arXiv subjects

Zhida Li

Publications and source records attributed to Zhida Li.

3 recordsLinked to original sources

arXiv2026

Quantitative measurements of biological/chemical concentrations using smartphone cameras

This paper presents a smartphone-based imaging system capable of quantifying the concentration of an assortment of biological/chemical assay samples. The main objective is to construct an image database which characterizes the relationship between color information and concentrations of the biological/chemical assay sample. For this aim, a designated optical setup combined with image processing and data analyzing techniques was implemented. A series of experiments conducted on selected assays, including fluorescein, RNA Mango, homogenized milk and yeast have demonstrated that the proposed system estimates the concentration of fluorescent materials and colloidal mixtures comparable to currently used commercial and laboratory instruments. Furthermore, by utilizing the camera and computational power of smartphones, eventual development can be directed toward extremely compact, inexpensive and portable analysis and diagnostic systems which will allow experiments and tests to be conducted in remote or impoverished areas.

eess.IV↗

arXiv2026

OpenPort Protocol: A Security Governance Specification for AI Agent Tool Access

AI agents increasingly require direct, structured access to application data and actions, but production deployments still struggle to express and verify the governance properties that matter in practice: least-privilege authorization, controlled write execution, predictable failure handling, abuse resistance, and auditability. This paper introduces OpenPort Protocol (OPP), a governance-first specification for exposing application tools through a secure server-side gateway that is model- and runtime-neutral and can bind to existing tool ecosystems. OpenPort defines authorization-dependent discovery, stable response envelopes with machine-actionable \texttt{agent.*} reason codes, and an authorization model combining integration credentials, scoped permissions, and ABAC-style policy constraints. For write operations, OpenPort specifies a risk-gated lifecycle that defaults to draft creation and human review, supports time-bounded auto-execution under explicit policy, and enforces high-risk safeguards including preflight impact binding and idempotency. To address time-of-check/time-of-use drift in delayed approval flows, OpenPort also specifies an optional State Witness profile that revalidates execution-time preconditions and fails closed on state mismatch. Operationally, the protocol requires admission control (rate limits/quotas) with stable 429 semantics and structured audit events across allow/deny/fail paths so that client recovery and incident analysis are deterministic. We present a reference runtime and an executable governance toolchain (layered conformance profiles, negative security tests, fuzz/abuse regression, and release-gate scans) and evaluate the core profile at a pinned release tag using artifact-based, externally reproducible validation.

cs.CR↗

arXiv2021

COSINE: A Web Server for Clonal and Subclonal Structure Inference and Evolution in Cancer Genomics

Cancers evolve from mutation of a single cell with sequential clonal and subclonal expansion of somatic mutation acquisition. Inferring clonal and subclonal structures from bulk or single cell tumor genomic sequencing data has a huge impact on cancer evolution studies. Clonal state and mutational order can provide detailed insight into tumor origin and its future development. In the past decade, a variety of methods have been developed for subclonal reconstruction using bulk tumor sequencing data. As these methods have been developed in different programming languages and using different input data formats, their use and comparison can be problematic. Therefore, we established a web server for clonal and subclonal structure inference and evolution of cancer genomic data (COSINE), which included 12 popular subclonal reconstruction methods. We decomposed each method via a detailed workflow of single processing steps with a user-friendly interface. To the best of our knowledge, this is the first web server providing online subclonal inference, including the most popular subclonal reconstruction methods. COSINE is freely accessible at www.clab-cosine.net or http://bio.rj.run:48996/cun-web.

q-bio.GN↗