With the massive proliferation of data-driven algorithms, such as deep learning-based approaches, the availability of high-quality data is of great interest. Volumetric data is very important in medicine, as it ranges from disease diagnoses to therapy monitoring. When the dataset is sufficient, models can be trained to help doctors with these tasks. Unfortunately, there are scenarios where large amounts of data is unavailable. For example, rare diseases and privacy issues can lead to restricted data availability. In non-medical fields, the high cost of obtaining enough high-quality data can also be a concern. A solution to these problems can be the generation of realistic synthetic data using Generative Adversarial Networks (GANs). The existence of these mechanisms is a good asset, especially in healthcare, as the data must be of good quality, realistic, and without privacy issues. Therefore, most of the publications on volumetric GANs are within the medical domain. In this review, we provide a summary of works that generate realistic volumetric synthetic data using GANs. We therefore outline GAN-based methods in these areas with common architectures, loss functions and evaluation metrics, including their advantages and disadvantages. We present a novel taxonomy, evaluations, challenges, and research opportunities to provide a holistic overview of the current state of volumetric GANs.

We construct pseudorandom error-correcting codes (or simply pseudorandom codes), which are error-correcting codes with the property that any polynomial number of codewords are pseudorandom to any computationally-bounded adversary. Efficient decoding of corrupted codewords is possible with the help of a decoding key. We build pseudorandom codes that are robust to substitution and deletion errors, where pseudorandomness rests on standard cryptographic assumptions. Specifically, pseudorandomness is based on either $2^{O(\sqrt{n})}$-hardness of LPN, or polynomial hardness of LPN and the planted XOR problem at low density. As our primary application of pseudorandom codes, we present an undetectable watermarking scheme for outputs of language models that is robust to cropping and a constant rate of random substitutions and deletions. The watermark is undetectable in the sense that any number of samples of watermarked text are computationally indistinguishable from text output by the original model. This is the first undetectable watermarking scheme that can tolerate a constant rate of errors. Our second application is to steganography, where a secret message is hidden in innocent-looking content. We present a constant-rate stateless steganography scheme with robustness to a constant rate of substitutions. Ours is the first stateless steganography scheme with provable steganographic security and any robustness to errors.

Protein research is crucial in various fundamental disciplines, but understanding their intricate structure-function relationships remains challenging. Recent Large Language Models (LLMs) have made significant strides in comprehending task-specific knowledge, suggesting the potential for ChatGPT-like systems specialized in protein to facilitate basic research. In this work, we introduce ProtChatGPT, which aims at learning and understanding protein structures via natural languages. ProtChatGPT enables users to upload proteins, ask questions, and engage in interactive conversations to produce comprehensive answers. The system comprises protein encoders, a Protein-Language Pertaining Transformer (PLP-former), a projection adapter, and an LLM. The protein first undergoes protein encoders and PLP-former to produce protein embeddings, which are then projected by the adapter to conform with the LLM. The LLM finally combines user questions with projected embeddings to generate informative answers. Experiments show that ProtChatGPT can produce promising responses to proteins and their corresponding questions. We hope that ProtChatGPT could form the basis for further exploration and application in protein research. Code and our pre-trained model will be publicly available.

Lung cancer (LC) remains the primary cause of cancer-related mortality, largely due to late-stage diagnoses. Effective strategies for early detection are therefore of paramount importance. In recent years, machine learning (ML) has demonstrated considerable potential in healthcare by facilitating the detection of various diseases. In this retrospective development and validation study, we developed an ML model based on dynamic ensemble selection (DES) for LC detection. The model leverages standard blood sample analysis and smoking history data from a large population at risk in Denmark. The study includes all patients examined on suspicion of LC in the Region of Southern Denmark from 2009 to 2018. We validated and compared the predictions by the DES model with diagnoses provided by five pulmonologists. Among the 38,944 patients, 9,940 had complete data of which 2,505 (25\%) had LC. The DES model achieved an area under the roc curve of 0.77$\pm$0.01, sensitivity of 76.2\%$\pm$2.4\%, specificity of 63.8\%$\pm$2.3\%, positive predictive value of 41.6\%$\pm$1.2\%, and F\textsubscript{1}-score of 53.8\%$\pm$1.1\%. The DES model outperformed all five pulmonologists, achieving a sensitivity 9\% higher than their average. The model identified smoking status, age, total calcium levels, neutrophil count, and lactate dehydrogenase as the most important factors for the detection of LC. The results highlight the successful application of the ML approach in detecting LC, surpassing pulmonologists' performance. Incorporating clinical and laboratory data in future risk assessment models can improve decision-making and facilitate timely referrals.

Quantum machine learning provides a fundamentally novel and promising approach to analyzing data. However, many data sets are too complex for currently available quantum computers. Consequently, quantum machine learning applications conventionally resort to dimensionality reduction algorithms, e.g., auto-encoders, before passing data through the quantum models. We show that using a classical auto-encoder as an independent preprocessing step can significantly decrease the classification performance of a quantum machine learning algorithm. To ameliorate this issue, we design an architecture that unifies the preprocessing and quantum classification algorithms into a single trainable model: the guided quantum compression model. The utility of this model is demonstrated by using it to identify the Higgs boson in proton-proton collisions at the LHC, where the conventional approach proves ineffective. Conversely, the guided quantum compression model excels at solving this classification problem, achieving a good accuracy. Additionally, the model developed herein shows better performance compared to the classical benchmark when using only low-level kinematic features.

Model-based planners for partially observable problems must accommodate both model uncertainty during planning and goal uncertainty during objective inference. However, model-based planners may be brittle under these types of uncertainty because they rely on an exact model and tend to commit to a single optimal behavior. Inspired by results in the model-free setting, we propose an entropy-regularized model-based planner for partially observable problems. Entropy regularization promotes policy robustness for planning and objective inference by encouraging policies to be no more committed to a single action than necessary. We evaluate the robustness and objective inference performance of entropy-regularized policies in three problem domains. Our results show that entropy-regularized policies outperform non-entropy-regularized baselines in terms of higher expected returns under modeling errors and higher accuracy during objective inference.

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with pre-defined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.

Rib fractures are a common and potentially severe injury that can be challenging and labor-intensive to detect in CT scans. While there have been efforts to address this field, the lack of large-scale annotated datasets and evaluation benchmarks has hindered the development and validation of deep learning algorithms. To address this issue, the RibFrac Challenge was introduced, providing a benchmark dataset of over 5,000 rib fractures from 660 CT scans, with voxel-level instance mask annotations and diagnosis labels for four clinical categories (buckle, nondisplaced, displaced, or segmental). The challenge includes two tracks: a detection (instance segmentation) track evaluated by an FROC-style metric and a classification track evaluated by an F1-style metric. During the MICCAI 2020 challenge period, 243 results were evaluated, and seven teams were invited to participate in the challenge summary. The analysis revealed that several top rib fracture detection solutions achieved performance comparable or even better than human experts. Nevertheless, the current rib fracture classification solutions are hardly clinically applicable, which can be an interesting area in the future. As an active benchmark and research resource, the data and online evaluation of the RibFrac Challenge are available at the challenge website. As an independent contribution, we have also extended our previous internal baseline by incorporating recent advancements in large-scale pretrained networks and point-based rib segmentation techniques. The resulting FracNet+ demonstrates competitive performance in rib fracture detection, which lays a foundation for further research and development in AI-assisted rib fracture detection and diagnosis.

Objective: Firearm injury research necessitates using data from often-exploited vulnerable populations of Black and Brown Americans. In order to minimize distrust, this study provides a framework for establishing AI trust and transparency with the general population. Methods: We propose a Model Facts template that is easily extendable and decomposes accuracy and demographics into standardized and minimally complex values. This framework allows general users to assess the validity and biases of a model without diving into technical model documentation. Examples: We apply the Model Facts template on two previously published models, a violence risk identification model and a suicide risk prediction model. We demonstrate the ease of accessing the appropriate information when the data is structured appropriately. Discussion: The Model Facts template is limited in its current form to human based data and biases. Like nutrition facts, it also will require some educational resources for users to grasp its full utility. Human computer interaction experiments should be conducted to ensure that the interaction between user interface and model interface is as desired. Conclusion: The Model Facts label is the first framework dedicated to establishing trust with end users and general population consumers. Implementation of Model Facts into firearm injury research will provide public health practitioners and those impacted by firearm injury greater faith in the tools the research provides.

Harmful algal blooms (HABs) are episodes of high concentrations of algae that are potentially toxic for human consumption. Mollusc farming can be affected by HABs because, as filter feeders, they can accumulate high concentrations of marine biotoxins in their tissues. To avoid the risk to human consumption, harvesting is prohibited when toxicity is detected. At present, the closure of production areas is based on expert knowledge and the existence of a predictive model would help when conditions are complex and sampling is not possible. Although the concentration of toxin in meat is the method most commonly used by experts in the control of shellfish production areas, it is rarely used as a target by automatic prediction models. This is largely due to the irregularity of the data due to the established sampling programs. As an alternative, the activity status of production areas has been proposed as a target variable based on whether mollusc meat has a toxicity level below or above the legal limit. This new option is the most similar to the actual functioning of the control of shellfish production areas. For this purpose, we have made a comparison between hybrid machine learning models like Neural-Network-Adding Bootstrap (BAGNET) and Discriminative Nearest Neighbor Classification (SVM-KNN) when estimating the state of production areas. The study has been carried out in several estuaries with different levels of complexity in the episodes of algal blooms to demonstrate the generalization capacity of the models in bloom detection. As a result, we could observe that, with an average recall value of 93.41% and without dropping below 90% in any of the estuaries, BAGNET outperforms the other models both in terms of results and robustness.