StarCoder 2 and The Stack v2: The Next Generation

The BigCode project, an open-scientific collaboration focused on the responsible development of Large Language Models for Code (Code LLMs), introduces StarCoder2. In partnership with Software Heritage (SWH), we build The Stack v2 on top of the digital commons of their source code archive. Alongside the SWH repositories spanning 619 programming languages, we carefully select other high-quality data sources, such as GitHub pull requests, Kaggle notebooks, and code documentation. This results in a training set that is 4x larger than the first StarCoder dataset. We train StarCoder2 models with 3B, 7B, and 15B parameters on 3.3 to 4.3 trillion tokens and thoroughly evaluate them on a comprehensive set of Code LLM benchmarks. We find that our small model, StarCoder2-3B, outperforms other Code LLMs of similar size on most benchmarks, and also outperforms StarCoderBase-15B. Our large model, StarCoder2- 15B, significantly outperforms other models of comparable size. In addition, it matches or outperforms CodeLlama-34B, a model more than twice its size. Although DeepSeekCoder- 33B is the best-performing model at code completion for high-resource languages, we find that StarCoder2-15B outperforms it on math and code reasoning benchmarks, as well as several low-resource languages. We make the model weights available under an OpenRAIL license and ensure full transparency regarding the training data by releasing the SoftWare Heritage persistent IDentifiers (SWHIDs) of the source code data.

SciGraphQA: A Large-Scale Synthetic Multi-Turn Question-Answering Dataset for Scientific Graphs

In this work, we present SciGraphQA, a synthetic multi-turn question-answer dataset related to academic graphs. SciGraphQA is 13 times larger than ChartVQA, the previously largest chart-visual question-answering dataset. It is also the largest open-sourced chart VQA dataset with non-synthetic charts. To build our dataset, we selected 290,000 Computer Science or Machine Learning ArXiv papers published between 2010 and 2020, and then used Palm-2 to generate 295K samples of open-vocabulary multi-turn question-answering dialogues about the graphs. As context, we provided the text-only Palm-2 with paper title, abstract, paragraph mentioning the graph, and rich text contextual data from the graph itself, obtaining dialogues with an average 2.23 question-answer turns for each graph. We asked GPT-4 to assess the matching quality of our question-answer turns given the paper's context, obtaining an average rating of 8.7/10 on our 3K test set. We evaluated the 0-shot capability of the most popular MLLM models such as LLaVa, mPLUGowl, BLIP-2, and openFlamingo's on our dataset, finding LLaVA-13B being the most performant with a CIDEr score of 0.08. We further enriched the question prompts for LLAVA by including the serialized data tables extracted from the graphs using the DePlot model, boosting LLaVA's 0-shot CIDEr to 0.15. To verify the validity of our dataset, we also fine-tuned LLaVa using our dataset, reaching a substantially higher CIDEr score of 0.26. We anticipate further accuracy improvement by including segmentation mask tokens and leveraging larger LLM backbones coupled with emergent prompting techniques. Our code and data are open-sourced.

MDT-Net: Multi-domain Transfer by Perceptual Supervision for Unpaired Images in OCT Scan

Deep learning models tend to underperform in the presence of domain shifts. Domain transfer has recently emerged as a promising approach wherein images exhibiting a domain shift are transformed into other domains for augmentation or adaptation. However, with the absence of paired and annotated images, most domain transfer methods mainly rely on adversarial networks and weak cycle consistency, which could result in incomplete domain transfer or poor adherence to the original image content. In this paper, we introduce MDT-Net to address the limitations above through a multi-domain transfer model based on perceptual supervision. Specifically, our model consists of an encoder-decoder network, which aims to preserve anatomical structures, and multiple domain-specific transfer modules, which guide the domain transition through feature transformation. During the inference, MDT-Net can directly transfer images from the source domain to multiple target domains at one time without any reference image. To demonstrate the performance of MDT-Net, we evaluate it on RETOUCH dataset, comprising OCT scans from three different scanner devices (domains), for multi-domain transfer. We also take the transformed results as additional training images for fluid segmentation in OCT scans in the tasks of domain adaptation and data augmentation. Experimental results show that MDT-Net can outperform other domain transfer models qualitatively and quantitatively. Furthermore, the significant improvement in dice scores over multiple segmentation models also demonstrates the effectiveness and efficiency of our proposed method.

A Location-Sensitive Local Prototype Network for Few-Shot Medical Image Segmentation

Despite the tremendous success of deep neural networks in medical image segmentation, they typically require a large amount of costly, expert-level annotated data. Few-shot segmentation approaches address this issue by learning to transfer knowledge from limited quantities of labeled examples. Incorporating appropriate prior knowledge is critical in designing high-performance few-shot segmentation algorithms. Since strong spatial priors exist in many medical imaging modalities, we propose a prototype-based method -- namely, the location-sensitive local prototype network -- that leverages spatial priors to perform few-shot medical image segmentation. Our approach divides the difficult problem of segmenting the entire image with global prototypes into easily solvable subproblems of local region segmentation with local prototypes. For organ segmentation experiments on the VISCERAL CT image dataset, our method outperforms the state-of-the-art approaches by 10% in the mean Dice coefficient. Extensive ablation studies demonstrate the substantial benefits of incorporating spatial information and confirm the effectiveness of our approach.

Extreme Consistency: Overcoming Annotation Scarcity and Domain Shifts

Supervised learning has proved effective for medical image analysis. However, it can utilize only the small labeled portion of data; it fails to leverage the large amounts of unlabeled data that is often available in medical image datasets. Supervised models are further handicapped by domain shifts, when the labeled dataset, despite being large enough, fails to cover different protocols or ethnicities. In this paper, we introduce \emph{extreme consistency}, which overcomes the above limitations, by maximally leveraging unlabeled data from the same or a different domain in a teacher-student semi-supervised paradigm. Extreme consistency is the process of sending an extreme transformation of a given image to the student network and then constraining its prediction to be consistent with the teacher network's prediction for the untransformed image. The extreme nature of our consistency loss distinguishes our method from related works that yield suboptimal performance by exercising only mild prediction consistency. Our method is 1) auto-didactic, as it requires no extra expert annotations; 2) versatile, as it handles both domain shift and limited annotation problems; 3) generic, as it is readily applicable to classification, segmentation, and detection tasks; and 4) simple to implement, as it requires no adversarial training. We evaluate our method for the tasks of lesion and retinal vessel segmentation in skin and fundus images. Our experiments demonstrate a significant performance gain over both modern supervised networks and recent semi-supervised models. This performance is attributed to the strong regularization enforced by extreme consistency, which enables the student network to learn how to handle extreme variants of both labeled and unlabeled images. This enhances the network's ability to tackle the inevitable same- and cross-domain data variability during inference.

Computer Aided Detection for Pulmonary Embolism Challenge (CAD-PE)

Rationale: Computer aided detection (CAD) algorithms for Pulmonary Embolism (PE) algorithms have been shown to increase radiologists' sensitivity with a small increase in specificity. However, CAD for PE has not been adopted into clinical practice, likely because of the high number of false positives current CAD software produces. Objective: To generate a database of annotated computed tomography pulmonary angiographies, use it to compare the sensitivity and false positive rate of current algorithms and to develop new methods that improve such metrics. Methods: 91 Computed tomography pulmonary angiography scans were annotated by at least one radiologist by segmenting all pulmonary emboli visible on the study. 20 annotated CTPAs were open to the public in the form of a medical image analysis challenge. 20 more were kept for evaluation purposes. 51 were made available post-challenge. 8 submissions, 6 of them novel, were evaluated on the 20 evaluation CTPAs. Performance was measured as per embolus sensitivity vs. false positives per scan curve. Results: The best algorithms achieved a per-embolus sensitivity of 75% at 2 false positives per scan (fps) or of 70% at 1 fps, outperforming the state of the art. Deep learning approaches outperformed traditional machine learning ones, and their performance improved with the number of training cases. Significance: Through this work and challenge we have improved the state-of-the art of computer aided detection algorithms for pulmonary embolism. An open database and an evaluation benchmark for such algorithms have been generated, easing the development of further improvements. Implications on clinical practice will need further research.

UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects -- an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.

ErrorNet: Learning error representations from limited data to improve vascular segmentation

Deep convolutional neural networks have proved effective in segmenting lesions and anatomies in various medical imaging modalities. However, in the presence of small sample size and domain shift problems, these models often produce masks with non-intuitive segmentation mistakes. In this paper, we propose a segmentation framework called ErrorNet, which learns to correct these segmentation mistakes through the repeated process of injecting systematic segmentation errors to a segmentation mask based on a learned shape prior, followed by attempting to predict the injected error. During inference, ErrorNet corrects the segmentation mistakes by adding the predicted error map to the initial segmentation mask. ErrorNet has advantages over alternatives based on domain adaptation or CRF-based post processing, because it requires neither domain-specific parameter tuning nor any data from the target domains. We have evaluated ErrorNet using five public datasets for the task of retinal vessel segmentation. The selected datasets differ in size and patient population, allowing us to evaluate the effectiveness of ErrorNet in handling small sample size and domain shift problems. Our experiments demonstrate that ErrorNet outperforms a base segmentation model, a CRF-based post processing scheme, and a domain adaptation method, with a greater performance gain in the presence of dataset limitations above.