Background We aim to use Natural Language Processing (NLP) to automate the extraction and classification of thyroid cancer risk factors from pathology reports. Methods We analyzed 1,410 surgical pathology reports from adult papillary thyroid cancer patients at Mayo Clinic, Rochester, MN, from 2010 to 2019. Structured and non-structured reports were used to create a consensus-based ground truth dictionary and categorized them into modified recurrence risk levels. Non-structured reports were narrative, while structured reports followed standardized formats. We then developed ThyroPath, a rule-based NLP pipeline, to extract and classify thyroid cancer features into risk categories. Training involved 225 reports (150 structured, 75 unstructured), with testing on 170 reports (120 structured, 50 unstructured) for evaluation. The pipeline's performance was assessed using both strict and lenient criteria for accuracy, precision, recall, and F1-score. Results In extraction tasks, ThyroPath achieved overall strict F-1 scores of 93% for structured reports and 90 for unstructured reports, covering 18 thyroid cancer pathology features. In classification tasks, ThyroPath-extracted information demonstrated an overall accuracy of 93% in categorizing reports based on their corresponding guideline-based risk of recurrence: 76.9% for high-risk, 86.8% for intermediate risk, and 100% for both low and very low-risk cases. However, ThyroPath achieved 100% accuracy across all thyroid cancer risk categories with human-extracted pathology information. Conclusions ThyroPath shows promise in automating the extraction and risk recurrence classification of thyroid pathology reports at large scale. It offers a solution to laborious manual reviews and advancing virtual registries. However, it requires further validation before implementation.

We introduce an evaluation system designed to compute PARSEVAL measures, offering a viable alternative to \texttt{evalb} commonly used for constituency parsing evaluation. The widely used \texttt{evalb} script has traditionally been employed for evaluating the accuracy of constituency parsing results, albeit with the requirement for consistent tokenization and sentence boundaries. In contrast, our approach, named \texttt{jp-evalb}, is founded on an alignment method. This method aligns sentences and words when discrepancies arise. It aims to overcome several known issues associated with \texttt{evalb} by utilizing the `jointly preprocessed (JP)' alignment-based method. We introduce a more flexible and adaptive framework, ultimately contributing to a more accurate assessment of constituency parsing performance.

The advent of high-contrast imaging instruments combined with medium-resolution spectrographs allows spectral and temporal dimensions to be combined with spatial dimensions to detect and potentially characterize exoplanets with higher sensitivity. We develop a new method to effectively leverage the spectral and spatial dimensions in integral-field spectroscopy (IFS) datasets using a supervised deep-learning algorithm to improve the detection sensitivity to high-contrast exoplanets. We begin by applying a data transform whereby the IFS datasets are replaced by cross-correlation coefficient tensors obtained by cross-correlating our data with young gas giant spectral template spectra. This transformed data is then used to train machine learning (ML) algorithms. We train a 2D CNN and 3D LSTM with our data. We compare the ML models with a non-ML algorithm, based on the STIM map of arXiv:1810.06895. We test our algorithms on simulated young gas giants in a dataset that contains no known exoplanet, and explore the sensitivity of algorithms to detect these exoplanets at contrasts ranging from 1e-3 to 1e-4 at different radial separations. We quantify the sensitivity using modified receiver operating characteristic curves (mROC). We discover that the ML algorithms produce fewer false positives and have a higher true positive rate than the STIM-based algorithm, and the true positive rate of ML algorithms is less impacted by changing radial separation. We discover that the velocity dimension is an important differentiating factor. Through this paper, we demonstrate that ML techniques have the potential to improve the detection limits and reduce false positives for directly imaged planets in IFS datasets, after transforming the spectral dimension into a radial velocity dimension through a cross-correlation operation.

We consider the task of retraining machine learning (ML) models when new batches of data become available. Existing methods focus largely on greedy approaches to find the best-performing model for each batch, without considering the stability of the model's structure across retraining iterations. In this study, we propose a methodology for finding sequences of ML models that are stable across retraining iterations. We develop a mixed-integer optimization formulation that is guaranteed to recover Pareto optimal models (in terms of the predictive power-stability trade-off) and an efficient polynomial-time algorithm that performs well in practice. We focus on retaining consistent analytical insights - which is important to model interpretability, ease of implementation, and fostering trust with users - by using custom-defined distance metrics that can be directly incorporated into the optimization problem. Our method shows stronger stability than greedily trained models with a small, controllable sacrifice in predictive power, as evidenced through a real-world case study in a major hospital system in Connecticut.

Defect reduction planning plays a vital role in enhancing software quality and minimizing software maintenance costs. By training a black box machine learning model and "explaining" its predictions, explainable AI for software engineering aims to identify the code characteristics that impact maintenance risks. However, post-hoc explanations do not always faithfully reflect what the original model computes. In this paper, we introduce CounterACT, a Counterfactual ACTion rule mining approach that can generate defect reduction plans without black-box models. By leveraging action rules, CounterACT provides a course of action that can be considered as a counterfactual explanation for the class (e.g., buggy or not buggy) assigned to a piece of code. We compare the effectiveness of CounterACT with the original action rule mining algorithm and six established defect reduction approaches on 9 software projects. Our evaluation is based on (a) overlap scores between proposed code changes and actual developer modifications; (b) improvement scores in future releases; and (c) the precision, recall, and F1-score of the plans. Our results show that, compared to competing approaches, CounterACT's explainable plans achieve higher overlap scores at the release level (median 95%) and commit level (median 85.97%), and they offer better trade-off between precision and recall (median F1-score 88.12%). Finally, we venture beyond planning and explore leveraging Large Language models (LLM) for generating code edits from our generated plans. Our results show that suggested LLM code edits supported by our plans are actionable and are more likely to pass relevant test cases than vanilla LLM code recommendations.

With the increasing use of large language models (LLMs) in daily life, concerns have emerged regarding their potential misuse and societal impact. Watermarking is proposed to trace the usage of specific models by injecting patterns into their generated texts. An ideal watermark should produce outputs that are nearly indistinguishable from those of the original LLM (imperceptibility), while ensuring a high detection rate (efficacy), even when the text is partially altered (robustness). Despite many methods having been proposed, none have simultaneously achieved all three properties, revealing an inherent trade-off. This paper utilizes a key-centered scheme to unify existing watermarking techniques by decomposing a watermark into two distinct modules: a key module and a mark module. Through this decomposition, we demonstrate for the first time that the key module significantly contributes to the trade-off issues observed in prior methods. Specifically, this reflects the conflict between the scale of the key sampling space during generation and the complexity of key restoration during detection. To this end, we introduce \textbf{WaterPool}, a simple yet effective key module that preserves a complete key sampling space required by imperceptibility while utilizing semantics-based search to improve the key restoration process. WaterPool can integrate with most watermarks, acting as a plug-in. Our experiments with three well-known watermarking techniques show that WaterPool significantly enhances their performance, achieving near-optimal imperceptibility and markedly improving efficacy and robustness (+12.73\% for KGW, +20.27\% for EXP, +7.27\% for ITS).

This paper presents the first systematic study of evalution of Deep Neural Network (DNN) designed and trained to predict the evolution of a stochastic dynamical system, using wildfire prediction as a case study. We show that traditional evaluation methods based on threshold based classification metrics and error-based scoring rules assess a DNN's ability to replicate the observed ground truth (GT), but do not measure the fidelity of the DNN's learning of the underlying stochastic process. To address this gap, we propose a new system property: Statistic-GT, representing the GT of the stochastic process, and an evaluation metric that exclusively assesses fidelity to Statistic-GT. Utilizing a synthetic dataset, we introduce a stochastic framework to characterize this property and establish criteria for a metric to be a valid measure of the proposed property. We formally show that Expected Calibration Error (ECE) tests the necessary condition for fidelity to Statistic-GT. We perform empirical experiments, differentiating ECE's behavior from conventional metrics and demonstrate that ECE exclusively measures fidelity to the stochastic process. Extending our analysis to real-world wildfire data, we highlight the limitations of traditional evaluation methods and discuss the utility of evaluating fidelity to the stochastic process alongside existing metrics.

Serial sectioning Optical Coherence Tomography (sOCT) is a high-throughput, label free microscopic imaging technique that is becoming increasingly popular to study post-mortem neurovasculature. Quantitative analysis of the vasculature requires highly accurate segmentation; however, sOCT has low signal-to-noise-ratio and displays a wide range of contrasts and artifacts that depend on acquisition parameters. Furthermore, labeled data is scarce and extremely time consuming to generate. Here, we leverage synthetic datasets of vessels to train a deep learning segmentation model. We construct the vessels with semi-realistic splines that simulate the vascular geometry and compare our model with realistic vascular labels generated by constrained constructive optimization. Both approaches yield similar Dice scores, although with very different false positive and false negative rates. This method addresses the complexity inherent in OCT images and paves the way for more accurate and efficient analysis of neurovascular structures.

The new generation of observatories and instruments (VLT/ERIS, JWST, ELT) motivate the development of robust methods to detect and characterise faint and close-in exoplanets. Molecular mapping and cross-correlation for spectroscopy use molecular templates to isolate a planet's spectrum from its host star. However, reliance on signal-to-noise ratio (S/N) metrics can lead to missed discoveries, due to strong assumptions of Gaussian independent and identically distributed noise. We introduce machine learning for cross-correlation spectroscopy (MLCCS); the method aims to leverage weak assumptions on exoplanet characterisation, such as the presence of specific molecules in atmospheres, to improve detection sensitivity for exoplanets. MLCCS methods, including a perceptron and unidimensional convolutional neural networks, operate in the cross-correlated spectral dimension, in which patterns from molecules can be identified. We test on mock datasets of synthetic planets inserted into real noise from SINFONI at K-band. The results from MLCCS show outstanding improvements. The outcome on a grid of faint synthetic gas giants shows that for a false discovery rate up to 5%, a perceptron can detect about 26 times the amount of planets compared to an S/N metric. This factor increases up to 77 times with convolutional neural networks, with a statistical sensitivity shift from 0.7% to 55.5%. In addition, MLCCS methods show a drastic improvement in detection confidence and conspicuity on imaging spectroscopy. Once trained, MLCCS methods offer sensitive and rapid detection of exoplanets and their molecular species in the spectral dimension. They handle systematic noise and challenging seeing conditions, can adapt to many spectroscopic instruments and modes, and are versatile regarding atmospheric characteristics, which can enable identification of various planets in archival and future data.

In this paper, we introduce a simple yet effective tabular data watermarking mechanism with statistical guarantees. We show theoretically that the proposed watermark can be effectively detected, while faithfully preserving the data fidelity, and also demonstrates appealing robustness against additive noise attack. The general idea is to achieve the watermarking through a strategic embedding based on simple data binning. Specifically, it divides the feature's value range into finely segmented intervals and embeds watermarks into selected ``green list" intervals. To detect the watermarks, we develop a principled statistical hypothesis-testing framework with minimal assumptions: it remains valid as long as the underlying data distribution has a continuous density function. The watermarking efficacy is demonstrated through rigorous theoretical analysis and empirical validation, highlighting its utility in enhancing the security of synthetic and real-world datasets.