ST-NeRP: Spatial-Temporal Neural Representation Learning with Prior Embedding for Patient-specific Imaging Study

During and after a course of therapy, imaging is routinely used to monitor the disease progression and assess the treatment responses. Despite of its significance, reliably capturing and predicting the spatial-temporal anatomic changes from a sequence of patient-specific image series presents a considerable challenge. Thus, the development of a computational framework becomes highly desirable for a multitude of practical applications. In this context, we propose a strategy of Spatial-Temporal Neural Representation learning with Prior embedding (ST-NeRP) for patient-specific imaging study. Our strategy involves leveraging an Implicit Neural Representation (INR) network to encode the image at the reference time point into a prior embedding. Subsequently, a spatial-temporally continuous deformation function is learned through another INR network. This network is trained using the whole patient-specific image sequence, enabling the prediction of deformation fields at various target time points. The efficacy of the ST-NeRP model is demonstrated through its application to diverse sequential image series, including 4D CT and longitudinal CT datasets within thoracic and abdominal imaging. The proposed ST-NeRP model exhibits substantial potential in enabling the monitoring of anatomical changes within a patient throughout the therapeutic journey.

Multi-sensor Learning Enables Information Transfer across Different Sensory Data and Augments Multi-modality Imaging

Multi-modality imaging is widely used in clinical practice and biomedical research to gain a comprehensive understanding of an imaging subject. Currently, multi-modality imaging is accomplished by post hoc fusion of independently reconstructed images under the guidance of mutual information or spatially registered hardware, which limits the accuracy and utility of multi-modality imaging. Here, we investigate a data-driven multi-modality imaging (DMI) strategy for synergetic imaging of CT and MRI. We reveal two distinct types of features in multi-modality imaging, namely intra- and inter-modality features, and present a multi-sensor learning (MSL) framework to utilize the crossover inter-modality features for augmented multi-modality imaging. The MSL imaging approach breaks down the boundaries of traditional imaging modalities and allows for optimal hybridization of CT and MRI, which maximizes the use of sensory data. We showcase the effectiveness of our DMI strategy through synergetic CT-MRI brain imaging. The principle of DMI is quite general and holds enormous potential for various DMI applications across disciplines.

Automated radiotherapy treatment planning guided by GPT-4Vision

Radiotherapy treatment planning is a time-consuming and potentially subjective process that requires the iterative adjustment of model parameters to balance multiple conflicting objectives. Recent advancements in large foundation models offer promising avenues for addressing the challenges in planning and clinical decision-making. This study introduces GPT-RadPlan, a fully automated treatment planning framework that harnesses prior radiation oncology knowledge encoded in multi-modal large language models, such as GPT-4Vision (GPT-4V) from OpenAI. GPT-RadPlan is made aware of planning protocols as context and acts as an expert human planner, capable of guiding a treatment planning process. Via in-context learning, we incorporate clinical protocols for various disease sites as prompts to enable GPT-4V to acquire treatment planning domain knowledge. The resulting GPT-RadPlan agent is integrated into our in-house inverse treatment planning system through an API. The efficacy of the automated planning system is showcased using multiple prostate and head & neck cancer cases, where we compared GPT-RadPlan results to clinical plans. In all cases, GPT-RadPlan either outperformed or matched the clinical plans, demonstrating superior target coverage and organ-at-risk sparing. Consistently satisfying the dosimetric objectives in the clinical protocol, GPT-RadPlan represents the first multimodal large language model agent that mimics the behaviors of human planners in radiation oncology clinics, achieving remarkable results in automating the treatment planning process without the need for additional training.

Constrained Decoding for Secure Code Generation

Code Large Language Models (Code LLMs) have been increasingly used by developers to boost productivity, but they often generate vulnerable code. Thus, there is an urgent need to ensure that code generated by Code LLMs is correct and secure. Previous research has primarily focused on generating secure code, overlooking the fact that secure code also needs to be correct. This oversight can lead to a false sense of security. Currently, the community lacks a method to measure actual progress in this area, and we need solutions that address both security and correctness of code generation. This paper introduces a new benchmark, CodeGuard+, along with two new metrics, secure-pass@k and secure@$k_{\text{pass}}$, to measure Code LLMs' ability to generate both secure and correct code. Using our new evaluation methods, we show that the state-of-the-art defense technique, prefix tuning, may not be as strong as previously believed, since it generates secure code but sacrifices functional correctness. We also demonstrate that different decoding methods significantly affect the security of Code LLMs. Furthermore, we explore a new defense direction: constrained decoding for secure code generation. We propose new constrained decoding techniques to generate code that satisfies security and correctness constraints simultaneously. Our results reveal that constrained decoding is more effective than prefix tuning to improve the security of Code LLMs, without requiring a specialized training dataset. Moreover, constrained decoding can be used together with prefix tuning to further improve the security of Code LLMs.

Vulnerability Detection with Code Language Models: How Far Are We?

In the context of the rising interest in code language models (code LMs) and vulnerability detection, we study the effectiveness of code LMs for detecting vulnerabilities. Our analysis reveals significant shortcomings in existing vulnerability datasets, including poor data quality, low label accuracy, and high duplication rates, leading to unreliable model performance in realistic vulnerability detection scenarios. Additionally, the evaluation methods used with these datasets are not representative of real-world vulnerability detection. To address these challenges, we introduce PrimeVul, a new dataset for training and evaluating code LMs for vulnerability detection. PrimeVul incorporates a novel set of data labeling techniques that achieve comparable label accuracy to human-verified benchmarks while significantly expanding the dataset. It also implements a rigorous data de-duplication and chronological data splitting strategy to mitigate data leakage issues, alongside introducing more realistic evaluation metrics and settings. This comprehensive approach aims to provide a more accurate assessment of code LMs' performance in real-world conditions. Evaluating code LMs on PrimeVul reveals that existing benchmarks significantly overestimate the performance of these models. For instance, a state-of-the-art 7B model scored 68.26% F1 on BigVul but only 3.09% F1 on PrimeVul. Attempts to improve performance through advanced training techniques and larger models like GPT-3.5 and GPT-4 were unsuccessful, with results akin to random guessing in the most stringent settings. These findings underscore the considerable gap between current capabilities and the practical requirements for deploying code LMs in security roles, highlighting the need for more innovative research in this domain.

2L3: Lifting Imperfect Generated 2D Images into Accurate 3D

Reconstructing 3D objects from a single image is an intriguing but challenging problem. One promising solution is to utilize multi-view (MV) 3D reconstruction to fuse generated MV images into consistent 3D objects. However, the generated images usually suffer from inconsistent lighting, misaligned geometry, and sparse views, leading to poor reconstruction quality. To cope with these problems, we present a novel 3D reconstruction framework that leverages intrinsic decomposition guidance, transient-mono prior guidance, and view augmentation to cope with the three issues, respectively. Specifically, we first leverage to decouple the shading information from the generated images to reduce the impact of inconsistent lighting; then, we introduce mono prior with view-dependent transient encoding to enhance the reconstructed normal; and finally, we design a view augmentation fusion strategy that minimizes pixel-level loss in generated sparse views and semantic loss in augmented random views, resulting in view-consistent geometry and detailed textures. Our approach, therefore, enables the integration of a pre-trained MV image generator and a neural network-based volumetric signed distance function (SDF) representation for a single image to 3D object reconstruction. We evaluate our framework on various datasets and demonstrate its superior performance in both quantitative and qualitative assessments, signifying a significant advancement in 3D object reconstruction. Compared with the latest state-of-the-art method Syncdreamer~\cite{liu2023syncdreamer}, we reduce the Chamfer Distance error by about 36\% and improve PSNR by about 30\% .

DiverseVul: A New Vulnerable Source Code Dataset for Deep Learning Based Vulnerability Detection

We propose and release a new vulnerable source code dataset. We curate the dataset by crawling security issue websites, extracting vulnerability-fixing commits and source codes from the corresponding projects. Our new dataset contains 150 CWEs, 26,635 vulnerable functions, and 352,606 non-vulnerable functions extracted from 7,861 commits. Our dataset covers 305 more projects than all previous datasets combined. We show that increasing the diversity and volume of training data improves the performance of deep learning models for vulnerability detection. Combining our new dataset with previous datasets, we present an analysis of the challenges and promising research directions of using deep learning for detecting software vulnerabilities. We study 11 model architectures belonging to 4 families. Our results show that deep learning is still not ready for vulnerability detection, due to high false positive rate, low F1 score, and difficulty of detecting hard CWEs. In particular, we demonstrate an important generalization challenge for the deployment of deep learning-based models. However, we also identify hopeful future research directions. We demonstrate that large language models (LLMs) are the future for vulnerability detection, outperforming Graph Neural Networks (GNNs) with manual feature engineering. Moreover, developing source code specific pre-training objectives is a promising research direction to improve the vulnerability detection performance.

Continuous Learning for Android Malware Detection

Machine learning methods can detect Android malware with very high accuracy. However, these classifiers have an Achilles heel, concept drift: they rapidly become out of date and ineffective, due to the evolution of malware apps and benign apps. Our research finds that, after training an Android malware classifier on one year's worth of data, the F1 score quickly dropped from 0.99 to 0.76 after 6 months of deployment on new test samples. In this paper, we propose new methods to combat the concept drift problem of Android malware classifiers. Since machine learning technique needs to be continuously deployed, we use active learning: we select new samples for analysts to label, and then add the labeled samples to the training set to retrain the classifier. Our key idea is, similarity-based uncertainty is more robust against concept drift. Therefore, we combine contrastive learning with active learning. We propose a new hierarchical contrastive learning scheme, and a new sample selection technique to continuously train the Android malware classifier. Our evaluation shows that this leads to significant improvements, compared to previously published methods for active learning. Our approach reduces the false negative rate from 16% (for the best baseline) to 10%, while maintaining the same false positive rate (0.6%). Also, our approach maintains more consistent performance across a seven-year time period than past methods.

Part-Based Models Improve Adversarial Robustness

We show that combining human prior knowledge with end-to-end learning can improve the robustness of deep neural networks by introducing a part-based model for object classification. We believe that the richer form of annotation helps guide neural networks to learn more robust features without requiring more samples or larger models. Our model combines a part segmentation model with a tiny classifier and is trained end-to-end to simultaneously segment objects into parts and then classify the segmented object. Empirically, our part-based models achieve both higher accuracy and higher adversarial robustness than a ResNet-50 baseline on all three datasets. For instance, the clean accuracy of our part models is up to 15 percentage points higher than the baseline's, given the same level of robustness. Our experiments indicate that these models also reduce texture bias and yield better robustness against common corruptions and spurious correlations. The code is publicly available at https://github.com/chawins/adv-part-model.

Learning Security Classifiers with Verified Global Robustness Properties

Recent works have proposed methods to train classifiers with local robustness properties, which can provably eliminate classes of evasion attacks for most inputs, but not all inputs. Since data distribution shift is very common in security applications, e.g., often observed for malware detection, local robustness cannot guarantee that the property holds for unseen inputs at the time of deploying the classifier. Therefore, it is more desirable to enforce global robustness properties that hold for all inputs, which is strictly stronger than local robustness. In this paper, we present a framework and tools for training classifiers that satisfy global robustness properties. We define new notions of global robustness that are more suitable for security classifiers. We design a novel booster-fixer training framework to enforce global robustness properties. We structure our classifier as an ensemble of logic rules and design a new verifier to verify the properties. In our training algorithm, the booster increases the classifier's capacity, and the fixer enforces verified global robustness properties following counterexample guided inductive synthesis. To the best of our knowledge, the only global robustness property that has been previously achieved is monotonicity. Several previous works have defined global robustness properties, but their training techniques failed to achieve verified global robustness. In comparison, we show that we can train classifiers to satisfy different global robustness properties for three security datasets, and even multiple properties at the same time, with modest impact on the classifier's performance. For example, we train a Twitter spam account classifier to satisfy five global robustness properties, with 5.4% decrease in true positive rate, and 0.1% increase in false positive rate, compared to a baseline XGBoost model that doesn't satisfy any property.