Unlocking Insights: Semantic Search in Jupyter Notebooks

Semantic search, a process aimed at delivering highly relevant search results by comprehending the searcher's intent and the contextual meaning of terms within a searchable dataspace, plays a pivotal role in information retrieval. In this paper, we investigate the application of large language models to enhance semantic search capabilities, specifically tailored for the domain of Jupyter Notebooks. Our objective is to retrieve generated outputs, such as figures or tables, associated functions and methods, and other pertinent information. We demonstrate a semantic search framework that achieves a comprehensive semantic understanding of the entire notebook's contents, enabling it to effectively handle various types of user queries. Key components of this framework include: 1). A data preprocessor is designed to handle diverse types of cells within Jupyter Notebooks, encompassing both markdown and code cells. 2). An innovative methodology is devised to address token size limitations that arise with code-type cells. We implement a finer-grained approach to data input, transitioning from the cell level to the function level, effectively resolving these issues.

An objective comparison of methods for augmented reality in laparoscopic liver resection by preoperative-to-intraoperative image fusion

Augmented reality for laparoscopic liver resection is a visualisation mode that allows a surgeon to localise tumours and vessels embedded within the liver by projecting them on top of a laparoscopic image. Preoperative 3D models extracted from CT or MRI data are registered to the intraoperative laparoscopic images during this process. In terms of 3D-2D fusion, most of the algorithms make use of anatomical landmarks to guide registration. These landmarks include the liver's inferior ridge, the falciform ligament, and the occluding contours. They are usually marked by hand in both the laparoscopic image and the 3D model, which is time-consuming and may contain errors if done by a non-experienced user. Therefore, there is a need to automate this process so that augmented reality can be used effectively in the operating room. We present the Preoperative-to-Intraoperative Laparoscopic Fusion Challenge (P2ILF), held during the Medical Imaging and Computer Assisted Interventions (MICCAI 2022) conference, which investigates the possibilities of detecting these landmarks automatically and using them in registration. The challenge was divided into two tasks: 1) A 2D and 3D landmark detection task and 2) a 3D-2D registration task. The teams were provided with training data consisting of 167 laparoscopic images and 9 preoperative 3D models from 9 patients, with the corresponding 2D and 3D landmark annotations. A total of 6 teams from 4 countries participated, whose proposed methods were evaluated on 16 images and two preoperative 3D models from two patients. All the teams proposed deep learning-based methods for the 2D and 3D landmark segmentation tasks and differentiable rendering-based methods for the registration task. Based on the experimental outcomes, we propose three key hypotheses that determine current limitations and future directions for research in this domain.

Twice Class Bias Correction for Imbalanced Semi-Supervised Learning

Differing from traditional semi-supervised learning, class-imbalanced semi-supervised learning presents two distinct challenges: (1) The imbalanced distribution of training samples leads to model bias towards certain classes, and (2) the distribution of unlabeled samples is unknown and potentially distinct from that of labeled samples, which further contributes to class bias in the pseudo-labels during training. To address these dual challenges, we introduce a novel approach called \textbf{T}wice \textbf{C}lass \textbf{B}ias \textbf{C}orrection (\textbf{TCBC}). We begin by utilizing an estimate of the class distribution from the participating training samples to correct the model, enabling it to learn the posterior probabilities of samples under a class-balanced prior. This correction serves to alleviate the inherent class bias of the model. Building upon this foundation, we further estimate the class bias of the current model parameters during the training process. We apply a secondary correction to the model's pseudo-labels for unlabeled samples, aiming to make the assignment of pseudo-labels across different classes of unlabeled samples as equitable as possible. Through extensive experimentation on CIFAR10/100-LT, STL10-LT, and the sizable long-tailed dataset SUN397, we provide conclusive evidence that our proposed TCBC method reliably enhances the performance of class-imbalanced semi-supervised learning.

CLAF: Contrastive Learning with Augmented Features for Imbalanced Semi-Supervised Learning

Due to the advantages of leveraging unlabeled data and learning meaningful representations, semi-supervised learning and contrastive learning have been progressively combined to achieve better performances in popular applications with few labeled data and abundant unlabeled data. One common manner is assigning pseudo-labels to unlabeled samples and selecting positive and negative samples from pseudo-labeled samples to apply contrastive learning. However, the real-world data may be imbalanced, causing pseudo-labels to be biased toward the majority classes and further undermining the effectiveness of contrastive learning. To address the challenge, we propose Contrastive Learning with Augmented Features (CLAF). We design a class-dependent feature augmentation module to alleviate the scarcity of minority class samples in contrastive learning. For each pseudo-labeled sample, we select positive and negative samples from labeled data instead of unlabeled data to compute contrastive loss. Comprehensive experiments on imbalanced image classification datasets demonstrate the effectiveness of CLAF in the context of imbalanced semi-supervised learning.

KAER: A Knowledge Augmented Pre-Trained Language Model for Entity Resolution

Entity resolution has been an essential and well-studied task in data cleaning research for decades. Existing work has discussed the feasibility of utilizing pre-trained language models to perform entity resolution and achieved promising results. However, few works have discussed injecting domain knowledge to improve the performance of pre-trained language models on entity resolution tasks. In this study, we propose Knowledge Augmented Entity Resolution (KAER), a novel framework named for augmenting pre-trained language models with external knowledge for entity resolution. We discuss the results of utilizing different knowledge augmentation and prompting methods to improve entity resolution performance. Our model improves on Ditto, the existing state-of-the-art entity resolution method. In particular, 1) KAER performs more robustly and achieves better results on "dirty data", and 2) with more general knowledge injection, KAER outperforms the existing baseline models on the textual dataset and dataset from the online product domain. 3) KAER achieves competitive results on highly domain-specific datasets, such as citation datasets, requiring the injection of expert knowledge in future work.

Optimal Boxes: Boosting End-to-End Scene Text Recognition by Adjusting Annotated Bounding Boxes via Reinforcement Learning

Text detection and recognition are essential components of a modern OCR system. Most OCR approaches attempt to obtain accurate bounding boxes of text at the detection stage, which is used as the input of the text recognition stage. We observe that when using tight text bounding boxes as input, a text recognizer frequently fails to achieve optimal performance due to the inconsistency between bounding boxes and deep representations of text recognition. In this paper, we propose Box Adjuster, a reinforcement learning-based method for adjusting the shape of each text bounding box to make it more compatible with text recognition models. Additionally, when dealing with cross-domain problems such as synthetic-to-real, the proposed method significantly reduces mismatches in domain distribution between the source and target domains. Experiments demonstrate that the performance of end-to-end text recognition systems can be improved when using the adjusted bounding boxes as the ground truths for training. Specifically, on several benchmark datasets for scene text understanding, the proposed method outperforms state-of-the-art text spotters by an average of 2.0% F-Score on end-to-end text recognition tasks and 4.6% F-Score on domain adaptation tasks.

I-BERT: Inductive Generalization of Transformer to Arbitrary Context Lengths

Self-attention has emerged as a vital component of state-of-the-art sequence-to-sequence models for natural language processing in recent years, brought to the forefront by pre-trained bi-directional Transformer models. Its effectiveness is partly due to its non-sequential architecture, which promotes scalability and parallelism but limits the model to inputs of a bounded length. In particular, such architectures perform poorly on algorithmic tasks, where the model must learn a procedure which generalizes to input lengths unseen in training, a capability we refer to as inductive generalization. Identifying the computational limits of existing self-attention mechanisms, we propose I-BERT, a bi-directional Transformer that replaces positional encodings with a recurrent layer. The model inductively generalizes on a variety of algorithmic tasks where state-of-the-art Transformer models fail to do so. We also test our method on masked language modeling tasks where training and validation sets are partitioned to verify inductive generalization. Out of three algorithmic and two natural language inductive generalization tasks, I-BERT achieves state-of-the-art results on four tasks.