmentation map. The entire base framework, SAM, requires no additional training or fine-tuning but could produce an end-to-end result for two fundamental segmentation tasks in pathology. Our method compares with state-of-the-art models in F1 score for nuclei detection and binary/multiclass panoptic(bPQ/mPQ) and mask quality(dice) for segmentation quality on the PanNuke dataset while offering end-to-end efficiency. Our model also achieves remarkable Average Precision (+4.5%) on the secondary dataset (HuBMAP Kidney) compared to Faster RCNN. The code is publicly available at https://github.com/learner-codec/autoprom_sam.

cs.CV↗

arXiv2022

Network medicine framework reveals generic herb-symptom effectiveness of Traditional Chinese Medicine

Traditional Chinese medicine (TCM) relies on natural medical products to treat symptoms and diseases. While clinical data have demonstrated the effectiveness of selected TCM-based treatments, the mechanistic root of how TCM herbs treat diseases remains largely unknown. More importantly, current approaches focus on single herbs or prescriptions, missing the high-level general principles of TCM. To uncover the mechanistic nature of TCM on a system level, in this work we establish a generic network medicine framework for TCM from the human protein interactome. Applying our framework reveals a network pattern between symptoms (diseases) and herbs in TCM. We first observe that genes associated with a symptom are not distributed randomly in the interactome, but cluster into localized modules; furthermore, a short network distance between two symptom modules is indicative of the symptoms' co-occurrence and similarity. Next, we show that the network proximity of a herb's targets to a symptom module is predictive of the herb's effectiveness in treating the symptom. We validate our framework with real-world hospital patient data by showing that (1) shorter network distance between symptoms of inpatients correlates with higher relative risk (co-occurrence), and (2) herb-symptom network proximity is indicative of patients' symptom recovery rate after herbal treatment. Finally, we identified novel herb-symptom pairs in which the herb's effectiveness in treating the symptom is predicted by network and confirmed in hospital data, but previously unknown to the TCM community. These predictions highlight our framework's potential in creating herb discovery or repurposing opportunities. In conclusion, network medicine offers a powerful novel platform to understand the mechanism of traditional medicine and to predict novel herbal treatment against diseases.

q-bio.MN↗

arXiv2021

Parity and time-reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks

We present new applications of parity inversion and time-reversal to the emergence of complex behavior from simple dynamical rules in stochastic discrete models. Our parity-based encoding of causal relationships and time-reversal construction efficiently reveal discrete analogs of stable and unstable manifolds. We demonstrate their predictive power by studying decision-making in systems biology and statistical physics models. These applications underpin a novel attractor identification algorithm implemented for Boolean networks under stochastic dynamics. Its speed enables resolving a longstanding open question of how attractor count in critical random Boolean networks scales with network size, and whether the scaling matches biological observations. Via 80-fold improvement in probed network size ($N=16,384$), we find the surprisingly low scaling exponent of $0.12\pm 0.05$ -- approximately one tenth the analytical upper bound. We demonstrate a general principle: a system's relationship to its time-reversal and state-space inversion constrains its repertoire of emergent behaviors.

nlin.AO↗

arXiv2020

Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19

The current pandemic has highlighted the need for methodologies that can quickly and reliably prioritize clinically approved compounds for their potential effectiveness for SARS-CoV-2 infections. In the past decade, network medicine has developed and validated multiple predictive algorithms for drug repurposing, exploiting the sub-cellular network-based relationship between a drug's targets and disease genes. Here, we deployed algorithms relying on artificial intelligence, network diffusion, and network proximity, tasking each of them to rank 6,340 drugs for their expected efficacy against SARS-CoV-2. To test the predictions, we used as ground truth 918 drugs that had been experimentally screened in VeroE6 cells, and the list of drugs under clinical trial, that capture the medical community's assessment of drugs with potential COVID-19 efficacy. We find that while most algorithms offer predictive power for these ground truth data, no single method offers consistently reliable outcomes across all datasets and metrics. This prompted us to develop a multimodal approach that fuses the predictions of all algorithms, showing that a consensus among the different predictive methods consistently exceeds the performance of the best individual pipelines. We find that 76 of the 77 drugs that successfully reduced viral infection do not bind the proteins targeted by SARS-CoV-2, indicating that these drugs rely on network-based actions that cannot be identified using docking-based strategies. These advances offer a methodological pathway to identify repurposable drugs for future pathogens and neglected diseases underserved by the costs and extended timeline of de novo drug development.

q-bio.MN↗