arXiv subjects

Ali Kamali

Publications and source records attributed to Ali Kamali.

5 recordsLinked to original sources

arXiv2026

GOLDMARK: Governed Outcome-Linked Diagnostic Model Assessment Reference Kit

Computational biomarkers (CBs) are histopathology-derived patterns extracted from hematoxylin-eosin (H&E) whole-slide images (WSIs) using artificial intelligence (AI) to predict therapeutic response or prognosis. Recently, slide-level multiple-instance learning (MIL) with pathology foundation models (PFMs) has become the standard baseline for CB development. While these methods have improved predictive performance, computational pathology lacks standardized intermediate data formats, provenance tracking, checkpointing conventions, and reproducible evaluation metrics required for clinical-grade deployment. We introduce GOLDMARK (https://artificialintelligencepathology.org), a standardized benchmarking framework built on a curated TCGA cohort with clinically actionable OncoKB level 1-3 biomarker labels. GOLDMARK releases structured intermediate representations, including tile coordinate maps, per-slide feature embeddings from canonical PFMs, quality-control metadata, predefined patient-level splits, trained slide-level models, and evaluation outputs. Models are trained on TCGA and evaluated on an independent MSKCC cohort with reciprocal testing. Across 33 tumor-biomarker tasks, mean AUROC was 0.689 (TCGA) and 0.630 (MSKCC). Restricting to the eight highest-performing tasks yielded mean AUROCs of 0.831 and 0.801, respectively. These tasks correspond to established morphologic-genomic associations (e.g., LGG IDH1, COAD MSI/BRAF, THCA BRAF/NRAS, BLCA FGFR3, UCEC PTEN) and showed the most stable cross-site performance. Differences between canonical encoders were modest relative to task-specific variability. GOLDMARK establishes a shared experimental substrate for computational pathology, enabling reproducible benchmarking and direct comparison of methods across datasets and models.

cs.CV↗

arXiv2024

GPT-4o System Card

GPT-4o is an autoregressive omni model that accepts as input any combination of text, audio, image, and video, and generates any combination of text, audio, and image outputs. It's trained end-to-end across text, vision, and audio, meaning all inputs and outputs are processed by the same neural network. GPT-4o can respond to audio inputs in as little as 232 milliseconds, with an average of 320 milliseconds, which is similar to human response time in conversation. It matches GPT-4 Turbo performance on text in English and code, with significant improvement on text in non-English languages, while also being much faster and 50\% cheaper in the API. GPT-4o is especially better at vision and audio understanding compared to existing models. In line with our commitment to building AI safely and consistent with our voluntary commitments to the White House, we are sharing the GPT-4o System Card, which includes our Preparedness Framework evaluations. In this System Card, we provide a detailed look at GPT-4o's capabilities, limitations, and safety evaluations across multiple categories, focusing on speech-to-speech while also evaluating text and image capabilities, and measures we've implemented to ensure the model is safe and aligned. We also include third-party assessments on dangerous capabilities, as well as discussion of potential societal impacts of GPT-4o's text and vision capabilities.

cs.CL↗

arXiv2023

Physics-informed UNets for Discovering Hidden Elasticity in Heterogeneous Materials

Soft biological tissues often have complex mechanical properties due to variation in structural components. In this paper, we develop a novel UNet-based neural network model for inversion in elasticity (El-UNet) to infer the spatial distributions of mechanical parameters from strain maps as input images, normal stress boundary conditions, and domain physics information. We show superior performance, both in terms of accuracy and computational cost, by El-UNet compared to fully-connected physics-informed neural networks in estimating unknown parameters and stress distributions for isotropic linear elasticity. We characterize different variations of El-UNet and propose a self-adaptive spatial loss weighting approach. To validate our inversion models, we performed various finite-element simulations of isotropic domains with heterogenous distributions of material parameters to generate synthetic data. El-UNet is faster and more accurate than the fully-connected physics-informed implementation in resolving the distribution of unknown fields. Among the tested models, the self-adaptive spatially weighted models had the most accurate reconstructions in equal computation times. The learned spatial weighting distribution visibly corresponded to regions that the unweighted models were resolving inaccurately. Our work demonstrates a computationally efficient inversion algorithm for elasticity imaging using convolutional neural networks and presents a potential fast framework for three-dimensional inverse elasticity problems that have proven unachievable through previously proposed methods.

cs.LG↗

arXiv2022

A unit-based symbolic execution method for detecting memory corruption vulnerabilities in executable codes

Memory corruption is a serious class of software vulnerabilities, which requires careful attention to be detected and removed from applications before getting exploited and harming the system users. Symbolic execution is a well-known method for analyzing programs and detecting various vulnerabilities, e.g., memory corruption. Although this method is sound and complete in theory, it faces some challenges, such as path explosion, when applied to real-world complex programs. In this paper, we present a method for improving the efficiency of symbolic execution and detecting four classes of memory corruption vulnerabilities in executable codes, i.e., heap-based buffer overflow, stack-based buffer overflow, use-after-free, and double-free. We perform symbolic execution only on test units rather than the whole program to lower the chance of path explosion. In our method, test units are considered parts of the program's code, which might contain vulnerable statements and are statically identified based on the specifications of memory corruption vulnerabilities. Then, each test unit is symbolically executed to calculate path and vulnerability constraints of each statement of the unit, which determine the conditions on unit input data for executing that statement or activating vulnerabilities in it, respectively. Solving these constraints gives us input values for the test unit, which execute the desired statements and reveal vulnerabilities in them. Finally, we use machine learning to approximate the correlation between system and unit input data. Thereby, we generate system inputs that enter the program, reach vulnerable instructions in the desired test unit, and reveal vulnerabilities in them. This method is implemented as a plugin for angr framework and evaluated using a group of benchmark programs. The experiments show its superiority over similar tools in accuracy and performance.

cs.CR↗

arXiv2022

Hyperacute pathophysiology of traumatic and vascular brain injury captured by ultrasound, photoacoustic, and magnetic resonance imaging

Cerebrovascular dynamics and pathomechanisms that evolve in the minutes and hours following traumatic vascular injury in the brain remain largely unknown. We investigated the pathophysiology evolution within the first three hours after closed-head traumatic brain injury (TBI) and subarachnoid hemorrhage (SAH), two common traumatic vascular injuries, in mice. We took a multi-modal imaging approach using photoacoustic, color Doppler, and magnetic resonance imaging (MRI) in mice. Brain oxygenation (%sO2) and velocity-weighted volume of blood flow (VVF) values significantly decreased from baseline to fifteen minutes after both TBI and SAH. TBI resulted in 19.2% and 41.0% ipsilateral %sO2 and VVF reductions 15 minutes post injury while SAH resulted in 43.9% %sO2 and 85.0% VVF reduction ipsilaterally (p<0.001). We found partial recovery of %sO2 from 15 minutes to 3-hours after injury for TBI but not SAH. Hemorrhage, edema, reduced perfusion, and altered diffusivity were evident from MRI scans acquired 90-150 minutes after injury in both models although the spatial distribution was mostly focal for TBI and diffuse for SAH. The results reveal that the cerebral %sO2 deficits immediately following injuries are reversible for TBI and irreversible for SAH. Our findings can inform future studies on mitigating these early responses to improve long-term recovery.

q-bio.QM↗