Over the past 40 years, the discovery and development of therapeutic antibodies to treat disease has become common practice. However, as therapeutic antibody constructs are becoming more sophisticated (e.g., multi-specifics), conventional approaches to optimisation are increasingly inefficient. Machine learning (ML) promises to open up an in silico route to antibody discovery and help accelerate the development of drug products using a reduced number of experiments and hence cost. Over the past few years, we have observed rapid developments in the field of ML-guided antibody discovery and development (D&D). However, many of the results are difficult to compare or hard to assess for utility by other experts in the field due to the high diversity in the datasets and evaluation techniques and metrics that are across industry and academia. This limitation of the literature curtails the broad adoption of ML across the industry and slows down overall progress in the field, highlighting the need to develop standards and guidelines that may help improve the reproducibility of ML models across different research groups. To address these challenges, we set out in this perspective to critically review current practices, explain common pitfalls, and clearly define a set of method development and evaluation guidelines that can be applied to different types of ML-based techniques for therapeutic antibody D&D. Specifically, we address in an end-to-end analysis, challenges associated with all aspects of the ML process and recommend a set of best practices for each stage.

Benchmark datasets for digital dermatology unwittingly contain inaccuracies that reduce trust in model performance estimates. We propose a resource-efficient data-cleaning protocol to identify issues that escaped previous curation. The protocol leverages an existing algorithmic cleaning strategy and is followed by a confirmation process terminated by an intuitive stopping criterion. Based on confirmation by multiple dermatologists, we remove irrelevant samples and near duplicates and estimate the percentage of label errors in six dermatology image datasets for model evaluation promoted by the International Skin Imaging Collaboration. Along with this paper, we publish revised file lists for each dataset which should be used for model evaluation. Our work paves the way for more trustworthy performance assessment in digital dermatology.

Despite the remarkable advances in deep learning technology, achieving satisfactory performance in lung sound classification remains a challenge due to the scarcity of available data. Moreover, the respiratory sound samples are collected from a variety of electronic stethoscopes, which could potentially introduce biases into the trained models. When a significant distribution shift occurs within the test dataset or in a practical scenario, it can substantially decrease the performance. To tackle this issue, we introduce cross-domain adaptation techniques, which transfer the knowledge from a source domain to a distinct target domain. In particular, by considering different stethoscope types as individual domains, we propose a novel stethoscope-guided supervised contrastive learning approach. This method can mitigate any domain-related disparities and thus enables the model to distinguish respiratory sounds of the recording variation of the stethoscope. The experimental results on the ICBHI dataset demonstrate that the proposed methods are effective in reducing the domain dependency and achieving the ICBHI Score of 61.71%, which is a significant improvement of 2.16% over the baseline.

Asset owner identification is an important first step for any information security organization, allowing organizations the ability to identify and detect data breaches and losses, vulnerabilities, possible attack surfaces, and define effective countermeasures. Using existing asset ownership data, the research utilized an assortment of machine learning algorithms to determine the best classification model to predict an asset's owner. The research ran separate analyses for each enumerated team, then ran a 100 iteration Monte Carlo Cross Validation across Adaboost, Logistic Regression, Naive Bayes, Classification and Regression Trees, and Random Forests. Finally, a visualization dashboard was created to help users understand the asset inventory through interactive exploratory data analysis as well as the ability to understand model evaluation metrics including accuracy, sensitivity, and specificity for each model. Overall, Adaboost performed the best across all owners with low testing errors below 5% while Naive Bayes performed the worst. The remaining models performed similarly. The fully qualified domain name (FQDN), Classless Inter-Domain Routing (CIDR) CIDR/16, and location were among the most important features.

Automatic text simplification (TS) aims to automate the process of rewriting text to make it easier for people to read. A pre-requisite for TS to be useful is that it should convey information that is consistent with the meaning of the original text. However, current TS evaluation protocols assess system outputs for simplicity and meaning preservation without regard for the document context in which output sentences occur and for how people understand them. In this work, we introduce a human evaluation framework to assess whether simplified texts preserve meaning using reading comprehension questions. With this framework, we conduct a thorough human evaluation of texts by humans and by nine automatic systems. Supervised systems that leverage pre-training knowledge achieve the highest scores on the reading comprehension (RC) tasks amongst the automatic controllable TS systems. However, even the best-performing supervised system struggles with at least 14% of the questions, marking them as "unanswerable'' based on simplified content. We further investigate how existing TS evaluation metrics and automatic question-answering systems approximate the human judgments we obtained.

While coresets have been growing in terms of their application, barring few exceptions, they have mostly been limited to unsupervised settings. We consider supervised classification problems, and non-decomposable evaluation measures in such settings. We show that stratified uniform sampling based coresets have excellent empirical performance that are backed by theoretical guarantees too. We focus on the F1 score and Matthews Correlation Coefficient, two widely used non-decomposable objective functions that are nontrivial to optimize for and show that uniform coresets attain a lower bound for coreset size, and have good empirical performance, comparable with ``smarter'' coreset construction strategies.

This report proposes a model to predict the location of the most deprived areas in a city using data from the census. A census data is very high dimensional and needs to be simplified. We use a novel algorithm to reduce dimensionality and find patterns: The diffusion map. Features are defined by eigenvectors of the Laplacian matrix that defines the diffusion map. Eigenvectors corresponding to the smallest eigenvalues indicate specific population features. Previous work has found qualitatively that the second most important dimension for describing the census data in Bristol is linked to deprivation. In this report, we analyse how good this dimension is as a model for predicting deprivation by comparing with the recognised measures. The Pearson correlation coefficient was found to be over 0.7. The top 10 per cent of deprived areas in the UK which also locate in Bristol are extracted to test the accuracy of the model. There are 52 most deprived areas, and 38 areas are correctly identified by comparing to the model. The influence of scores of IMD domains that do not correlate with the models, Eigenvector 2 entries of non-deprived OAs and orthogonality of Eigenvectors cause the model to fail the prediction of 14 deprived areas. However, overall, the model shows a high performance to predict the future deprivation of overall areas where the project considers. This project is expected to support the government to allocate resources and funding.

Artificial Intelligence (AI) based image analysis has an immense potential to support diagnostic histopathology, including cancer diagnostics. However, developing supervised AI methods requires large-scale annotated datasets. A potentially powerful solution is to augment training data with synthetic data. Latent diffusion models, which can generate high-quality, diverse synthetic images, are promising. However, the most common implementations rely on detailed textual descriptions, which are not generally available in this domain. This work proposes a method that constructs structured textual prompts from automatically extracted image features. We experiment with the PCam dataset, composed of tissue patches only loosely annotated as healthy or cancerous. We show that including image-derived features in the prompt, as opposed to only healthy and cancerous labels, improves the Fr\'echet Inception Distance (FID) from 178.8 to 90.2. We also show that pathologists find it challenging to detect synthetic images, with a median sensitivity/specificity of 0.55/0.55. Finally, we show that synthetic data effectively trains AI models.

Efficient and effective Out-of-Distribution (OOD) detection is essential for the safe deployment of AI in latency-critical applications. Recently, studies have revealed that detecting OOD based on feature space information can be highly effective. Despite their effectiveness, however, exiting feature space OOD methods may incur non-negligible computational overhead, given their reliance on auxiliary models built from training features. In this paper, we aim to obviate auxiliary models to optimize computational efficiency while leveraging the rich information embedded in the feature space. We investigate from the novel perspective of decision boundaries and propose to detect OOD using the feature distance to decision boundaries. To minimize the cost of measuring the distance, we introduce an efficient closed-form estimation, analytically proven to tightly lower bound the distance. We observe that ID features tend to reside further from the decision boundaries than OOD features. Our observation aligns with the intuition that models tend to be more decisive on ID samples, considering that distance to decision boundaries quantifies model uncertainty. From our understanding, we propose a hyperparameter-free, auxiliary model-free OOD detector. Our OOD detector matches or surpasses the effectiveness of state-of-the-art methods across extensive experiments. Meanwhile, our OOD detector incurs practically negligible overhead in inference latency. Overall, we significantly enhance the efficiency-effectiveness trade-off in OOD detection.

Machine-Learned Likelihoods (MLL) combines machine-learning classification techniques with likelihood-based inference tests to estimate the experimental sensitivity of high-dimensional data sets. We extend the MLL method by including Kernel Density Estimators (KDE) to avoid binning the classifier output to extract the resulting one-dimensional signal and background probability density functions. We first test our method on toy models generated with multivariate Gaussian distributions, where the true probability distribution functions are known. Later, we apply the method to two cases of interest at the LHC: a search for exotic Higgs bosons, and a $Z'$ boson decaying into lepton pairs. In contrast to physical-based quantities, the typical fluctuations of the ML outputs give non-smooth probability distributions for pure-signal and pure-background samples. The non-smoothness is propagated into the density estimation due to the good performance and flexibility of the KDE method. We study its impact on the final significance computation, and we compare the results using the average of several independent ML output realizations, which allows us to obtain smoother distributions. We conclude that the significance estimation turns out to be not sensible to this issue.