Daily Papers

Drug mechanism-of-action (MoA) modeling commonly relies on perturbational transcriptomes, but matched microRNA (miRNA) measurements are often unavailable. Inferred regulatory features offer a scalable way to reuse these data. Here, we present MIRCID, a framework comparing gene expression with inferred transcription factor (TF) activity and miRNA expression across pathway classification and similarity-based MoA retrieval. HubmiRNet infers 414 pan-cancer hub miRNAs (HubmiRs) from 977 L1000 landmark genes, achieving a Pearson correlation coefficient of 87.72%; its 1,298-output variant also outperformed SiCmiR on the full-miRNA task (71.21% versus 67.30%). In the evaluated comparisons, miRNA augmentation provided more consistent gains than TF activity. Generic embedding controls showed model-dependent utility, while complementarity analyses identified a distinct, partially linearly recoverable representation that retained gene-derived structure. Illustrative rescue cases linked improved classification to biologically plausible miRNA patterns in samples with weak transcriptional signatures. These findings support inferred HubmiRs as a biologically informed recoding of transcriptomic data for perturbational drug modeling, while leaving recovery of measured perturbational miRNA responses to further validation.

From a falcon detecting prey to humans recognizing faces, many species exhibit extraordinary abilities in rapid visual localization and classification. These are made possible by a specialized retinal region called the fovea, which provides high acuity at the center of vision while maintaining lower resolution in the periphery. This distinctive spatial organization, preserved along the early visual pathway through retinotopic mapping, is fundamental to biological vision, yet remains largely unexplored in machine learning. Our study investigates how incorporating foveated retinotopy may benefit deep convolutional neural networks (CNNs) in image classification tasks. By implementing a foveated retinotopic transformation in the input layer of standard ResNet models and re-training them, we maintain comparable classification accuracy while enhancing the network's robustness to scale and rotational perturbations. Although this architectural modification introduces increased sensitivity to fixation point shifts, we demonstrate how this apparent limitation becomes advantageous: variations in classification probabilities across different gaze positions serve as effective indicators for object localization. Our findings suggest that foveated retinotopic mapping encodes implicit knowledge about visual object geometry, offering an efficient solution to the visual search problem - a capability crucial for many living species.

This paper introduces a novel sector-based methodology for star-galaxy classification, leveraging the latest Sloan Digital Sky Survey data (SDSS-DR18). By strategically segmenting the sky into sectors aligned with SDSS observational patterns and employing a dedicated convolutional neural network (CNN), we achieve state-of-the-art performance for star galaxy classification. Our preliminary results demonstrate a promising pathway for efficient and precise astronomical analysis, especially in real-time observational settings.

Large-scale multi-label text classification assigns a small subset of relevant labels to each document from a vocabulary containing thousands or tens of thousands of candidate labels. Although pretrained language models have improved semantic text representations, most representation-based approaches center their prediction pipelines on a primary encoder or combine auxiliary features within a single ranker. The complementarity between heterogeneous language models therefore remains insufficiently explored. We propose DualMLC, a dual-branch framework that processes the same document through an autoregressive decoder-only language model and a bidirectional encoder. Each branch maintains its own representation pathway and independently estimates relevance scores over the shared label space. DualMLC combines the two score vectors through late logit fusion, allowing shared evidence to reinforce relevant labels and branch-specific evidence to compensate for limitations in the other branch's representation. DualMLC achieves state-of-the-art results on three widely used large-scale multi-label text classification benchmarks. Ablation results further confirm that integrating the heterogeneous predictors produces stronger rankings than either branch alone. The source code is publicly available at https://github.com/huiyegit/DualMLC.

The detection of bias in natural language processing (NLP) is a critical challenge, particularly with the increasing use of large language models (LLMs) in various domains. This paper introduces GUS-Net, an innovative approach to bias detection that focuses on three key types of biases: (G)eneralizations, (U)nfairness, and (S)tereotypes. GUS-Net leverages generative AI and automated agents to create a comprehensive synthetic dataset, enabling robust multi-label token classification. Our methodology enhances traditional bias detection methods by incorporating the contextual encodings of pre-trained models, resulting in improved accuracy and depth in identifying biased entities. Through extensive experiments, we demonstrate that GUS-Net outperforms state-of-the-art techniques, achieving superior performance in terms of accuracy, F1-score, and Hamming Loss. The findings highlight GUS-Net's effectiveness in capturing a wide range of biases across diverse contexts, making it a valuable tool for social bias detection in text. This study contributes to the ongoing efforts in NLP to address implicit bias, providing a pathway for future research and applications in various fields. The Jupyter notebooks used to create the dataset and model are available at: https://github.com/Ethical-Spectacle/fair-ly/tree/main/resources. Warning: This paper contains examples of harmful language, and reader discretion is recommended.

Scientific figures and tables encode essential experimental evidence, yet remain difficult for digital libraries and multimodal AI systems to retrieve and interpret. The ALD/E-ImageMiner benchmark and ICDAR 2026 Competition on Information Extraction from Atomic Layer Deposition/Etching Scientific Figures provide 1,951 figures from 205 publications, expert-annotated for classification, data table extraction, summarization, and visual question answering. In these companion proceedings, we present a forward-looking perspective on how the benchmark can guide future scientific-image challenges. We examine how its tasks probe capabilities from visual and quantitative reading to domain-grounded reasoning and evidential justification, and how Bloom-informed question design can support deeper scientific understanding. We propose "scientific conceptual understanding from images" as a long-term benchmark objective, with future directions including broader domains and figure types, contextual and cross-document synthesis, hypothesis evaluation, provenance, uncertainty, counterfactual grounding, and open-ended multimodal research. This perspective connects the ICDAR 2026 challenge to a broader agenda for machine-actionable scientific visual knowledge and verifiable multimodal scientific AI.

Recent research on time series foundation models has primarily focused on forecasting, leaving it unclear how generalizable their learned representations are. In this study, we examine whether frozen pre-trained forecasting models can provide effective representations for classification. To this end, we compare different representation extraction strategies and introduce two model-agnostic embedding augmentations. Our experiments show that the best forecasting models achieve classification accuracy that matches or even surpasses that of state-of-the-art models pre-trained specifically for classification. Moreover, we observe a positive correlation between forecasting and classification performance. These findings challenge the assumption that task-specific pre-training is necessary, and suggest that learning to forecast may provide a powerful route toward constructing general-purpose time series foundation models.

While deep learning has achieved remarkable success across many domains, it has historically underperformed on tabular learning tasks, which remain dominated by gradient boosting decision trees (GBDTs). However, recent advancements are paving the way for Tabular Foundation Models, which can leverage real-world knowledge and generalize across diverse datasets, particularly when the data contains free-text. Although incorporating language model capabilities into tabular tasks has been explored, most existing methods utilize static, target-agnostic textual representations, limiting their effectiveness. We introduce TabSTAR: a Foundation Tabular Model with Semantically Target-Aware Representations. TabSTAR is designed to enable transfer learning on tabular data with textual features, with an architecture free of dataset-specific parameters. It unfreezes a pretrained text encoder and takes as input target tokens, which provide the model with the context needed to learn task-specific embeddings. TabSTAR achieves state-of-the-art performance for both medium- and large-sized datasets across known benchmarks of classification tasks with text features, and its pretraining phase exhibits scaling laws in the number of datasets, offering a pathway for further performance improvements.

Biologically-informed neural networks typically leverage pathway annotations to enhance performance in biomedical applications. We hypothesized that the benefits of pathway integration does not arise from its biological relevance, but rather from the sparsity it introduces. We conducted a comprehensive analysis of all relevant pathway-based neural network models for predictive tasks, critically evaluating each study's contributions. From this review, we curated a subset of methods for which the source code was publicly available. The comparison of the biologically informed state-of-the-art deep learning models and their randomized counterparts showed that models based on randomized information performed equally well as biologically informed ones across different metrics and datasets. Notably, in 3 out of the 15 analyzed models, the randomized versions even outperformed their biologically informed counterparts. Moreover, pathway-informed models did not show any clear advantage in interpretability, as randomized models were still able to identify relevant disease biomarkers despite lacking explicit pathway information. Our findings suggest that pathway annotations may be too noisy or inadequately explored by current methods. Therefore, we propose a methodology that can be applied to different domains and can serve as a robust benchmark for systematically comparing novel pathway-informed models against their randomized counterparts. This approach enables researchers to rigorously determine whether observed performance improvements can be attributed to biological insights.

Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

Machine learning classification problems are widespread in bioinformatics, but the technical knowledge required to perform model training, optimization, and inference can prevent researchers from utilizing this technology. This article presents an automated tool for machine learning classification problems to simplify the process of training models and producing results while providing informative visualizations and insights into the data. This tool supports both binary and multiclass classification problems, and it provides access to a variety of models and methods. Synthetic data can be generated within the interface to fill missing values, balance class labels, or generate entirely new datasets. It also provides support for feature evaluation and generates explainability scores to indicate which features influence the output the most. We present CLASSify, an open-source tool for simplifying the user experience of solving classification problems without the need for knowledge of machine learning.

E-commerce platforms categorize their products into a multi-level taxonomy tree with thousands of leaf categories. Conventional methods for product categorization are typically based on machine learning classification algorithms. These algorithms take product information as input (e.g., titles and descriptions) to classify a product into a leaf category. In this paper, we propose a new paradigm based on machine translation. In our approach, we translate a product's natural language description into a sequence of tokens representing a root-to-leaf path in a product taxonomy. In our experiments on two large real-world datasets, we show that our approach achieves better predictive accuracy than a state-of-the-art classification system for product categorization. In addition, we demonstrate that our machine translation models can propose meaningful new paths between previously unconnected nodes in a taxonomy tree, thereby transforming the taxonomy into a directed acyclic graph (DAG). We discuss how the resultant taxonomy DAG promotes user-friendly navigation, and how it is more adaptable to new products.

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of the fusion. On the histopathology side, K learnable morphological prototypes, trained end-to-end with the survival objective, serve as the slide representation itself: patches flow into prototype tokens via soft assignment, compressing variable-length patch sets into fixed task-adaptive tokens. On the genomic side, a bipartite graph neural network encodes gene expression within the Reactome pathway hierarchy, producing pathway embeddings that reflect both constituent genes and their broader biological context through bidirectional message passing over a shared gene--pathway graph. Cross-modal attention then operates over a compact prototype times pathway matrix in which prototypes query pathways, modeling the biological direction in which molecular programs give rise to tissue morphology. Because both axes carry stable task-learned identity, the attention matrix is itself an interpretability output, yielding native inference-time attribution across the full biological hierarchy, from genes through pathways and prototypes to spatial tissue maps. We evaluate on five TCGA cancer cohorts, demonstrating competitive or superior survival prediction with substantially improved biological interpretability and reduced computational cost, with interpretability claims validated through fold-stratified rank-based population-level analysis. Our source code, model weights, and Reactome pathways, together with a unified codebase reimplementing all multimodal survival baselines under identical preprocessing and evaluation, are available at: https://github.com/AmayaGS/ProtoPathway.

Scientific progress depends on sequences of enabling contributions, yet existing AI4Science benchmarks largely focus on citation prediction, literature retrieval, or idea generation rather than the dependencies that make progress possible. In this paper, we introduce discovery pathway forecasting: given a target scientific contribution and the prior literature available at a specified time, the task is to (1) identify the enabling contributions required to realize it and (2) ground each in prior work when such prior work exists. We present SciPaths, a benchmark of 262 expert-annotated gold pathways and 2,444 silver pathways constructed from machine learning and natural language processing papers, where each pathway records enabling contributions, roles, rationales, and prior-work groundings or unmapped decisions. Evaluating frontier and open-weight language models, we find that the best model reaches only 0.189 F1 under strict semantic matching, with core methodological dependencies hardest to recover. Prior-work grounding improves substantially when gold enabling contributions are provided, showing that decomposition quality is a major bottleneck for end-to-end pathway recovery. SciPaths therefore shifts evaluation toward a missing capability in scientific forecasting: reasoning backward from a target contribution to the enabling scientific building blocks and prior-work dependencies that make it feasible.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

Subject classification schemes are foundational to the organization, evaluation, and navigation of scientific knowledge. While expert-curated systems like Scopus provide widely used taxonomies, they often suffer from coarse granularity, subjectivity, and limited adaptability to emerging interdisciplinary fields. Data-driven alternatives based on citation networks show promise but lack rigorous, external validation against the semantic content of scientific literature. Here, we propose a novel quantitative framework that leverages classification tasks to evaluate the effectiveness of journal classification schemes. Using over 23 million paper abstracts, we demonstrate that labels derived from k-means clustering on Periodical2Vec (P2V)--a periodical embedding learned from paper-level citations--yield significantly higher classification performance than both Scopus and other data-driven baselines (e.g., citation, co-citation, and Node2Vec variants). By comparing journal partitions across classification schemes, two structural patterns emerge on the map of science: (1) the reorganization of disciplinary boundaries--splitting overly broad categories (e.g., "Medicine" into "Oncology", "Cardiology", and other specialties) while merging artificially fragmented ones (e.g., "Chemistry" and "Chemical Engineering"); and (2) the identification of coherent interdisciplinary clusters--such as "Biomedical Engineering", "Medical Ethics", and "Information Management"--that are dispersed across multiple categories but unified in citation space. These findings underscore that citation-derived periodical embeddings not only outperform traditional taxonomies in predictive validity but also offer a dynamic, fine-grained map of science that better reflects both the specialization and interdisciplinarity inherent in contemporary research.

Convolutional Neural Networks (CNNs) have exhibited great performance in discriminative feature learning for complex visual tasks. Besides discrimination power, interpretability is another important yet under-explored property for CNNs. One difficulty in the CNN interpretability is that filters and image classes are entangled. In this paper, we introduce a novel pathway to alleviate the entanglement between filters and image classes. The proposed pathway groups the filters in a late conv-layer of CNN into class-specific clusters. Clusters and classes are in a one-to-one relationship. Specifically, we use the Bernoulli sampling to generate the filter-cluster assignment matrix from a learnable filter-class correspondence matrix. To enable end-to-end optimization, we develop a novel reparameterization trick for handling the non-differentiable Bernoulli sampling. We evaluate the effectiveness of our method on ten widely used network architectures (including nine CNNs and a ViT) and five benchmark datasets. Experimental results have demonstrated that our method PICNN (the combination of standard CNNs with our proposed pathway) exhibits greater interpretability than standard CNNs while achieving higher or comparable discrimination power.

Link prediction is a very fundamental task on graphs. Inspired by traditional path-based methods, in this paper we propose a general and flexible representation learning framework based on paths for link prediction. Specifically, we define the representation of a pair of nodes as the generalized sum of all path representations, with each path representation as the generalized product of the edge representations in the path. Motivated by the Bellman-Ford algorithm for solving the shortest path problem, we show that the proposed path formulation can be efficiently solved by the generalized Bellman-Ford algorithm. To further improve the capacity of the path formulation, we propose the Neural Bellman-Ford Network (NBFNet), a general graph neural network framework that solves the path formulation with learned operators in the generalized Bellman-Ford algorithm. The NBFNet parameterizes the generalized Bellman-Ford algorithm with 3 neural components, namely INDICATOR, MESSAGE and AGGREGATE functions, which corresponds to the boundary condition, multiplication operator, and summation operator respectively. The NBFNet is very general, covers many traditional path-based methods, and can be applied to both homogeneous graphs and multi-relational graphs (e.g., knowledge graphs) in both transductive and inductive settings. Experiments on both homogeneous graphs and knowledge graphs show that the proposed NBFNet outperforms existing methods by a large margin in both transductive and inductive settings, achieving new state-of-the-art results.

Pancreatic cancer is one of the leading causes of cancer-related death. Accurate detection, segmentation, and differential diagnosis of the full taxonomy of pancreatic lesions, i.e., normal, seven major types of lesions, and other lesions, is critical to aid the clinical decision-making of patient management and treatment. However, existing works focus on segmentation and classification for very specific lesion types (PDAC) or groups. Moreover, none of the previous work considers using lesion prevalence-related non-imaging patient information to assist the differential diagnosis. To this end, we develop a meta-information-aware dual-path transformer and exploit the feasibility of classification and segmentation of the full taxonomy of pancreatic lesions. Specifically, the proposed method consists of a CNN-based segmentation path (S-path) and a transformer-based classification path (C-path). The S-path focuses on initial feature extraction by semantic segmentation using a UNet-based network. The C-path utilizes both the extracted features and meta-information for patient-level classification based on stacks of dual-path transformer blocks that enhance the modeling of global contextual information. A large-scale multi-phase CT dataset of 3,096 patients with pathology-confirmed pancreatic lesion class labels, voxel-wise manual annotations of lesions from radiologists, and patient meta-information, was collected for training and evaluations. Our results show that our method can enable accurate classification and segmentation of the full taxonomy of pancreatic lesions, approaching the accuracy of the radiologist's report and significantly outperforming previous baselines. Results also show that adding the common meta-information, i.e., gender and age, can boost the model's performance, thus demonstrating the importance of meta-information for aiding pancreatic disease diagnosis.

We consider the hierarchical representation of documents as graphs and use geometric deep learning to classify them into different categories. While graph neural networks can efficiently handle the variable structure of hierarchical documents using the permutation invariant message passing operations, we show that we can gain extra performance improvements using our proposed selective graph pooling operation that arises from the fact that some parts of the hierarchy are invariable across different documents. We applied our model to classify clinical trial (CT) protocols into completed and terminated categories. We use bag-of-words based, as well as pre-trained transformer-based embeddings to featurize the graph nodes, achieving f1-scores around 0.85 on a publicly available large scale CT registry of around 360K protocols. We further demonstrate how the selective pooling can add insights into the CT termination status prediction. We make the source code and dataset splits accessible.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

Hierarchical Text Classification (HTC) is a natural language processing task with the objective to classify text documents into a set of classes from a structured class hierarchy. Many HTC approaches have been proposed which attempt to leverage the class hierarchy information in various ways to improve classification performance. Machine learning-based classification approaches require large amounts of training data and are most-commonly compared through three established benchmark datasets, which include the Web Of Science (WOS), Reuters Corpus Volume 1 Version 2 (RCV1-V2) and New York Times (NYT) datasets. However, apart from the RCV1-V2 dataset which is well-documented, these datasets are not accompanied with detailed description methodologies. In this paper, we introduce three new HTC benchmark datasets in the domain of research publications which comprise the titles and abstracts of papers from the Web of Science publication database. We first create two baseline datasets which use existing journal-and citation-based classification schemas. Due to the respective shortcomings of these two existing schemas, we propose an approach which combines their classifications to improve the reliability and robustness of the dataset. We evaluate the three created datasets with a clustering-based analysis and show that our proposed approach results in a higher quality dataset where documents that belong to the same class are semantically more similar compared to the other datasets. Finally, we provide the classification performance of four state-of-the-art HTC approaches on these three new datasets to provide baselines for future studies on machine learning-based techniques for scientific publication classification.

Automated classification of metadata of research data by their discipline(s) of research can be used in scientometric research, by repository service providers, and in the context of research data aggregation services. Openly available metadata of the DataCite index for research data were used to compile a large training and evaluation set comprised of 609,524 records, which is published alongside this paper. These data allow to reproducibly assess classification approaches, such as tree-based models and neural networks. According to our experiments with 20 base classes (multi-label classification), multi-layer perceptron models perform best with a f1-macro score of 0.760 closely followed by Long Short-Term Memory models (f1-macro score of 0.755). A possible application of the trained classification models is the quantitative analysis of trends towards interdisciplinarity of digital scholarly output or the characterization of growth patterns of research data, stratified by discipline of research. Both applications perform at scale with the proposed models which are available for re-use.

Identifying travelers' transportation modes is important in transportation science and location-based services. It's appealing for researchers to leverage GPS trajectory data to infer transportation modes with the popularity of GPS-enabled devices, e.g., smart phones. Existing studies frame this problem as classification task. The dominant two-stage studies divide the trip into single-one mode segments first and then categorize these segments. The over segmentation strategy and inevitable error propagation bring difficulties to classification stage and make optimizing the whole system hard. The recent one-stage works throw out trajectory segmentation entirely to avoid these by directly conducting point-wise classification for the trip, whereas leaving predictions dis-continuous. To solve above-mentioned problems, inspired by YOLO and SSD in object detection, we propose to reframe change point detection and segment classification as a unified regression task instead of the existing classification task. We directly regress coordinates of change points and classify associated segments. In this way, our method divides the trip into segments under a supervised manner and leverage more contextual information, obtaining predictions with high accuracy and continuity. Two frameworks, TrajYOLO and TrajSSD, are proposed to solve the regression task and various feature extraction backbones are exploited. Exhaustive experiments on GeoLife dataset show that the proposed method has competitive overall identification accuracy of 0.853 when distinguishing five modes: walk, bike, bus, car, train. As for change point detection, our method increases precision at the cost of drop in recall. All codes are available at https://github.com/RadetzkyLi/TrajYOLO-SSD.

Graph neural networks (GNNs) have recently become the standard approach for learning with graph-structured data. Prior work has shed light into their potential, but also their limitations. Unfortunately, it was shown that standard GNNs are limited in their expressive power. These models are no more powerful than the 1-dimensional Weisfeiler-Leman (1-WL) algorithm in terms of distinguishing non-isomorphic graphs. In this paper, we propose Path Neural Networks (PathNNs), a model that updates node representations by aggregating paths emanating from nodes. We derive three different variants of the PathNN model that aggregate single shortest paths, all shortest paths and all simple paths of length up to K. We prove that two of these variants are strictly more powerful than the 1-WL algorithm, and we experimentally validate our theoretical results. We find that PathNNs can distinguish pairs of non-isomorphic graphs that are indistinguishable by 1-WL, while our most expressive PathNN variant can even distinguish between 3-WL indistinguishable graphs. The different PathNN variants are also evaluated on graph classification and graph regression datasets, where in most cases, they outperform the baseline methods.

Training machine learning models in a meaningful order, from the easy samples to the hard ones, using curriculum learning can provide performance improvements over the standard training approach based on random data shuffling, without any additional computational costs. Curriculum learning strategies have been successfully employed in all areas of machine learning, in a wide range of tasks. However, the necessity of finding a way to rank the samples from easy to hard, as well as the right pacing function for introducing more difficult data can limit the usage of the curriculum approaches. In this survey, we show how these limits have been tackled in the literature, and we present different curriculum learning instantiations for various tasks in machine learning. We construct a multi-perspective taxonomy of curriculum learning approaches by hand, considering various classification criteria. We further build a hierarchical tree of curriculum learning methods using an agglomerative clustering algorithm, linking the discovered clusters with our taxonomy. At the end, we provide some interesting directions for future work.

Metabolomics knowledge is distributed across heterogeneous resources and remains difficult to translate into predictive representations. We developed MetaboLLM, a metabolomics-specialized large language model adapted through continual pretraining, supervised fine-tuning, and structured retrieval, together with MetaboLLM-GIN, which converts generated biochemical descriptions into metabolite graphs for patient-level prediction using a graph isomorphism network. Across four backbone families, MetaboLLM outperformed corresponding base and medically adapted models on metabolomics knowledge, relational, and description tasks, and transferred to an external public benchmark. MetaboLLM-GIN achieved the highest AUC for stress hyperglycemia prediction after coronary artery bypass grafting (0.8616) and postmenopausal hormone-regimen classification (0.8123), outperforming conventional models, alternative graph constructions, and graphs generated from unadapted or non-retrieval LLM configurations. Model interpretation further produced biologically meaningful findings in both applications. These results show that domain-specialized language models can organize heterogeneous biochemical knowledge into predictive and interpretable metabolite graph representations.

We propose to improve transformers of a specific modality with irrelevant data from other modalities, e.g., improve an ImageNet model with audio or point cloud datasets. We would like to highlight that the data samples of the target modality are irrelevant to the other modalities, which distinguishes our method from other works utilizing paired (e.g., CLIP) or interleaved data of different modalities. We propose a methodology named Multimodal Pathway - given a target modality and a transformer designed for it, we use an auxiliary transformer trained with data of another modality and construct pathways to connect components of the two models so that data of the target modality can be processed by both models. In this way, we utilize the universal sequence-to-sequence modeling abilities of transformers obtained from two modalities. As a concrete implementation, we use a modality-specific tokenizer and task-specific head as usual but utilize the transformer blocks of the auxiliary model via a proposed method named Cross-Modal Re-parameterization, which exploits the auxiliary weights without any inference costs. On the image, point cloud, video, and audio recognition tasks, we observe significant and consistent performance improvements with irrelevant data from other modalities. The code and models are available at https://github.com/AILab-CVC/M2PT.

Predicting spatial gene expression from H&E histology offers a scalable and clinically accessible alternative to sequencing, but realizing clinical impact requires models that generalize across cancer types and capture biologically coherent signals. Prior work is often limited to per-cancer settings and variance-based evaluation, leaving functional relevance underexplored. We introduce HistoPrism, an efficient transformer-based architecture for pan-cancer prediction of gene expression from histology. To evaluate biological meaning, we introduce a pathway-level benchmark, shifting assessment from isolated gene-level variance to coherent functional pathways. HistoPrism not only surpasses prior state-of-the-art models on highly variable genes , but also more importantly, achieves substantial gains on pathway-level prediction, demonstrating its ability to recover biologically coherent transcriptomic patterns. With strong pan-cancer generalization and improved efficiency, HistoPrism establishes a new standard for clinically relevant transcriptomic modeling from routinely available histology.

Large language model (LLM) routers improve the efficiency of multi-model systems by directing each query to the most appropriate model while leveraging the diverse strengths of heterogeneous LLMs. Most existing approaches frame routing as a classification problem based solely on the input query. While this reduces overhead by avoiding inference across all models, it overlooks valuable information that could be gleaned from potential outputs and fails to capture implicit intent or contextual nuances that often emerge only during response generation. These limitations can result in suboptimal routing decisions, particularly for complex or ambiguous queries that require deeper semantic understanding. To address this challenge, we propose Lookahead, a routing framework that "foresees" potential model outputs by predicting their latent representations and uses these predictions to guide model selection, thus enabling more informed routing without full inference. Within this framework, we implement two approaches based on causal and masked language models. Empirical evaluations across seven public benchmarks - spanning instruction following, mathematical reasoning, and code generation - show that Lookahead consistently outperforms existing routing baselines, achieving an average performance gain of 7.7% over the state-of-the-art. Our code is available at https://github.com/huangcb01/lookahead-routing.

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

Neural message passing algorithms for semi-supervised classification on graphs have recently achieved great success. However, for classifying a node these methods only consider nodes that are a few propagation steps away and the size of this utilized neighborhood is hard to extend. In this paper, we use the relationship between graph convolutional networks (GCN) and PageRank to derive an improved propagation scheme based on personalized PageRank. We utilize this propagation procedure to construct a simple model, personalized propagation of neural predictions (PPNP), and its fast approximation, APPNP. Our model's training time is on par or faster and its number of parameters on par or lower than previous models. It leverages a large, adjustable neighborhood for classification and can be easily combined with any neural network. We show that this model outperforms several recently proposed methods for semi-supervised classification in the most thorough study done so far for GCN-like models. Our implementation is available online.

The continual growth of high speed networks is a challenge for real-time network analysis systems. The real time traffic classification is an issue for corporations and ISPs (Internet Service Providers). This work presents the design and implementation of a real time flow-based network traffic classification system. The classifier monitor acts as a pipeline consisting of three modules: packet capture and pre-processing, flow reassembly, and classification with Machine Learning (ML). The modules are built as concurrent processes with well defined data interfaces between them so that any module can be improved and updated independently. In this pipeline, the flow reassembly function becomes the bottleneck of the performance. In this implementation, was used a efficient method of reassembly which results in a average delivery delay of 0.49 seconds, approximately. For the classification module, the performances of the K-Nearest Neighbor (KNN), C4.5 Decision Tree, Naive Bayes (NB), Flexible Naive Bayes (FNB) and AdaBoost Ensemble Learning Algorithm are compared in order to validate our approach.

We present the design and implementation of a custom discrete optimization technique for building rule lists over a categorical feature space. Our algorithm produces rule lists with optimal training performance, according to the regularized empirical risk, with a certificate of optimality. By leveraging algorithmic bounds, efficient data structures, and computational reuse, we achieve several orders of magnitude speedup in time and a massive reduction of memory consumption. We demonstrate that our approach produces optimal rule lists on practical problems in seconds. Our results indicate that it is possible to construct optimal sparse rule lists that are approximately as accurate as the COMPAS proprietary risk prediction tool on data from Broward County, Florida, but that are completely interpretable. This framework is a novel alternative to CART and other decision tree methods for interpretable modeling.

There is a rapidly growing number of open-source Large Language Models (LLMs) and benchmark datasets to compare them. While some models dominate these benchmarks, no single model typically achieves the best accuracy in all tasks and use cases. In this work, we address the challenge of selecting the best LLM out of a collection of models for new tasks. We propose a new formulation for the problem, in which benchmark datasets are repurposed to learn a "router" model for this LLM selection, and we show that this problem can be reduced to a collection of binary classification tasks. We demonstrate the utility and limitations of learning model routers from various benchmark datasets, where we consistently improve performance upon using any single model for all tasks.

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives. The data and code are available here: https://github.com/azminewasi/Drug-Classification-NLP.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

To improve the prognosis of patients suffering from pulmonary diseases, such as lung cancer, early diagnosis and treatment are crucial. The analysis of CT images is invaluable for diagnosis, whereas high quality segmentation of the airway tree are required for intervention planning and live guidance during bronchoscopy. Recently, the Multi-domain Airway Tree Modeling (ATM'22) challenge released a large dataset, both enabling training of deep-learning based models and bringing substantial improvement of the state-of-the-art for the airway segmentation task. However, the ATM'22 dataset includes few patients with severe pathologies affecting the airway tree anatomy. In this study, we introduce a new public benchmark dataset (AeroPath), consisting of 27 CT images from patients with pathologies ranging from emphysema to large tumors, with corresponding trachea and bronchi annotations. Second, we present a multiscale fusion design for automatic airway segmentation. Models were trained on the ATM'22 dataset, tested on the AeroPath dataset, and further evaluated against competitive open-source methods. The same performance metrics as used in the ATM'22 challenge were used to benchmark the different considered approaches. Lastly, an open web application is developed, to easily test the proposed model on new data. The results demonstrated that our proposed architecture predicted topologically correct segmentations for all the patients included in the AeroPath dataset. The proposed method is robust and able to handle various anomalies, down to at least the fifth airway generation. In addition, the AeroPath dataset, featuring patients with challenging pathologies, will contribute to development of new state-of-the-art methods. The AeroPath dataset and the web application are made openly available.

Precision oncology requires accurate molecular insights, yet obtaining these directly from genomics is costly and time-consuming for broad clinical use. Predicting complex molecular features and patient prognosis directly from routine whole-slide images (WSI) remains a major challenge for current deep learning methods. Here we introduce PathLUPI, which uses transcriptomic privileged information during training to extract genome-anchored histological embeddings, enabling effective molecular prediction using only WSIs at inference. Through extensive evaluation across 49 molecular oncology tasks using 11,257 cases among 20 cohorts, PathLUPI demonstrated superior performance compared to conventional methods trained solely on WSIs. Crucially, it achieves AUC geq 0.80 in 14 of the biomarker prediction and molecular subtyping tasks and C-index geq 0.70 in survival cohorts of 5 major cancer types. Moreover, PathLUPI embeddings reveal distinct cellular morphological signatures associated with specific genotypes and related biological pathways within WSIs. By effectively encoding molecular context to refine WSI representations, PathLUPI overcomes a key limitation of existing models and offers a novel strategy to bridge molecular insights with routine pathology workflows for wider clinical application.

Large language models' significant advances in capabilities are accompanied by significant increases in inference costs. Model routing is a simple technique for reducing inference cost, wherein one maintains a pool of candidate LLMs, and learns to route each prompt to the smallest feasible LLM. Existing works focus on learning a router for a fixed pool of LLMs. In this paper, we consider the problem of dynamic routing, where new, previously unobserved LLMs are available at test time. We propose a new approach to this problem that relies on representing each LLM as a feature vector, derived based on predictions on a set of representative prompts. Based on this, we detail two effective strategies, relying on cluster-based routing and a learned cluster map respectively. We prove that these strategies are estimates of a theoretically optimal routing rule, and provide an excess risk bound to quantify their errors. Experiments on a range of public benchmarks show the effectiveness of the proposed strategies in routing amongst more than 30 unseen LLMs.

We introduce Llama Guard, an LLM-based input-output safeguard model geared towards Human-AI conversation use cases. Our model incorporates a safety risk taxonomy, a valuable tool for categorizing a specific set of safety risks found in LLM prompts (i.e., prompt classification). This taxonomy is also instrumental in classifying the responses generated by LLMs to these prompts, a process we refer to as response classification. For the purpose of both prompt and response classification, we have meticulously gathered a dataset of high quality. Llama Guard, a Llama2-7b model that is instruction-tuned on our collected dataset, albeit low in volume, demonstrates strong performance on existing benchmarks such as the OpenAI Moderation Evaluation dataset and ToxicChat, where its performance matches or exceeds that of currently available content moderation tools. Llama Guard functions as a language model, carrying out multi-class classification and generating binary decision scores. Furthermore, the instruction fine-tuning of Llama Guard allows for the customization of tasks and the adaptation of output formats. This feature enhances the model's capabilities, such as enabling the adjustment of taxonomy categories to align with specific use cases, and facilitating zero-shot or few-shot prompting with diverse taxonomies at the input. We are making Llama Guard model weights available and we encourage researchers to further develop and adapt them to meet the evolving needs of the community for AI safety.

Prompt routing dynamically selects the most appropriate large language model from a pool of candidates for each query, optimizing performance while managing costs. As model pools scale to include dozens of frontier models with narrow performance gaps, existing approaches face significant challenges: manually defined task taxonomies cannot capture fine-grained capability distinctions, while monolithic routers struggle to differentiate subtle differences across diverse tasks. We propose a two-stage routing architecture that addresses these limitations through automated fine-grained task discovery and task-aware quality estimation. Our first stage employs graph-based clustering to discover latent task types and trains a classifier to assign prompts to discovered tasks. The second stage uses a mixture-of-experts architecture with task-specific prediction heads for specialized quality estimates. At inference, we aggregate predictions from both stages to balance task-level stability with prompt-specific adaptability. Evaluated on 10 benchmarks with 11 frontier models, our method consistently outperforms existing baselines and surpasses the strongest individual model while incurring less than half its cost.

Motivation: Phenotype concept recognition (CR) is a fundamental task in biomedical text mining. However, existing methods either require ontology-specific training, making them struggle to generalize across diverse text styles and evolving biomedical terminology, or depend on general-purpose large language models (LLMs) that lack necessary domain knowledge. Results: To address these limitations, we propose AutoPCR, a prompt-based phenotype CR method designed to automatically generalize to new ontologies and unseen data without ontology-specific training. To further boost performance, we also introduce an optional self-supervised training strategy. Experiments show that AutoPCR achieves the best average and most robust performance across datasets. Further ablation and transfer studies demonstrate its inductive capability and generalizability to new ontologies. Availability and Implementation: Our code is available at https://github.com/yctao7/AutoPCR. Contact: drjieliu@umich.edu

We propose a filtering feature selection framework that considers subsets of features as paths in a graph, where a node is a feature and an edge indicates pairwise (customizable) relations among features, dealing with relevance and redundancy principles. By two different interpretations (exploiting properties of power series of matrices and relying on Markov chains fundamentals) we can evaluate the values of paths (i.e., feature subsets) of arbitrary lengths, eventually go to infinite, from which we dub our framework Infinite Feature Selection (Inf-FS). Going to infinite allows to constrain the computational complexity of the selection process, and to rank the features in an elegant way, that is, considering the value of any path (subset) containing a particular feature. We also propose a simple unsupervised strategy to cut the ranking, so providing the subset of features to keep. In the experiments, we analyze diverse settings with heterogeneous features, for a total of 11 benchmarks, comparing against 18 widely-known comparative approaches. The results show that Inf-FS behaves better in almost any situation, that is, when the number of features to keep are fixed a priori, or when the decision of the subset cardinality is part of the process.

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

Path-finding over knowledge graphs has become an effective way to ground LLM reasoning on multi-hop questions. However, biomedical QA introduces two distinct challenges that general-domain methods are not designed for: (i) queries do not expose intermediate reasoning and can be answered through multiple valid pathways, and (ii) biomedical knowledge graphs are densely connected, so path-finding methods easily take wrong turns. To address these challenges, we propose AdaPath, a path-finding framework that retrieves query-adaptive meta-paths from Path-Bank, which captures both query semantics and biomedical knowledge graph structure. AdaPath provides the missing cues in biomedical queries while effectively pruning dense knowledge graph neighborhoods during multi-hop reasoning. We further release BioStrat-QA, a biomedical KGQA benchmark that stratifies multi-hop queries by how much intermediate reasoning they expose. Across biomedical KGQA benchmarks, AdaPath consistently outperforms baselines, sustaining meaningful path-finding even when multi-hop queries expose less surface information. The source code is available at https://github.com/Jun-Hyeong-Kim/AdaPath.

In this paper, we discuss a different type of semi-supervised setting: a coarse level of labeling is available for all observations but the model has to learn a fine level of latent annotation for each one of them. Problems in this setting are likely to be encountered in many domains such as text categorization, protein function prediction, image classification as well as in exploratory scientific studies such as medical and genomics research. We consider this setting as simultaneously performed supervised classification (per the available coarse labels) and unsupervised clustering (within each one of the coarse labels) and propose a novel output layer modification called auto-clustering output layer (ACOL) that allows concurrent classification and clustering based on Graph-based Activity Regularization (GAR) technique. As the proposed output layer modification duplicates the softmax nodes at the output layer for each class, GAR allows for competitive learning between these duplicates on a traditional error-correction learning framework to ultimately enable a neural network to learn the latent annotations in this partially supervised setup. We demonstrate how the coarse label supervision impacts performance and helps propagate useful clustering information between sub-classes. Comparative tests on three of the most popular image datasets MNIST, SVHN and CIFAR-100 rigorously demonstrate the effectiveness and competitiveness of the proposed approach.

For many segmentation tasks, especially for the biomedical image, the topological prior is vital information which is useful to exploit. The containment/nesting is a typical inter-class geometric relationship. In the MICCAI Brain tumor segmentation challenge, with its three hierarchically nested classes 'whole tumor', 'tumor core', 'active tumor', the nested classes relationship is introduced into the 3D-residual-Unet architecture. The network comprises a context aggregation pathway and a localization pathway, which encodes increasingly abstract representation of the input as going deeper into the network, and then recombines these representations with shallower features to precisely localize the interest domain via a localization path. The nested-class-prior is combined by proposing the multi-class activation function and its corresponding loss function. The model is trained on the training dataset of Brats2018, and 20% of the dataset is regarded as the validation dataset to determine parameters. When the parameters are fixed, we retrain the model on the whole training dataset. The performance achieved on the validation leaderboard is 86%, 77% and 72% Dice scores for the whole tumor, enhancing tumor and tumor core classes without relying on ensembles or complicated post-processing steps. Based on the same start-of-the-art network architecture, the accuracy of nested-class (enhancing tumor) is reasonably improved from 69% to 72% compared with the traditional Softmax-based method which blind to topological prior.

Over the years, network traffic analysis and generation have advanced significantly. From traditional statistical methods, the field has progressed to sophisticated deep learning techniques. This progress has improved the ability to detect complex patterns and security threats, as well as to test and optimize network performance. However, obstacles persist, such as the dependence on labeled data for analysis and the difficulty of generating traffic samples that follow realistic patterns. Pre-trained deep neural networks have emerged as powerful tools to resolve these issues, offering improved performance by learning robust data representations from large unlabeled datasets. Despite their benefits, existing pre-trained models face challenges like token length limitation, which restricts their usefulness in comprehensive traffic analysis and realistic traffic generation. To address these challenges, we introduce TrafficGPT, a deep learning model that can tackle complex challenges related to long flow classification and generation tasks. This model uses generative pre-training with the linear attention mechanism, which allows for a substantially increased capacity of up to 12,032 tokens from the previous limit of only 512 tokens. TrafficGPT demonstrates superior performance in classification tasks, reaching state-of-the-art levels. In generation tasks, it closely resembles real traffic flows, with low JS divergence and an F1 score close to 0.5 (representing a random guess) in discriminating generated data. These advancements hold promise for future applications in both traffic flow classification and generation tasks.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

Many court systems are overwhelmed all over the world, leading to huge backlogs of pending cases. Effective triage systems, like those in emergency rooms, could ensure proper prioritization of open cases, optimizing time and resource allocation in the court system. In this work, we introduce the Criticality Prediction dataset, a novel resource for evaluating case prioritization. Our dataset features a two-tier labeling system: (1) the binary LD-Label, identifying cases published as Leading Decisions (LD), and (2) the more granular Citation-Label, ranking cases by their citation frequency and recency, allowing for a more nuanced evaluation. Unlike existing approaches that rely on resource-intensive manual annotations, we algorithmically derive labels leading to a much larger dataset than otherwise possible. We evaluate several multilingual models, including both smaller fine-tuned models and large language models in a zero-shot setting. Our results show that the fine-tuned models consistently outperform their larger counterparts, thanks to our large training set. Our results highlight that for highly domain-specific tasks like ours, large training sets are still valuable.

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

Classification is one of the most widespread tasks in AI applications, serving often as the first step in filtering, sorting, and categorizing data. Since modern AI systems must handle large volumes of input data and early pipeline stages can propagate errors downstream, achieving high efficiency and accuracy is critical. Moreover, classification requirements can change dynamically based on user needs, necessitating models with strong zero-shot capabilities. While generative LLMs have become mainstream for zero-shot classification due to their versatility, they suffer from inconsistent instruction following and computational inefficiency. Cross-encoders, commonly used as rerankers in RAG pipelines, face a different bottleneck: they must process text-label pairs sequentially, significantly reducing efficiency with large label sets. Embedding-based approaches offer good efficiency but struggle with complex scenarios involving logical and semantic constraints. We propose GLiClass, a novel method that adapts the GLiNER architecture for sequence classification tasks. Our approach achieves strong accuracy and efficiency comparable to embedding-based methods, while maintaining the flexibility needed for zero-shot and few-shot learning scenarios. Additionally, we adapted proximal policy optimization (PPO) for multi-label text classification, enabling training classifiers in data-sparse conditions or from human feedback.

The National Comprehensive Cancer Network (NCCN) provides evidence-based guidelines for cancer treatment. Translating complex patient presentations into guideline-compliant treatment recommendations is time-intensive, requires specialized expertise, and is prone to error. Advances in large language model (LLM) capabilities promise to reduce the time required to generate treatment recommendations and improve accuracy. We present an LLM agent-based approach to automatically generate guideline-concordant treatment trajectories for patients with non-small cell lung cancer (NSCLC). Our contributions are threefold. First, we construct a novel longitudinal dataset of 121 cases of NSCLC patients that includes clinical encounters, diagnostic results, and medical histories, each expertly annotated with the corresponding NCCN guideline trajectories by board-certified oncologists. Second, we demonstrate that existing LLMs possess domain-specific knowledge that enables high-quality proxy benchmark generation for both model development and evaluation, achieving strong correlation (Spearman coefficient r=0.88, RMSE = 0.08) with expert-annotated benchmarks. Third, we develop a hybrid approach combining expensive human annotations with model consistency information to create both the agent framework that predicts the relevant guidelines for a patient, as well as a meta-classifier that verifies prediction accuracy with calibrated confidence scores for treatment recommendations (AUROC=0.800), a critical capability for communicating the accuracy of outputs, custom-tailoring tradeoffs in performance, and supporting regulatory compliance. This work establishes a framework for clinically viable LLM-based guideline adherence systems that balance accuracy, interpretability, and regulatory requirements while reducing annotation costs, providing a scalable pathway toward automated clinical decision support.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

With the rise of the Internet, there is a growing need to build intelligent systems that are capable of efficiently dealing with early risk detection (ERD) problems on social media, such as early depression detection, early rumor detection or identification of sexual predators. These systems, nowadays mostly based on machine learning techniques, must be able to deal with data streams since users provide their data over time. In addition, these systems must be able to decide when the processed data is sufficient to actually classify users. Moreover, since ERD tasks involve risky decisions by which people's lives could be affected, such systems must also be able to justify their decisions. However, most standard and state-of-the-art supervised machine learning models are not well suited to deal with this scenario. This is due to the fact that they either act as black boxes or do not support incremental classification/learning. In this paper we introduce SS3, a novel supervised learning model for text classification that naturally supports these aspects. SS3 was designed to be used as a general framework to deal with ERD problems. We evaluated our model on the CLEF's eRisk2017 pilot task on early depression detection. Most of the 30 contributions submitted to this competition used state-of-the-art methods. Experimental results show that our classifier was able to outperform these models and standard classifiers, despite being less computationally expensive and having the ability to explain its rationale.

Route Recommendation (RR) is a core task in route planning within online navigation applications, aiming to recommend the optimal route among candidate routes to users. Industrially, RR adopts the two-stage recall-and-rank framework instead of traditional route planning algorithms primarily for computational efficiency. However, RR fundamentally differs from traditional recommendation systems that follow this paradigm. First, a primary challenge is that route items cannot be assigned unique identifiers. Additionally, RR fundamentally differs from traditional recommendation systems in its approach to feature interaction. These differences render conventional recommendation approaches inadequate for route recommendation scenarios, necessitating specialized methods that can effectively handle route-specific challenges. To address these challenges, we propose a novel method called Comprehensive Comparison Network (CCN) for route recommendation. CCN constructs comparative features by comparing non-overlapping segments between route pairs, enabling difference learning without the infinite scalability issues of ID embeddings. Furthermore, CCN employs a specially designed Comprehensive Comparison Block (CCB) that differs from previous item attention methods to achieve effective cross-interaction between routes using comparison-level features. Moreover, we develop an interpretable Pair Scoring Network (PSN) for route recommendation and introduce a more comprehensive route recommendation dataset to advance research in this field. Experimental results demonstrate the effectiveness of our method, and CCN has been successfully deployed in AMAP for over a year, demonstrating its value in route recommendation.

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

The task of Legal Statute Identification (LSI) aims to identify the legal statutes that are relevant to a given description of Facts or evidence of a legal case. Existing methods only utilize the textual content of Facts and legal articles to guide such a task. However, the citation network among case documents and legal statutes is a rich source of additional information, which is not considered by existing models. In this work, we take the first step towards utilising both the text and the legal citation network for the LSI task. We curate a large novel dataset for this task, including Facts of cases from several major Indian Courts of Law, and statutes from the Indian Penal Code (IPC). Modeling the statutes and training documents as a heterogeneous graph, our proposed model LeSICiN can learn rich textual and graphical features, and can also tune itself to correlate these features. Thereafter, the model can be used to inductively predict links between test documents (new nodes whose graphical features are not available to the model) and statutes (existing nodes). Extensive experiments on the dataset show that our model comfortably outperforms several state-of-the-art baselines, by exploiting the graphical structure along with textual features. The dataset and our codes are available at https://github.com/Law-AI/LeSICiN.

We present a novel dataset collected by ASOS (a major online fashion retailer) to address the challenge of predicting customer returns in a fashion retail ecosystem. With the release of this substantial dataset we hope to motivate further collaboration between research communities and the fashion industry. We first explore the structure of this dataset with a focus on the application of Graph Representation Learning in order to exploit the natural data structure and provide statistical insights into particular features within the data. In addition to this, we show examples of a return prediction classification task with a selection of baseline models (i.e. with no intermediate representation learning step) and a graph representation based model. We show that in a downstream return prediction classification task, an F1-score of 0.792 can be found using a Graph Neural Network (GNN), improving upon other models discussed in this work. Alongside this increased F1-score, we also present a lower cross-entropy loss by recasting the data into a graph structure, indicating more robust predictions from a GNN based solution. These results provide evidence that GNNs could provide more impactful and usable classifications than other baseline models on the presented dataset and with this motivation, we hope to encourage further research into graph-based approaches using the ASOS GraphReturns dataset.

The automatic classification of applications and services is an invaluable feature for new generation mobile networks. Here, we propose and validate algorithms to perform this task, at runtime, from the raw physical channel of an operative mobile network, without having to decode and/or decrypt the transmitted flows. Towards this, we decode Downlink Control Information (DCI) messages carried within the LTE Physical Downlink Control CHannel (PDCCH). DCI messages are sent by the radio cell in clear text and, in this paper, are utilized to classify the applications and services executed at the connected mobile terminals. Two datasets are collected through a large measurement campaign: one labeled, used to train the classification algorithms, and one unlabeled, collected from four radio cells in the metropolitan area of Barcelona, in Spain. Among other approaches, our Convolutional Neural Network (CNN) classifier provides the highest classification accuracy of 99%. The CNN classifier is then augmented with the capability of rejecting sessions whose patterns do not conform to those learned during the training phase, and is subsequently utilized to attain a fine grained decomposition of the traffic for the four monitored radio cells, in an online and unsupervised fashion.

We introduce Acacia, a graph foundation model, trained on the web graph. Acacia (i) supports arbitrary feature dimensionalities and semantics without additional training, (ii) supports a wide range of tasks, including node classification, link prediction, node clustering, and graph generation, without additional training, (iii) has in-context learning capabilities, and (iv) does not rely on pretrained LLMs. In particular, existing graph foundation models often require training additional classification heads or feature projectors to accommodate new graphs or new labels, whereas Acacia does not. Moreover, existing graph foundation models often gain their capabilities by being stitched together with pretrained LLMs, whereas Acacia is trained from scratch using only the Common Crawl web graph. This is also an important result because it provides evidence that graph models can acquire emergent capabilities from scratch like LLMs.

Pathology vision-language models (VLMs) have shown strong visual perception ability, but their robustness in the language domain remains poorly characterized. Existing pathology VLM benchmarks largely rely on canonical closed-set prompts or perturb only generic templates, treating language as a fixed evaluation component rather than a variable axis of model behavior. In clinical practice, however, diagnostic language varies across reports, institutions, and candidate diagnoses. We introduce PathLang, a language-centered and clinically grounded zero-shot benchmark. PathLang holds the underlying slides, ground-truth labels, and image-text evaluation direction fixed while systematically varying only the diagnostic language, so that performance differences reflect how a diagnosis is phrased rather than what is imaged. The language variation follows how pathologists actually rephrase diagnoses (terminology, specificity, and reporting style), and all prompts and candidate pools are validated by six board-certified pathologists. PathLang covers four task families: (1) zero-shot classification with image-text alignment analysis, (2) cross-modal retrieval, (3) paraphrase robustness, including semantic-equivalence paraphrases, length and reporting-style variation, and prompt ensembling, and (4) open-vocabulary diagnosis retrieval over four candidate pools with distinct forms of semantic competition. Across nine VLMs and five public datasets spanning four organs, we find that performance is highly sensitive to clinically equivalent paraphrases, varies substantially across forms of semantic competition, and that image-text alignment quality does not necessarily translate into inter-class separability. We release the prompt corpus, candidate pools, pre-computed text embeddings, and evaluation code at https://anonymous.4open.science/r/PathLang.

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

Classification of movement trajectories has many applications in transportation. Supervised neural models represent the current state-of-the-art. Recent security applications require this task to be rapidly employed in environments that may differ from the data used to train such models for which there is little training data. We provide a neuro-symbolic rule-based framework to conduct error correction and detection of these models to support eventual deployment in security applications. We provide a suite of experiments on several recent and state-of-the-art models and show an accuracy improvement of 1.7% over the SOTA model in the case where all classes are present in training and when 40% of classes are omitted from training, we obtain a 5.2% improvement (zero-shot) and 23.9% (few-shot) improvement over the SOTA model without resorting to retraining of the base model.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

In recent years, there has been an exponential growth in the number of complex documents and texts that require a deeper understanding of machine learning methods to be able to accurately classify texts in many applications. Many machine learning approaches have achieved surpassing results in natural language processing. The success of these learning algorithms relies on their capacity to understand complex models and non-linear relationships within data. However, finding suitable structures, architectures, and techniques for text classification is a challenge for researchers. In this paper, a brief overview of text classification algorithms is discussed. This overview covers different text feature extractions, dimensionality reduction methods, existing algorithms and techniques, and evaluations methods. Finally, the limitations of each technique and their application in the real-world problem are discussed.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

Large Language Models (LLM)-based systems, i.e. interconnected elements that include an LLM as a central component (e.g., conversational agents), are typically monolithic static architectures that rely on a single LLM for all user queries. However, they often require different preprocessing strategies, levels of reasoning, or knowledge. Generalist LLMs (i.e. GPT-4), trained on very large multi-topic corpora, can perform well in a variety of tasks. However, they require significant financial, energy, and hardware resources that may not be justified for basic tasks. This implies potentially investing in unnecessary costs for a given query. To overcome this problem, a routing mechanism routes user queries to the most suitable components, such as smaller LLMs or experts in specific topics. This approach may improve response quality while minimising costs. Routing can be expanded to other components of the conversational agent architecture, such as the selection of optimal embedding strategies. This paper explores key considerations for integrating routing into LLM-based systems, focusing on resource management, cost definition, and strategy selection. Our main contributions include a formalisation of the problem, a novel taxonomy of existing approaches emphasising relevance and resource efficiency, and a comparative analysis of these strategies in relation to industry practices. Finally, we identify critical challenges and directions for future research.

The Vehicle Routing Problem (VRP) is a widely studied combinatorial optimization problem and has been applied to various practical problems. While the explainability for VRP is significant for improving the reliability and interactivity in practical VRP applications, it remains unexplored. In this paper, we propose RouteExplainer, a post-hoc explanation framework that explains the influence of each edge in a generated route. Our framework realizes this by rethinking a route as the sequence of actions and extending counterfactual explanations based on the action influence model to VRP. To enhance the explanation, we additionally propose an edge classifier that infers the intentions of each edge, a loss function to train the edge classifier, and explanation-text generation by Large Language Models (LLMs). We quantitatively evaluate our edge classifier on four different VRPs. The results demonstrate its rapid computation while maintaining reasonable accuracy, thereby highlighting its potential for deployment in practical applications. Moreover, on the subject of a tourist route, we qualitatively evaluate explanations generated by our framework. This evaluation not only validates our framework but also shows the synergy between explanation frameworks and LLMs. See https://ntt-dkiku.github.io/xai-vrp for our code, datasets, models, and demo.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

The complexity and variability inherent in high-resolution pathological images present significant challenges in computational pathology. While pathology foundation models leveraging AI have catalyzed transformative advancements, their development demands large-scale datasets, considerable storage capacity, and substantial computational resources. Furthermore, ensuring their clinical applicability and generalizability requires rigorous validation across a broad spectrum of clinical tasks. Here, we present PathOrchestra, a versatile pathology foundation model trained via self-supervised learning on a dataset comprising 300K pathological slides from 20 tissue and organ types across multiple centers. The model was rigorously evaluated on 112 clinical tasks using a combination of 61 private and 51 public datasets. These tasks encompass digital slide preprocessing, pan-cancer classification, lesion identification, multi-cancer subtype classification, biomarker assessment, gene expression prediction, and the generation of structured reports. PathOrchestra demonstrated exceptional performance across 27,755 WSIs and 9,415,729 ROIs, achieving over 0.950 accuracy in 47 tasks, including pan-cancer classification across various organs, lymphoma subtype diagnosis, and bladder cancer screening. Notably, it is the first model to generate structured reports for high-incidence colorectal cancer and diagnostically complex lymphoma-areas that are infrequently addressed by foundational models but hold immense clinical potential. Overall, PathOrchestra exemplifies the feasibility and efficacy of a large-scale, self-supervised pathology foundation model, validated across a broad range of clinical-grade tasks. Its high accuracy and reduced reliance on extensive data annotation underline its potential for clinical integration, offering a pathway toward more efficient and high-quality medical services.

We present Singpath-VL, a vision-language large model, to fill the vacancy of AI assistant in cervical cytology. Recent advances in multi-modal large language models (MLLMs) have significantly propelled the field of computational pathology. However, their application in cytopathology, particularly cervical cytology, remains underexplored, primarily due to the scarcity of large-scale, high-quality annotated datasets. To bridge this gap, we first develop a novel three-stage pipeline to synthesize a million-scale image-description dataset. The pipeline leverages multiple general-purpose MLLMs as weak annotators, refines their outputs through consensus fusion and expert knowledge injection, and produces high-fidelity descriptions of cell morphology. Using this dataset, we then fine-tune the Qwen3-VL-4B model via a multi-stage strategy to create a specialized cytopathology MLLM. The resulting model, named Singpath-VL, demonstrates superior performance in fine-grained morphological perception and cell-level diagnostic classification. To advance the field, we will open-source a portion of the synthetic dataset and benchmark.

We propose a new graph neural network (GNN) module, based on relaxations of recently proposed geometric scattering transforms, which consist of a cascade of graph wavelet filters. Our learnable geometric scattering (LEGS) module enables adaptive tuning of the wavelets to encourage band-pass features to emerge in learned representations. The incorporation of our LEGS-module in GNNs enables the learning of longer-range graph relations compared to many popular GNNs, which often rely on encoding graph structure via smoothness or similarity between neighbors. Further, its wavelet priors result in simplified architectures with significantly fewer learned parameters compared to competing GNNs. We demonstrate the predictive performance of LEGS-based networks on graph classification benchmarks, as well as the descriptive quality of their learned features in biochemical graph data exploration tasks. Our results show that LEGS-based networks match or outperforms popular GNNs, as well as the original geometric scattering construction, on many datasets, in particular in biochemical domains, while retaining certain mathematical properties of handcrafted (non-learned) geometric scattering.

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

In this paper, we review recent developments and the role of Graph Neural Networks (GNNs) in computational drug discovery, including molecule generation, molecular property prediction, and drug-drug interaction prediction. By summarizing the most recent developments in this area, we underscore the capabilities of GNNs to comprehend intricate molecular patterns, while exploring both their current and prospective applications. We initiate our discussion by examining various molecular representations, followed by detailed discussions and categorization of existing GNN models based on their input types and downstream application tasks. We also collect a list of commonly used benchmark datasets for a variety of applications. We conclude the paper with brief discussions and summarize common trends in this important research area.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

Large language models (LLMs) are susceptible to a variety of risks, from non-faithful output to biased and toxic generations. Due to several limiting factors surrounding LLMs (training cost, API access, data availability, etc.), it may not always be feasible to impose direct safety constraints on a deployed model. Therefore, an efficient and reliable alternative is required. To this end, we present our ongoing efforts to create and deploy a library of detectors: compact and easy-to-build classification models that provide labels for various harms. In addition to the detectors themselves, we discuss a wide range of uses for these detector models - from acting as guardrails to enabling effective AI governance. We also deep dive into inherent challenges in their development and discuss future work aimed at making the detectors more reliable and broadening their scope.

Navigation and mobility are some of the major problems faced by visually impaired people in their daily lives. Advances in computer vision led to the proposal of some navigation systems. However, most of them require expensive and/or heavy hardware. In this paper we propose the use of convolutional neural networks (CNN), transfer learning, and semi-supervised learning (SSL) to build a framework aimed at the visually impaired aid. It has low computational costs and, therefore, may be implemented on current smartphones, without relying on any additional equipment. The smartphone camera can be used to automatically take pictures of the path ahead. Then, they will be immediately classified, providing almost instantaneous feedback to the user. We also propose a dataset to train the classifiers, including indoor and outdoor situations with different types of light, floor, and obstacles. Many different CNN architectures are evaluated as feature extractors and classifiers, by fine-tuning weights pre-trained on a much larger dataset. The graph-based SSL method, known as particle competition and cooperation, is also used for classification, allowing feedback from the user to be incorporated without retraining the underlying network. 92\% and 80\% classification accuracy is achieved in the proposed dataset in the best supervised and SSL scenarios, respectively.

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

Grokking, i.e., test performance keeps improving long after training loss converged, has been recently witnessed in neural network training, making the mechanism of generalization and other emerging capabilities such as reasoning mysterious. While prior studies usually train small models on a few toy or highly-specific tasks for thousands of epochs, we conduct the first study of grokking on checkpoints during one-pass pretraining of a 7B large language model (LLM), i.e., OLMoE. We compute the training loss and evaluate generalization on diverse benchmark tasks, including math reasoning, code generation, and commonsense/domain-specific knowledge retrieval tasks. Our study, for the first time, verifies that grokking still happens in the pretraining of large-scale foundation models, though different data may enter grokking stages asynchronously. We further demystify grokking's "emergence of generalization" by investigating LLM internal dynamics. Specifically, we find that training samples' pathways (i.e., expert choices across layers) evolve from random, instance-specific to more structured and shareable between samples during grokking. Also, the complexity of a sample's pathway reduces despite the converged loss. These indicate a memorization-to-generalization conversion, providing a mechanistic explanation of delayed generalization. In the study, we develop two novel metrics to quantify pathway distance and the complexity of a single pathway. We show their ability to predict the generalization improvement on diverse downstream tasks. They are efficient, simple to compute and solely dependent on training data. Hence, they have practical value for pretraining, enabling us to monitor the generalization performance without finetuning and test. Theoretically, we show that more structured pathways reduce model complexity and improve the generalization bound.

This paper highlights the need to bring document classification benchmarking closer to real-world applications, both in the nature of data tested (X: multi-channel, multi-paged, multi-industry; Y: class distributions and label set variety) and in classification tasks considered (f: multi-page document, page stream, and document bundle classification, ...). We identify the lack of public multi-page document classification datasets, formalize different classification tasks arising in application scenarios, and motivate the value of targeting efficient multi-page document representations. An experimental study on proposed multi-page document classification datasets demonstrates that current benchmarks have become irrelevant and need to be updated to evaluate complete documents, as they naturally occur in practice. This reality check also calls for more mature evaluation methodologies, covering calibration evaluation, inference complexity (time-memory), and a range of realistic distribution shifts (e.g., born-digital vs. scanning noise, shifting page order). Our study ends on a hopeful note by recommending concrete avenues for future improvements.}

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Generative retrieval has recently emerged as a new alternative of traditional information retrieval approaches. However, existing generative retrieval methods directly decode docid when a query is given, making it impossible to provide users with explanations as an answer for "Why this document is retrieved?". To address this limitation, we propose Hierarchical Category Path-Enhanced Generative Retrieval(HyPE), which enhances explainability by generating hierarchical category paths step-by-step before decoding docid. HyPE leverages hierarchical category paths as explanation, progressing from broad to specific semantic categories. This approach enables diverse explanations for the same document depending on the query by using shared category paths between the query and the document, and provides reasonable explanation by reflecting the document's semantic structure through a coarse-to-fine manner. HyPE constructs category paths with external high-quality semantic hierarchy, leverages LLM to select appropriate candidate paths for each document, and optimizes the generative retrieval model with path-augmented dataset. During inference, HyPE utilizes path-aware reranking strategy to aggregate diverse topic information, allowing the most relevant documents to be prioritized in the final ranked list of docids. Our extensive experiments demonstrate that HyPE not only offers a high level of explainability but also improves the retrieval performance in the document retrieval task.

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

In many binary classification applications such as disease diagnosis and spam detection, practitioners often face great needs to control type I errors (i.e., the conditional probability of misclassifying a class 0 observation as class 1) so that it remains below a desired threshold. To address this need, the Neyman-Pearson (NP) classification paradigm is a natural choice; it minimizes type II error (i.e., the conditional probability of misclassifying a class 1 observation as class 0) while enforcing an upper bound, α, on the type I error. Although the NP paradigm has a century-long history in hypothesis testing, it has not been well recognized and implemented in classification schemes. Common practices that directly limit the empirical type I error to no more than α do not satisfy the type I error control objective because the resulting classifiers are still likely to have type I errors much larger than α. As a result, the NP paradigm has not been properly implemented for many classification scenarios in practice. In this work, we develop the first umbrella algorithm that implements the NP paradigm for all scoring-type classification methods, including popular methods such as logistic regression, support vector machines and random forests. Powered by this umbrella algorithm, we propose a novel graphical tool for NP classification methods: NP receiver operating characteristic (NP-ROC) bands, motivated by the popular receiver operating characteristic (ROC) curves. NP-ROC bands will help choose α in a data adaptive way and compare different NP classifiers. We demonstrate the use and properties of the NP umbrella algorithm and NP-ROC bands, available in the R package nproc, through simulation and real data case studies.

We present a holistic approach to building a robust and useful natural language classification system for real-world content moderation. The success of such a system relies on a chain of carefully designed and executed steps, including the design of content taxonomies and labeling instructions, data quality control, an active learning pipeline to capture rare events, and a variety of methods to make the model robust and to avoid overfitting. Our moderation system is trained to detect a broad set of categories of undesired content, including sexual content, hateful content, violence, self-harm, and harassment. This approach generalizes to a wide range of different content taxonomies and can be used to create high-quality content classifiers that outperform off-the-shelf models.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

To understand the function of cortical circuits it is necessary to classify their underlying cellular diversity. Traditional attempts based on comparing anatomical or physiological features of neurons and glia, while productive, have not resulted in a unified taxonomy of neural cell types. The recent development of single-cell transcriptomics has enabled, for the first time, systematic high-throughput profiling of large numbers of cortical cells and the generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data have revealed the existence of clear clusters, many of which correspond to cell types defined by traditional criteria, and which are conserved across cortical areas and species. To capitalize on these innovations and advance the field, we, the Copenhagen Convention Group, propose the community adopts a transcriptome-based taxonomy of the cell types in the adult mammalian neocortex. This core classification should be ontological, hierarchical and use a standardized nomenclature. It should be configured to flexibly incorporate new data from multiple approaches, developmental stages and a growing number of species, enabling improvement and revision of the classification. This community-based strategy could serve as a common foundation for future detailed analysis and reverse engineering of cortical circuits and serve as an example for cell type classification in other parts of the nervous system and other organs.

We describe a method, based on Jennifer Nado's proposal for classification procedures as targets of conceptual engineering, that implements such procedures by prompting a large language model. We apply this method, using data from the Wikidata knowledge graph, to evaluate stipulative definitions related to two paradigmatic conceptual engineering projects: the International Astronomical Union's redefinition of PLANET and Haslanger's ameliorative analysis of WOMAN. Our results show that classification procedures built using our approach can exhibit good classification performance and, through the generation of rationales for their classifications, can contribute to the identification of issues in either the definitions or the data against which they are being evaluated. We consider objections to this method, and discuss implications of this work for three aspects of theory and practice of conceptual engineering: the definition of its targets, empirical methods for their investigation, and their practical roles. The data and code used for our experiments, together with the experimental results, are available in a Github repository.

Object categories are typically organized into a multi-granularity taxonomic hierarchy. When classifying categories at different hierarchy levels, traditional uni-modal approaches focus primarily on image features, revealing limitations in complex scenarios. Recent studies integrating Vision-Language Models (VLMs) with class hierarchies have shown promise, yet they fall short of fully exploiting the hierarchical relationships. These efforts are constrained by their inability to perform effectively across varied granularity of categories. To tackle this issue, we propose a novel framework (HGCLIP) that effectively combines CLIP with a deeper exploitation of the Hierarchical class structure via Graph representation learning. We explore constructing the class hierarchy into a graph, with its nodes representing the textual or image features of each category. After passing through a graph encoder, the textual features incorporate hierarchical structure information, while the image features emphasize class-aware features derived from prototypes through the attention mechanism. Our approach demonstrates significant improvements on 11 diverse visual recognition benchmarks. Our codes are fully available at https://github.com/richard-peng-xia/HGCLIP.

Diabetes is a prevalent chronic disease with significant health and economic burdens worldwide. Early prediction and diagnosis can aid in effective management and prevention of complications. This study explores the use of machine learning models to predict diabetes based on lifestyle factors using data from the Behavioral Risk Factor Surveillance System (BRFSS) 2015 survey. The dataset consists of 21 lifestyle and health-related features, capturing aspects such as physical activity, diet, mental health, and socioeconomic status. Three classification models, Decision Tree, K-Nearest Neighbors (KNN), and Logistic Regression, are implemented and evaluated to determine their predictive performance. The models are trained and tested using a balanced dataset, and their performances are assessed based on accuracy, precision, recall, and F1-score. The results indicate that the Decision Tree, KNN, and Logistic Regression achieve an accuracy of 0.74, 0.72, and 0.75, respectively, with varying strengths in precision and recall. The findings highlight the potential of machine learning in diabetes prediction and suggest future improvements through feature selection and ensemble learning techniques.

We develop information geometric techniques to understand the representations learned by deep networks when they are trained on different tasks using supervised, meta-, semi-supervised and contrastive learning. We shed light on the following phenomena that relate to the structure of the space of tasks: (1) the manifold of probabilistic models trained on different tasks using different representation learning methods is effectively low-dimensional; (2) supervised learning on one task results in a surprising amount of progress even on seemingly dissimilar tasks; progress on other tasks is larger if the training task has diverse classes; (3) the structure of the space of tasks indicated by our analysis is consistent with parts of the Wordnet phylogenetic tree; (4) episodic meta-learning algorithms and supervised learning traverse different trajectories during training but they fit similar models eventually; (5) contrastive and semi-supervised learning methods traverse trajectories similar to those of supervised learning. We use classification tasks constructed from the CIFAR-10 and Imagenet datasets to study these phenomena.

Historical maps are invaluable for analyzing long-term changes in transportation and spatial development, offering a rich source of data for evolutionary studies. However, digitizing and classifying road networks from these maps is often expensive and time-consuming, limiting their widespread use. Recent advancements in deep learning have made automatic road extraction from historical maps feasible, yet these methods typically require large amounts of labeled training data. To address this challenge, we introduce a novel framework that integrates deep learning with geoinformation, computer-based painting, and image processing methodologies. This framework enables the extraction and classification of roads from historical maps using only road geometries without needing road class labels for training. The process begins with training of a binary segmentation model to extract road geometries, followed by morphological operations, skeletonization, vectorization, and filtering algorithms. Synthetic training data is then generated by a painting function that artificially re-paints road segments using predefined symbology for road classes. Using this synthetic data, a deep ensemble is trained to generate pixel-wise probabilities for road classes to mitigate distribution shift. These predictions are then discretized along the extracted road geometries. Subsequently, further processing is employed to classify entire roads, enabling the identification of potential changes in road classes and resulting in a labeled road class dataset. Our method achieved completeness and correctness scores of over 94% and 92%, respectively, for road class 2, the most prevalent class in the two Siegfried Map sheets from Switzerland used for testing. This research offers a powerful tool for urban planning and transportation decision-making by efficiently extracting and classifying roads from historical maps.

Due to their high predictive performance and flexibility, machine learning models are an appropriate and efficient tool for ecologists. However, implementing a machine learning model is not yet a trivial task and may seem intimidating to ecologists with no previous experience in this area. Here we provide a series of tips to help ecologists in implementing machine learning models. We focus on classification problems as many ecological studies aim to assign data into predefined classes such as ecological states or biological entities. Each of the nine tips identifies a common error, trap or challenge in developing machine learning models and provides recommendations to facilitate their use in ecological studies.

Graph mining is an important area in data mining and machine learning that involves extracting valuable information from graph-structured data. In recent years, significant progress has been made in this field through the development of graph neural networks (GNNs). However, GNNs are still deficient in generalizing to diverse graph data. Aiming to this issue, Large Language Models (LLMs) could provide new solutions for graph mining tasks with their superior semantic understanding. In this review, we systematically review the combination and application techniques of LLMs and GNNs and present a novel taxonomy for research in this interdisciplinary field, which involves three main categories: GNN-driving-LLM, LLM-driving-GNN, and GNN-LLM-co-driving. Within this framework, we reveal the capabilities of LLMs in enhancing graph feature extraction as well as improving the effectiveness of downstream tasks such as node classification, link prediction, and community detection. Although LLMs have demonstrated their great potential in handling graph-structured data, their high computational requirements and complexity remain challenges. Future research needs to continue to explore how to efficiently fuse LLMs and GNNs to achieve more powerful graph learning and reasoning capabilities and provide new impetus for the development of graph mining techniques.

Occurrence reporting is a commonly used method in safety management systems to obtain insight in the prevalence of hazards and accident scenarios. In support of safety data analysis, reports are often categorized according to a taxonomy. However, the processing of the reports can require significant effort from safety analysts and a common problem is interrater variability in labeling processes. Also, in some cases, reports are not processed according to a taxonomy, or the taxonomy does not fully cover the contents of the documents. This paper explores various Natural Language Processing (NLP) methods to support the analysis of aviation safety occurrence reports. In particular, the problems studied are the automatic labeling of reports using a classification model, extracting the latent topics in a collection of texts using a topic model and the automatic generation of probable cause texts. Experimental results showed that (i) under the right conditions the labeling of occurrence reports can be effectively automated with a transformer-based classifier, (ii) topic modeling can be useful for finding the topics present in a collection of reports, and (iii) using a summarization model can be a promising direction for generating probable cause texts.

LLM routing has become a popular approach to improve the cost-quality trade-off of LLM services by dynamically selecting a model for each query. Recent work has explored a broad range of routing methods, including clustering-based routers, learned classifiers, pairwise ranking, and confidence-based approaches. Our extensive study of 21 routing methods across five benchmarks reveals a consistent phenomenon that we call the routing plateau: many methods, including kNN, achieve very similar accuracy and converge to a narrow performance range that remains far below the oracle router. Our investigation shows that the plateau is largely caused by a predictability bottleneck: current routers mainly learn global averaged model-performance trends rather than fine-grained query-specific routing signals. As a result, they solve overlapping easy queries but collectively fail on hard queries that require instance-specific routing decisions. We further study how to move beyond the plateau and find that larger training datasets, stronger encoders, and end-to-end fine-tuning can further improve routing accuracy. These findings characterize the common limits of current routing methods and provide insights and actionable directions for the community to build more effective routing systems.

Accurately predicting gene expression from histopathology images offers a scalable and non-invasive approach to molecular profiling, with significant implications for precision medicine and computational pathology. However, existing methods often underutilize the cross-modal representation alignment between histopathology images and gene expression profiles across multiple representational levels, thereby limiting their prediction performance. To address this, we propose Gene-DML, a unified framework that structures latent space through Dual-pathway Multi-Level discrimination to enhance correspondence between morphological and transcriptional modalities. The multi-scale instance-level discrimination pathway aligns hierarchical histopathology representations extracted at local, neighbor, and global levels with gene expression profiles, capturing scale-aware morphological-transcriptional relationships. In parallel, the cross-level instance-group discrimination pathway enforces structural consistency between individual (image/gene) instances and modality-crossed (gene/image, respectively) groups, strengthening the alignment across modalities. By jointly modelling fine-grained and structural-level discrimination, Gene-DML is able to learn robust cross-modal representations, enhancing both predictive accuracy and generalization across diverse biological contexts. Extensive experiments on public spatial transcriptomics datasets demonstrate that Gene-DML achieves state-of-the-art performance in gene expression prediction. The code and checkpoints will be released soon.

Next-generation sequencing technologies, including RNA-sequencing, provide genome-wide measurements of gene expression and enable broad explorations of biomarkers and mechanisms underlying disease and treatment response. Bioinformatics tools for processing this data, such as differential expression analysis, are largely univariate, linear, and rely on predefined pathway knowledge annotations, which limits their ability to capture nonlinear and multivariate gene interactions. This paper explores the application of causal discovery to characterizing transcriptional responses to radiation as a function of dose rate in human cells. By jointly modeling radiation perturbations and gene expression, we learn directed gene networks that capture important regulatory relationships beyond correlation and exhibit significant enrichment of known radiation response pathways compared to baseline approaches. We find that inferred causal graphs reveal structured network features such as high in-degree housekeeping genes and high out-degree transcription factors. Further analysis suggests a hierarchical organization of stress response pathways and triggered cell death pathways. This work highlights the potential of causal discovery in healthcare settings with applications to understanding response mechanisms, identifying regulatory targets, and improving interpretation of complex genomic data.

Gene set analysis (GSA) is a foundational approach for interpreting genomic data of diseases by linking genes to biological processes. However, conventional GSA methods overlook clinical context of the analyses, often generating long lists of enriched pathways with redundant, nonspecific, or irrelevant results. Interpreting these requires extensive, ad-hoc manual effort, reducing both reliability and reproducibility. To address this limitation, we introduce cGSA, a novel AI-driven framework that enhances GSA by incorporating context-aware pathway prioritization. cGSA integrates gene cluster detection, enrichment analysis, and large language models to identify pathways that are not only statistically significant but also biologically meaningful. Benchmarking on 102 manually curated gene sets across 19 diseases and ten disease-related biological mechanisms shows that cGSA outperforms baseline methods by over 30%, with expert validation confirming its increased precision and interpretability. Two independent case studies in melanoma and breast cancer further demonstrate its potential to uncover context-specific insights and support targeted hypothesis generation.

This paper proposes a novel framework to predict traffic flows' bandwidth ahead of time. Modern network management systems share a common issue: the network situation evolves between the moment the decision is made and the moment when actions (countermeasures) are applied. This framework converts packets from real-life traffic into flows containing relevant features. Machine learning models, including Decision Tree, Random Forest, XGBoost, and Deep Neural Network, are trained on these data to predict the bandwidth at the next time instance for every flow. Predictions can be fed to the management system instead of current flows bandwidth in order to take decisions on a more accurate network state. Experiments were performed on 981,774 flows and 15 different time windows (from 0.03s to 4s). They show that the Random Forest is the best performing and most reliable model, with a predictive performance consistently better than relying on the current bandwidth (+19.73% in mean absolute error and +18.00% in root mean square error). Experimental results indicate that this framework can help network management systems to take more informed decisions using a predicted network state.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Multi-omics sequences contain complex biological patterns, yet deciphering their mechanisms for automated scientific discovery remains challenging. As large language models (LLMs) interpret these sequences, evaluating both predictions and scientific reasoning is critical. However, existing benchmarks for multi-omics sequence tasks rely on classification and regression metrics, neglecting whether models grasp the underlying biological evidence. We introduce OmicsBench, the first reasoning benchmark for multi-omics sequences, comprising 1,160 expert-validated questions across six tasks spanning DNA regulation, RNA processing, and protein function. OmicsBench requires traceable evidence chains, evaluated using instance-specific rubrics developed with domain experts. Evaluating 17 LLMs reveals an inverse relationship: while scientific LLMs outperform general-purpose LLMs in sequence classification accuracy, they fail to provide valid evidence to support their predictions. One plausible interpretation is shortcut learning: specialized models may rely on statistical patterns rather than the biological mechanisms needed for scientific discovery. Motivated by this finding, we introduce tool-augmented on-policy distillation (TA-OPD), a post-training method to align sequence prediction with evidence-grounded biological reasoning. Across five Qwen3.5 models spanning 0.8B to 27B parameters, TA-OPD consistently strengthens biological evidence grounding while improving predictive performance on most tasks. These gains persist across model scales, indicating that stronger sequence reasoning does not arise solely from increased model capacity, but can be improved through evidence-aware training. Together, OmicsBench and TA-OPD provide a framework for diagnosing reasoning failures in multi-omics LLMs and a path toward models whose predictions are better grounded in biologically meaningful evidence.

This research presents a comprehensive approach to predicting the duration of traffic incidents and classifying them as short-term or long-term across the Sydney Metropolitan Area. Leveraging a dataset that encompasses detailed records of traffic incidents, road network characteristics, and socio-economic indicators, we train and evaluate a variety of advanced machine learning models including Gradient Boosted Decision Trees (GBDT), Random Forest, LightGBM, and XGBoost. The models are assessed using Root Mean Square Error (RMSE) for regression tasks and F1 score for classification tasks. Our experimental results demonstrate that XGBoost and LightGBM outperform conventional models with XGBoost achieving the lowest RMSE of 33.7 for predicting incident duration and highest classification F1 score of 0.62 for a 30-minute duration threshold. For classification, the 30-minute threshold balances performance with 70.84% short-term duration classification accuracy and 62.72% long-term duration classification accuracy. Feature importance analysis, employing both tree split counts and SHAP values, identifies the number of affected lanes, traffic volume, and types of primary and secondary vehicles as the most influential features. The proposed methodology not only achieves high predictive accuracy but also provides stakeholders with vital insights into factors contributing to incident durations. These insights enable more informed decision-making for traffic management and response strategies. The code is available by the link: https://github.com/Future-Mobility-Lab/SydneyIncidents

Graph neural networks achieve high accuracy in link prediction by jointly leveraging graph topology and node attributes. Topology, however, is represented indirectly; state-of-the-art methods based on subgraph classification label nodes with distance to the target link, so that, although topological information is present, it is tempered by pooling. This makes it challenging to leverage features like loops and motifs associated with network formation mechanisms. We propose a link prediction algorithm based on a new pooling scheme called WalkPool. WalkPool combines the expressivity of topological heuristics with the feature-learning ability of neural networks. It summarizes a putative link by random walk probabilities of adjacent paths. Instead of extracting transition probabilities from the original graph, it computes the transition matrix of a "predictive" latent graph by applying attention to learned features; this may be interpreted as feature-sensitive topology fingerprinting. WalkPool can leverage unsupervised node features or be combined with GNNs and trained end-to-end. It outperforms state-of-the-art methods on all common link prediction benchmarks, both homophilic and heterophilic, with and without node attributes. Applying WalkPool to a set of unsupervised GNNs significantly improves prediction accuracy, suggesting that it may be used as a general-purpose graph pooling scheme.

Cross-entropy pretraining and preference alignment update the same transformer weights, but leave geometrically distinct traces. We characterise this asymmetry with a relative-subspace-fraction probe that tracks how weight deltas align with residual-stream activation subspaces and with the prediction subspace defined by the unembedding. Alignment deltas concentrate in the read pathway (W_Q, W_K), along principal directions of attention-input activations, while remaining near-isotropic in the write pathway (W_O, W_2) relative to the prediction subspace. We explain this pattern through anisotropic gradient accumulation: updates to a matrix W are sums of outer products δ_t a_t^top, and inherit directional structure from whichever side has concentrated covariance. For read-pathway matrices, this side is the input activation a_t, whose covariance is spiked in trained transformers and therefore produces objective-agnostic concentration. For write-pathway matrices, the relevant side is the upstream gradient δ_t, whose anisotropy depends on the loss. Cross-entropy supplies the canonical sharp per-sample signal, inducing write-pathway prediction geometry during pretraining; alignment objectives typically add little further write-side concentration. We support this explanation with a within-checkpoint trajectory, a graded contrastive-objective control, and a closed-form rank-1 intervention with matched direction controls, providing causal evidence for the proposed weight-space geometry.

Hierarchical text classification (HTC) is the task of assigning labels to a text within a structured space organized as a hierarchy. Recent works treat HTC as a conventional multilabel classification problem, therefore evaluating it as such. We instead propose to evaluate models based on specifically designed hierarchical metrics and we demonstrate the intricacy of metric choice and prediction inference method. We introduce a new challenging dataset and we evaluate fairly, recent sophisticated models, comparing them with a range of simple but strong baselines, including a new theoretically motivated loss. Finally, we show that those baselines are very often competitive with the latest models. This highlights the importance of carefully considering the evaluation methodology when proposing new methods for HTC. Code implementation and dataset are available at https://github.com/RomanPlaud/revisitingHTC.

Skill Classification (SC) is the task of classifying job competences from job postings. This work is the first in SC applied to Danish job vacancy data. We release the first Danish job posting dataset: Kompetencer (en: competences), annotated for nested spans of competences. To improve upon coarse-grained annotations, we make use of The European Skills, Competences, Qualifications and Occupations (ESCO; le Vrang et al., 2014) taxonomy API to obtain fine-grained labels via distant supervision. We study two setups: The zero-shot and few-shot classification setting. We fine-tune English-based models and RemBERT (Chung et al., 2020) and compare them to in-language Danish models. Our results show RemBERT significantly outperforms all other models in both the zero-shot and the few-shot setting.

The growing use of generative models in daily life calls for efficient mechanisms to control their generation, to e.g., produce safe content or provide users with tools to explore style changes. Ideally, such mechanisms should require low volume of unpaired data (i.e., without explicit preference), and should be cheap, both at train and inference time, while preserving output quality. Recent research has shown that such mechanisms can be obtained by intervening exclusively on model activations, with the goal of correcting distributional differences between activations seen when using prompts from a source vs. a target set (e.g., toxic and non-toxic sentences). While cheap, these fast methods are inherently crude: their maps are tuned locally, not accounting for their impact on downstream layers, resulting in interventions that cause unintended shifts when used out-of-sample. We propose in this work linear end-to-end activation steering (LinEAS), an approach trained with a global loss that accounts simultaneously for all layer-wise distributional shifts. In addition to being more robust, the loss used to train LinEAS can be regularized with sparsifying norms, which can automatically carry out neuron selection. LinEAS only requires a handful of unpaired samples to be effective, and beats similar baselines on toxicity mitigation in language models, becoming competitive with oracle-dependent methods that have access to strong supervision. LinEAS is modality-agnostic and we empirically find that it outperforms existing activation steering methods at mitigating and including new concepts at the output of single-step text-to-image generation models.

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.

Vision Transformers (ViTs) are normally regarded as a stack of transformer layers. In this work, we propose a novel view of ViTs showing that they can be seen as ensemble networks containing multiple parallel paths with different lengths. Specifically, we equivalently transform the traditional cascade of multi-head self-attention (MSA) and feed-forward network (FFN) into three parallel paths in each transformer layer. Then, we utilize the identity connection in our new transformer form and further transform the ViT into an explicit multi-path ensemble network. From the new perspective, these paths perform two functions: the first is to provide the feature for the classifier directly, and the second is to provide the lower-level feature representation for subsequent longer paths. We investigate the influence of each path for the final prediction and discover that some paths even pull down the performance. Therefore, we propose the path pruning and EnsembleScale skills for improvement, which cut out the underperforming paths and re-weight the ensemble components, respectively, to optimize the path combination and make the short paths focus on providing high-quality representation for subsequent paths. We also demonstrate that our path combination strategies can help ViTs go deeper and act as high-pass filters to filter out partial low-frequency signals. To further enhance the representation of paths served for subsequent paths, self-distillation is applied to transfer knowledge from the long paths to the short paths. This work calls for more future research to explain and design ViTs from new perspectives.