Learning from Label Proportions (LLP) is a learning problem where only aggregate level labels are available for groups of instances, called bags, during training, and the aim is to get the best performance at the instance-level on the test data. This setting arises in domains like advertising and medicine due to privacy considerations. We propose a novel algorithmic framework for this problem that iteratively performs two main steps. For the first step (Pseudo Labeling) in every iteration, we define a Gibbs distribution over binary instance labels that incorporates a) covariate information through the constraint that instances with similar covariates should have similar labels and b) the bag level aggregated label. We then use Belief Propagation (BP) to marginalize the Gibbs distribution to obtain pseudo labels. In the second step (Embedding Refinement), we use the pseudo labels to provide supervision for a learner that yields a better embedding. In the final iteration, a classifier is trained using the pseudo labels. Our algorithm displays strong gains against several SOTA baselines (up to 15%) for the LLP Binary Classification problem on various dataset types - tabular and Image. We achieve these improvements with minimal computational overhead above standard supervised learning due to Belief Propagation, for large bag sizes, even for a million samples. Learning from Label Proportions (henceforth LLP) has seen renewed interest in recent times due to the rising concerns of privacy and leakage of sensitive information (Ardehaly & Culotta, 2017; Busa-Fekete et al., 2023; Zhang et al., 2022; Kobayashi et al., 2022; Yu et al., 2014). In the LLP binary classification setting, all the training instances are aggregated into bags and only the aggregated label count for a bag is available, i.e. proportion of 1's in a bag. Features of all instances are available. This can be seen as a form of weak supervision compared to providing instance-level labels.

Hyper-parameter optimization is the black art of tuning a learner's control parameters. In software analytics, a repeated result is that such tuning can result in dramatic performance improvements. Despite this, hyper-parameter optimization is often applied rarely or poorly in software analytics--perhaps due to the CPU cost of exploring all those parameter options can be prohibitive. We theorize that learners generalize better when the loss landscape is ``smooth''. This theory is useful since the influence on ``smoothness'' of different hyper-parameter choices can be tested very quickly (e.g. for a deep learner, after just one epoch). To test this theory, this paper implements and tests SMOOTHIE, a novel hyper-parameter optimizer that guides its optimizations via considerations of ``smothness''. The experiments of this paper test SMOOTHIE on numerous SE tasks including (a) GitHub issue lifetime prediction; (b) detecting false alarms in static code warnings; (c) defect prediction, and (d) a set of standard ML datasets. In all these experiments, SMOOTHIE out-performed state-of-the-art optimizers. Better yet, SMOOTHIE ran 300% faster than the prior state-of-the art. We hence conclude that this theory (that hyper-parameter optimization is best viewed as a ``smoothing'' function for the decision landscape), is both theoretically interesting and practically very useful. To support open science and other researchers working in this area, all our scripts and datasets are available on-line at https://github.com/yrahul3910/smoothness-hpo/.

In the realm of machine learning and statistical modeling, practitioners often work under the assumption of accessible, static, labeled data for evaluation and training. However, this assumption often deviates from reality where data may be private, encrypted, difficult- to-measure, or unlabeled. In this paper, we bridge this gap by adapting the Hui-Walter paradigm, a method traditionally applied in epidemiology and medicine, to the field of machine learning. This approach enables us to estimate key performance metrics such as false positive rate, false negative rate, and priors in scenarios where no ground truth is available. We further extend this paradigm for handling online data, opening up new possibilities for dynamic data environments. Our methodology involves partitioning data into latent classes to simulate multiple data populations (if natural populations are unavailable) and independently training models to replicate multiple tests. By cross-tabulating binary outcomes across ensemble categorizers and multiple populations, we are able to estimate unknown parameters through Gibbs sampling, eliminating the need for ground-truth or labeled data. This paper showcases the potential of our methodology to transform machine learning practices by allowing for accurate model assessment under dynamic and uncertain data conditions.

Antibody-drug conjugate (ADC) has revolutionized the field of cancer treatment in the era of precision medicine due to their ability to precisely target cancer cells and release highly effective drug. Nevertheless, the realization of rational design of ADC is very difficult because the relationship between their structures and activities is difficult to understand. In the present study, we introduce a unified deep learning framework called ADCNet to help design potential ADCs. The ADCNet highly integrates the protein representation learning language model ESM-2 and small-molecule representation learning language model FG-BERT models to achieve activity prediction through learning meaningful features from antigen and antibody protein sequences of ADC, SMILES strings of linker and payload, and drug-antibody ratio (DAR) value. Based on a carefully designed and manually tailored ADC data set, extensive evaluation results reveal that ADCNet performs best on the test set compared to baseline machine learning models across all evaluation metrics. For example, it achieves an average prediction accuracy of 87.12%, a balanced accuracy of 0.8689, and an area under receiver operating characteristic curve of 0.9293 on the test set. In addition, cross-validation, ablation experiments, and external independent testing results further prove the stability, advancement, and robustness of the ADCNet architecture. For the convenience of the community, we develop the first online platform (https://ADCNet.idruglab.cn) for the prediction of ADCs activity based on the optimal ADCNet model, and the source code is publicly available at https://github.com/idrugLab/ADCNet.

Graphs with heterophily have been regarded as challenging scenarios for Graph Neural Networks (GNNs), where nodes are connected with dissimilar neighbors through various patterns. In this paper, we present theoretical understandings of the impacts of different heterophily patterns for GNNs by incorporating the graph convolution (GC) operations into fully connected networks via the proposed Heterophilous Stochastic Block Models (HSBM), a general random graph model that can accommodate diverse heterophily patterns. Firstly, we show that by applying a GC operation, the separability gains are determined by two factors, i.e., the Euclidean distance of the neighborhood distributions and $\sqrt{\mathbb{E}\left[\operatorname{deg}\right]}$, where $\mathbb{E}\left[\operatorname{deg}\right]$ is the averaged node degree. It reveals that the impact of heterophily on classification needs to be evaluated alongside the averaged node degree. Secondly, we show that the topological noise has a detrimental impact on separability, which is equivalent to degrading $\mathbb{E}\left[\operatorname{deg}\right]$. Finally, when applying multiple GC operations, we show that the separability gains are determined by the normalized distance of the $l$-powered neighborhood distributions. It indicates that the nodes still possess separability as $l$ goes to infinity in a wide range of regimes. Extensive experiments on both synthetic and real-world data verify the effectiveness of our theory.

Brain tumor represents one of the most fatal cancers around the world, and is very common in children and the elderly. Accurate identification of the type and grade of tumor in the early stages plays an important role in choosing a precise treatment plan. The Magnetic Resonance Imaging (MRI) protocols of different sequences provide clinicians with important contradictory information to identify tumor regions. However, manual assessment is time-consuming and error-prone due to big amount of data and the diversity of brain tumor types. Hence, there is an unmet need for MRI automated brain tumor diagnosis. We observe that the predictive capability of uni-modality models is limited and their performance varies widely across modalities, and the commonly used modality fusion methods would introduce potential noise, which results in significant performance degradation. To overcome these challenges, we propose a novel cross-modality guidance-aided multi-modal learning with dual attention for addressing the task of MRI brain tumor grading. To balance the tradeoff between model efficiency and efficacy, we employ ResNet Mix Convolution as the backbone network for feature extraction. Besides, dual attention is applied to capture the semantic interdependencies in spatial and slice dimensions respectively. To facilitate information interaction among modalities, we design a cross-modality guidance-aided module where the primary modality guides the other secondary modalities during the process of training, which can effectively leverage the complementary information of different MRI modalities and meanwhile alleviate the impact of the possible noise.

Rules are widely used in Fintech institutions to make fraud prevention decisions, since rules are highly interpretable thanks to their intuitive if-then structure. In practice, a two-stage framework of fraud prevention decision rule set mining is usually employed in large Fintech institutions. This paper is concerned with finding high-quality rule subsets in a bi-objective space (such as precision and recall) from an initial pool of rules. To this end, we adopt the concept of Pareto optimality and aim to find a set of non-dominated rule subsets, which constitutes a Pareto front. We propose a heuristic-based framework called PORS and we identify that the core of PORS is the problem of solution selection on the front (SSF). We provide a systematic categorization of the SSF problem and a thorough empirical evaluation of various SSF methods on both public and proprietary datasets. We also introduce a novel variant of sequential covering algorithm called SpectralRules to encourage the diversity of the initial rule set and we empirically find that SpectralRules further improves the quality of the found Pareto front. On two real application scenarios within Alipay, we demonstrate the advantages of our proposed methodology compared to existing work.

Text normalization - the conversion of text from written to spoken form - is traditionally assumed to be an ill-formed task for language models. In this work, we argue otherwise. We empirically show the capacity of Large-Language Models (LLM) for text normalization in few-shot scenarios. Combining self-consistency reasoning with linguistic-informed prompt engineering, we find LLM based text normalization to achieve error rates around 40\% lower than top normalization systems. Further, upon error analysis, we note key limitations in the conventional design of text normalization tasks. We create a new taxonomy of text normalization errors and apply it to results from GPT-3.5-Turbo and GPT-4.0. Through this new framework, we can identify strengths and weaknesses of GPT-based TN, opening opportunities for future work.

Semantic similarity between natural language texts is typically measured either by looking at the overlap between subsequences (e.g., BLEU) or by using embeddings (e.g., BERTScore, S-BERT). Within this paper, we argue that when we are only interested in measuring the semantic similarity, it is better to directly predict the similarity using a fine-tuned model for such a task. Using a fine-tuned model for the Semantic Textual Similarity Benchmark tasks (STS-B) from the GLUE benchmark, we define the STSScore approach and show that the resulting similarity is better aligned with our expectations on a robust semantic similarity measure than other approaches.

The use of artificial intelligence to enable precision medicine and decision support systems through the analysis of pathology images has the potential to revolutionize the diagnosis and treatment of cancer. Such applications will depend on models' abilities to capture the diverse patterns observed in pathology images. To address this challenge, we present Virchow, a foundation model for computational pathology. Using self-supervised learning empowered by the DINOv2 algorithm, Virchow is a vision transformer model with 632 million parameters trained on 1.5 million hematoxylin and eosin stained whole slide images from diverse tissue and specimen types, which is orders of magnitude more data than previous works. The Virchow model enables the development of a pan-cancer detection system with 0.949 overall specimen-level AUC across 17 different cancer types, while also achieving 0.937 AUC on 7 rare cancer types. The Virchow model sets the state-of-the-art on the internal and external image tile level benchmarks and slide level biomarker prediction tasks. The gains in performance highlight the importance of training on massive pathology image datasets, suggesting scaling up the data and network architecture can improve the accuracy for many high-impact computational pathology applications where limited amounts of training data are available.