pwc-archive/papers-with-abstracts huggingface dataset:
TRIX: A More Expressive Model for Zero-shot Domain Transfer in Knowledge Graphs
Authors: Yucheng Zhang, Beatrice Bevilacqua, Mikhail Galkin, Bruno Ribeiro
Date: 2025-02-26 00:00:00
Tasks: Knowledge Graph Completion, Knowledge Graphs, Relation, Relation Prediction, Triplet

Fully inductive knowledge graph models can be trained on multiple domains and subsequently perform zero-shot knowledge graph completion (KGC) in new unseen domains. This is an important capability towards the goal of having foundation models for knowledge graphs. In this work, we introduce a more expressive and capable fully inductive model, dubbed TRIX, which not only yields strictly more expressive triplet embeddings (head entity, relation, tail entity) compared to state-of-the-art methods, but also introduces a new capability: directly handling both entity and relation prediction tasks in inductive settings. Empirically, we show that TRIX outperforms the state-of-the-art fully inductive models in zero-shot entity and relation predictions in new domains, and outperforms large-context LLMs in out-of-domain predictions. The source code is available at https://github.com/yuchengz99/TRIX.
Mixtraining: A Better Trade-Off Between Compute and Performance
Authors: Zexin Li, Jiancheng Zhang, Yinglun Zhu, Cong Liu
Date: 2025-02-26 00:00:00
Tasks: Multi-Task Learning, Representation Learning, Self-Supervised Learning

Incorporating self-supervised learning (SSL) before standard supervised learning (SL) has become a widely used strategy to enhance model performance, particularly in data-limited scenarios. However, this approach introduces a trade-off between computation and performance: while SSL helps with representation learning, it requires a separate, often time-consuming training phase, increasing computational overhead and limiting efficiency in resource-constrained settings. To address these challenges, we propose MixTraining, a novel framework that interleaves several SSL and SL epochs within a unified mixtraining training phase, featuring a smooth transition between two learning objectives. MixTraining enhances synergy between SSL and SL for improved accuracy and consolidates shared computation steps to reduce computation overhead. MixTraining is versatile and applicable to both single-task and multi-task learning scenarios. Extensive experiments demonstrate that MixTraining offers a superior compute-performance trade-off compared to conventional pipelines, achieving an 8.81% absolute accuracy gain (18.89% relative accuracy gain) on the TinyImageNet dataset while accelerating training by up to 1.29x with the ViT-Tiny model.
Analyzing Cost-Sensitive Surrogate Losses via $\mathcal{H}$-calibration
Authors: Sanket Shah, Milind Tambe, Jessie Finocchiaro
Date: 2025-02-26 00:00:00

This paper aims to understand whether machine learning models should be trained using cost-sensitive surrogates or cost-agnostic ones (e.g., cross-entropy). Analyzing this question through the lens of $\mathcal{H}$-calibration, we find that cost-sensitive surrogates can strictly outperform their cost-agnostic counterparts when learning small models under common distributional assumptions. Since these distributional assumptions are hard to verify in practice, we also show that cost-sensitive surrogates consistently outperform cost-agnostic surrogates on classification datasets from the UCI repository. Together, these make a strong case for using cost-sensitive surrogates in practice.
Extremely Greedy Equivalence Search
Authors: Achille Nazaret, David Blei
Date: 2025-02-26 00:00:00
Tasks: Causal Discovery, Model Selection

The goal of causal discovery is to learn a directed acyclic graph from data. One of the most well-known methods for this problem is Greedy Equivalence Search (GES). GES searches for the graph by incrementally and greedily adding or removing edges to maximize a model selection criterion. It has strong theoretical guarantees on infinite data but can fail in practice on finite data. In this paper, we first identify some of the causes of GES's failure, finding that it can get blocked in local optima, especially in denser graphs. We then propose eXtremely Greedy Equivalent Search (XGES), which involves a new heuristic to improve the search strategy of GES while retaining its theoretical guarantees. In particular, XGES favors deleting edges early in the search over inserting edges, which reduces the possibility of the search ending in local optima. A further contribution of this work is an efficient algorithmic formulation of XGES (and GES). We benchmark XGES on simulated datasets with known ground truth. We find that XGES consistently outperforms GES in recovering the correct graphs, and it is 10 times faster. XGES implementations in Python and C++ are available at https://github.com/ANazaret/XGES.
PhenoProfiler: Advancing Phenotypic Learning for Image-based Drug Discovery
Authors: Bo Li, Bob Zhang, Chengyang Zhang, Minghao Zhou, Weiliang Huang, Shihang Wang, Qing Wang, Mengran Li, Yong Zhang, Qianqian Song
Date: 2025-02-26 00:00:00
Tasks: Drug Discovery, Representation Learning

In the field of image-based drug discovery, capturing the phenotypic response of cells to various drug treatments and perturbations is a crucial step. However, existing methods require computationally extensive and complex multi-step procedures, which can introduce inefficiencies, limit generalizability, and increase potential errors. To address these challenges, we present PhenoProfiler, an innovative model designed to efficiently and effectively extract morphological representations, enabling the elucidation of phenotypic changes induced by treatments. PhenoProfiler is designed as an end-to-end tool that processes whole-slide multi-channel images directly into low-dimensional quantitative representations, eliminating the extensive computational steps required by existing methods. It also includes a multi-objective learning module to enhance robustness, accuracy, and generalization in morphological representation learning. PhenoProfiler is rigorously evaluated on large-scale publicly available datasets, including over 230,000 whole-slide multi-channel images in end-to-end scenarios and more than 8.42 million single-cell images in non-end-to-end settings. Across these benchmarks, PhenoProfiler consistently outperforms state-of-the-art methods by up to 20%, demonstrating substantial improvements in both accuracy and robustness. Furthermore, PhenoProfiler uses a tailored phenotype correction strategy to emphasize relative phenotypic changes under treatments, facilitating the detection of biologically meaningful signals. UMAP visualizations of treatment profiles demonstrate PhenoProfiler ability to effectively cluster treatments with similar biological annotations, thereby enhancing interpretability. These findings establish PhenoProfiler as a scalable, generalizable, and robust tool for phenotypic learning.
Improving Representation Learning of Complex Critical Care Data with ICU-BERT
Authors: Ricardo Santos, André V. Carreiro, Xi Peng, Hugo Gamboa, Holger Fröhlich
Date: 2025-02-26 00:00:00
Tasks: Feature Engineering, Language Modeling, Language Modelling, Large Language Model, Representation Learning

The multivariate, asynchronous nature of real-world clinical data, such as that generated in Intensive Care Units (ICUs), challenges traditional AI-based decision-support systems. These often assume data regularity and feature independence and frequently rely on limited data scopes and manual feature engineering. The potential of generative AI technologies has not yet been fully exploited to analyze clinical data. We introduce ICU-BERT, a transformer-based model pre-trained on the MIMIC-IV database using a multi-task scheme to learn robust representations of complex ICU data with minimal preprocessing. ICU-BERT employs a multi-token input strategy, incorporating dense embeddings from a biomedical Large Language Model to learn a generalizable representation of complex and multivariate ICU data. With an initial evaluation of five tasks and four additional ICU datasets, ICU-BERT results indicate that ICU-BERT either compares to or surpasses current performance benchmarks by leveraging fine-tuning. By integrating structured and unstructured data, ICU-BERT advances the use of foundational models in medical informatics, offering an adaptable solution for clinical decision support across diverse applications.
Introduction to Sequence Modeling with Transformers
Authors: Joni-Kristian Kämäräinen
Date: 2025-02-26 00:00:00
Tasks: Decoder

Understanding the transformer architecture and its workings is essential for machine learning (ML) engineers. However, truly understanding the transformer architecture can be demanding, even if you have a solid background in machine learning or deep learning. The main working horse is attention, which yields to the transformer encoder-decoder structure. However, putting attention aside leaves several programming components that are easy to implement but whose role for the whole is unclear. These components are 'tokenization', 'embedding' ('un-embedding'), 'masking', 'positional encoding', and 'padding'. The focus of this work is on understanding them. To keep things simple, the understanding is built incrementally by adding components one by one, and after each step investigating what is doable and what is undoable with the current model. Simple sequences of zeros (0) and ones (1) are used to study the workings of each step.
Learning Ensembles of Interpretable Simple Structure
Authors: Gaurav Arwade, Sigurdur Olafsson
Date: 2025-02-26 00:00:00
Tasks: Decision Making

Decision-making in complex systems often relies on machine learning models, yet highly accurate models such as XGBoost and neural networks can obscure the reasoning behind their predictions. In operations research applications, understanding how a decision is made is often as crucial as the decision itself. Traditional interpretable models, such as decision trees and logistic regression, provide transparency but may struggle with datasets containing intricate feature interactions. However, complexity in decision-making stem from interactions that are only relevant within certain subsets of data. Within these subsets, feature interactions may be simplified, forming simple structures where simple interpretable models can perform effectively. We propose a bottom-up simple structure-identifying algorithm that partitions data into interpretable subgroups known as simple structure, where feature interactions are minimized, allowing simple models to be trained within each subgroup. We demonstrate the robustness of the algorithm on synthetic data and show that the decision boundaries derived from simple structures are more interpretable and aligned with the intuition of the domain than those learned from a global model. By improving both explainability and predictive accuracy, our approach provides a principled framework for decision support in applications where model transparency is essential.
PRDP: Progressively Refined Differentiable Physics
Authors: Kanishk Bhatia, Felix Koehler, Nils Thuerey
Date: 2025-02-26 00:00:00
Tasks: Bilevel Optimization

The physics solvers employed for neural network training are primarily iterative, and hence, differentiating through them introduces a severe computational burden as iterations grow large. Inspired by works in bilevel optimization, we show that full accuracy of the network is achievable through physics significantly coarser than fully converged solvers. We propose Progressively Refined Differentiable Physics (PRDP), an approach that identifies the level of physics refinement sufficient for full training accuracy. By beginning with coarse physics, adaptively refining it during training, and stopping refinement at the level adequate for training, it enables significant compute savings without sacrificing network accuracy. Our focus is on differentiating iterative linear solvers for sparsely discretized differential operators, which are fundamental to scientific computing. PRDP is applicable to both unrolled and implicit differentiation. We validate its performance on a variety of learning scenarios involving differentiable physics solvers such as inverse problems, autoregressive neural emulators, and correction-based neural-hybrid solvers. In the challenging example of emulating the Navier-Stokes equations, we reduce training time by 62%.
Revealing Treatment Non-Adherence Bias in Clinical Machine Learning Using Large Language Models
Authors: Zhongyuan Liang, Arvind Suresh, Irene Y. Chen
Date: 2025-02-26 00:00:00
Tasks: Causal Inference, Language Modeling, Language Modelling, Large Language Model

Machine learning systems trained on electronic health records (EHRs) increasingly guide treatment decisions, but their reliability depends on the critical assumption that patients follow the prescribed treatments recorded in EHRs. Using EHR data from 3,623 hypertension patients, we investigate how treatment non-adherence introduces implicit bias that can fundamentally distort both causal inference and predictive modeling. By extracting patient adherence information from clinical notes using a large language model (LLM), we identify 786 patients (21.7%) with medication non-adherence. We further uncover key demographic and clinical factors associated with non-adherence, as well as patient-reported reasons including side effects and difficulties obtaining refills. Our findings demonstrate that this implicit bias can not only reverse estimated treatment effects, but also degrade model performance by up to 5% while disproportionately affecting vulnerable populations by exacerbating disparities in decision outcomes and model error rates. This highlights the importance of accounting for treatment non-adherence in developing responsible and equitable clinical machine learning systems.
Developing robust methods to handle missing data in real-world applications effectively
Authors: Youran Zhou, Mohamed Reda Bouadjenek, Sunil Arya
Date: 2025-02-27 00:00:00

Missing data is a pervasive challenge spanning diverse data types, including tabular, sensor data, time-series, images and so on. Its origins are multifaceted, resulting in various missing mechanisms. Prior research in this field has predominantly revolved around the assumption of the Missing Completely At Random (MCAR) mechanism. However, Missing At Random (MAR) and Missing Not At Random (MNAR) mechanisms, though equally prevalent, have often remained underexplored despite their significant influence. This PhD project presents a comprehensive research agenda designed to investigate the implications of diverse missing data mechanisms. The principal aim is to devise robust methodologies capable of effectively handling missing data while accommodating the unique characteristics of MCAR, MAR, and MNAR mechanisms. By addressing these gaps, this research contributes to an enriched understanding of the challenges posed by missing data across various industries and data modalities. It seeks to provide practical solutions that enable the effective management of missing data, empowering researchers and practitioners to leverage incomplete datasets confidently.
cMIM: A Contrastive Mutual Information Framework for Unified Generative and Discriminative Representation Learning
Authors: Micha Livne
Date: 2025-02-27 00:00:00
Tasks: Contrastive Learning, Data Augmentation, Decoder, Denoising, Representation Learning

Learning representations that are useful for unknown downstream tasks is a fundamental challenge in representation learning. Prominent approaches in this domain include contrastive learning, self-supervised masking, and denoising auto-encoders. In this paper, we introduce a novel method, termed contrastive Mutual Information Machine (cMIM), which aims to enhance the utility of learned representations for downstream tasks. cMIM integrates a new contrastive learning loss with the Mutual Information Machine (MIM) learning framework, a probabilistic auto-encoder that maximizes the mutual information between inputs and latent representations while clustering the latent codes. Despite MIM's potential, initial experiments indicated that the representations learned by MIM were less effective for discriminative downstream tasks compared to state-of-the-art (SOTA) models. The proposed cMIM method directly addresses this limitation. The main contributions of this work are twofold: (1) We propose a novel contrastive extension to MIM for learning discriminative representations which eliminates the need for data augmentation and is robust to variations in the number of negative examples (i.e., batch size). (2) We introduce a generic method for extracting informative embeddings from encoder-decoder models, which significantly improves performance in discriminative downstream tasks without requiring additional training. This method is applicable to any pre-trained encoder-decoder model. By presenting cMIM, we aim to offer a unified generative model that is effective for both generative and discriminative tasks. Our results demonstrate that the learned representations are valuable for downstream tasks while maintaining the generative capabilities of MIM.
Taxonomy, Opportunities, and Challenges of Representation Engineering for Large Language Models
Authors: Jan Wehner, Sahar Abdelnabi, Daniel Tan, David Krueger, Mario Fritz
Date: 2025-02-27 00:00:00

Representation Engineering (RepE) is a novel paradigm for controlling the behavior of LLMs. Unlike traditional approaches that modify inputs or fine-tune the model, RepE directly manipulates the model's internal representations. As a result, it may offer more effective, interpretable, data-efficient, and flexible control over models' behavior. We present the first comprehensive survey of RepE for LLMs, reviewing the rapidly growing literature to address key questions: What RepE methods exist and how do they differ? For what concepts and problems has RepE been applied? What are the strengths and weaknesses of RepE compared to other methods? To answer these, we propose a unified framework describing RepE as a pipeline comprising representation identification, operationalization, and control. We posit that while RepE methods offer significant potential, challenges remain, including managing multiple concepts, ensuring reliability, and preserving models' performance. Towards improving RepE, we identify opportunities for experimental and methodological improvements and construct a guide for best practices.
Unlocking Multi-Modal Potentials for Dynamic Text-Attributed Graph Representation
Authors: Yuanyuan Xu, Wenjie Zhang, Ying Zhang, Xuemin Lin, Xiwei Xu
Date: 2025-02-27 00:00:00
Tasks: Graph Learning

Dynamic Text-Attributed Graphs (DyTAGs) are a novel graph paradigm that captures evolving temporal edges alongside rich textual attributes. A prior approach to representing DyTAGs leverages pre-trained language models to encode text attributes and subsequently integrates them into dynamic graph models. However, it follows edge-centric modeling, as in dynamic graph learning, which is limited in local structures and fails to exploit the unique characteristics of DyTAGs, leading to suboptimal performance. We observe that DyTAGs inherently comprise three distinct modalities-temporal, textual, and structural-often exhibiting dispersed or even orthogonal distributions, with the first two largely overlooked in existing research. Building on this insight, we propose MoMent, a model-agnostic multi-modal framework that can seamlessly integrate with dynamic graph models for structural modality learning. The core idea is to shift from edge-centric to node-centric modeling, fully leveraging three modalities for node representation. Specifically, MoMent presents non-shared node-centric encoders based on the attention mechanism to capture global temporal and semantic contexts from temporal and textual modalities, together with local structure learning, thus generating modality-specific tokens. To prevent disjoint latent space, we propose a symmetric alignment loss, an auxiliary objective that aligns temporal and textual tokens, ensuring global temporal-semantic consistency with a theoretical guarantee. Last, we design a lightweight adaptor to fuse these tokens, generating comprehensive and cohesive node representations. We theoretically demonstrate that MoMent enhances discriminative power over exclusive edge-centric modeling. Extensive experiments across seven datasets and two downstream tasks show that MoMent achieves up to 33.62% improvement against the baseline using four dynamic graph models.
Variation Matters: from Mitigating to Embracing Zero-Shot NAS Ranking Function Variation
Authors: Pavel Rumiantsev, Mark Coates
Date: 2025-02-27 00:00:00
Tasks: Neural Architecture Search

Neural Architecture Search (NAS) is a powerful automatic alternative to manual design of a neural network. In the zero-shot version, a fast ranking function is used to compare architectures without training them. The outputs of the ranking functions often vary significantly due to different sources of randomness, including the evaluated architecture's weights' initialization or the batch of data used for calculations. A common approach to addressing the variation is to average a ranking function output over several evaluations. We propose taking into account the variation in a different manner, by viewing the ranking function output as a random variable representing a proxy performance metric. During the search process, we strive to construct a stochastic ordering of the performance metrics to determine the best architecture. Our experiments show that the proposed stochastic ordering can effectively boost performance of a search on standard benchmark search spaces.
Out-of-distribution Generalization for Total Variation based Invariant Risk Minimization
Authors: Yuanchao Wang, Zhao-Rong Lai, Tianqi Zhong
Date: 2025-02-27 00:00:00
Tasks: Out-of-Distribution Generalization

Invariant risk minimization is an important general machine learning framework that has recently been interpreted as a total variation model (IRM-TV). However, how to improve out-of-distribution (OOD) generalization in the IRM-TV setting remains unsolved. In this paper, we extend IRM-TV to a Lagrangian multiplier model named OOD-TV-IRM. We find that the autonomous TV penalty hyperparameter is exactly the Lagrangian multiplier. Thus OOD-TV-IRM is essentially a primal-dual optimization model, where the primal optimization minimizes the entire invariant risk and the dual optimization strengthens the TV penalty. The objective is to reach a semi-Nash equilibrium where the balance between the training loss and OOD generalization is maintained. We also develop a convergent primal-dual algorithm that facilitates an adversarial learning scheme. Experimental results show that OOD-TV-IRM outperforms IRM-TV in most situations.
Training Robust Graph Neural Networks by Modeling Noise Dependencies
Authors: Yeonjun In, Kanghoon Yoon, Sukwon Yun, Kibum Kim, Sungchul Kim, Chanyoung Park
Date: 2025-02-27 00:00:00
Tasks: Variational Inference

In real-world applications, node features in graphs often contain noise from various sources, leading to significant performance degradation in GNNs. Although several methods have been developed to enhance robustness, they rely on the unrealistic assumption that noise in node features is independent of the graph structure and node labels, thereby limiting their applicability. To this end, we introduce a more realistic noise scenario, dependency-aware noise on graphs (DANG), where noise in node features create a chain of noise dependencies that propagates to the graph structure and node labels. We propose a novel robust GNN, DA-GNN, which captures the causal relationships among variables in the data generating process (DGP) of DANG using variational inference. In addition, we present new benchmark datasets that simulate DANG in real-world applications, enabling more practical research on robust GNNs. Extensive experiments demonstrate that DA-GNN consistently outperforms existing baselines across various noise scenarios, including both DANG and conventional noise models commonly considered in this field.