pwc-archive/papers-with-abstracts huggingface dataset:
Perforated Backpropagation: A Neuroscience Inspired Extension to Artificial Neural Networks
Authors: Rorry Brenner, Laurent Itti
Date: 2025-01-29 00:00:00
Tasks: Drug Discovery, Language Modeling, Model Compression, Stock Trend Prediction

The neurons of artificial neural networks were originally invented when much less was known about biological neurons than is known today. Our work explores a modification to the core neuron unit to make it more parallel to a biological neuron. The modification is made with the knowledge that biological dendrites are not simply passive activation funnels, but also compute complex non-linear functions as they transmit activation to the cell body. The paper explores a novel system of "Perforated" backpropagation empowering the artificial neurons of deep neural networks to achieve better performance coding for the same features they coded for in the original architecture. After an initial network training phase, additional "Dendrite Nodes" are added to the network and separately trained with a different objective: to correlate their output with the remaining error of the original neurons. The trained Dendrite Nodes are then frozen, and the original neurons are further trained, now taking into account the additional error signals provided by the Dendrite Nodes. The cycle of training the original neurons and then adding and training Dendrite Nodes can be repeated several times until satisfactory performance is achieved. Our algorithm was successfully added to modern state-of-the-art PyTorch networks across multiple domains, improving upon original accuracies and allowing for significant model compression without a loss in accuracy.
A Proximal Operator for Inducing 2:4-Sparsity
Authors: Jonas M Kübler, Yu-Xiang Wang, Shoham Sabach, Navid Ansari, Matthäus Kleindessner, Kailash Budhathoki, Volkan Cevher, George Karypis
Date: 2025-01-29 00:00:00

Recent hardware advancements in AI Accelerators and GPUs allow to efficiently compute sparse matrix multiplications, especially when 2 out of 4 consecutive weights are set to zero. However, this so-called 2:4 sparsity usually comes at a decreased accuracy of the model. We derive a regularizer that exploits the local correlation of features to find better sparsity masks in trained models. We minimize the regularizer jointly with a local squared loss by deriving the proximal operator for which we show that it has an efficient solution in the 2:4-sparse case. After optimizing the mask, we use maskedgradient updates to further minimize the local squared loss. We illustrate our method on toy problems and apply it to pruning entire large language models up to 70B parameters. On models up to 13B we improve over previous state of the art algorithms, whilst on 70B models we match their performance.
Fault Localization via Fine-tuning Large Language Models with Mutation Generated Stack Traces
Authors: Neetha Jambigi, Bartosz Bogacz, Moritz Mueller, Thomas Bach, Michael Felderer
Date: 2025-01-29 00:00:00
Tasks: Fault localization

Abrupt and unexpected terminations of software are termed as software crashes. They can be challenging to analyze. Finding the root cause requires extensive manual effort and expertise to connect information sources like stack traces, source code, and logs. Typical approaches to fault localization require either test failures or source code. Crashes occurring in production environments, such as that of SAP HANA, provide solely crash logs and stack traces. We present a novel approach to localize faults based only on the stack trace information and no additional runtime information, by fine-tuning large language models (LLMs). We address complex cases where the root cause of a crash differs from the technical cause, and is not located in the innermost frame of the stack trace. As the number of historic crashes is insufficient to fine-tune LLMs, we augment our dataset by leveraging code mutators to inject synthetic crashes into the code base. By fine-tuning on 64,369 crashes resulting from 4.1 million mutations of the HANA code base, we can correctly predict the root cause location of a crash with an accuracy of 66.9\% while baselines only achieve 12.6% and 10.6%. We substantiate the generalizability of our approach by evaluating on two additional open-source databases, SQLite and DuckDB, achieving accuracies of 63% and 74%, respectively. Across all our experiments, fine-tuning consistently outperformed prompting non-finetuned LLMs for localizing faults in our datasets.
InnerThoughts: Disentangling Representations and Predictions in Large Language Models
Authors: Didier Chételat, Joseph Cotnareanu, Rylee Thompson, Yingxue Zhang, Mark Coates
Date: 2025-01-29 00:00:00
Tasks: Multiple-choice, Position, Question Answering

Large language models (LLMs) contain substantial factual knowledge which is commonly elicited by multiple-choice question-answering prompts. Internally, such models process the prompt through multiple transformer layers, building varying representations of the problem within its hidden states. Ultimately, however, only the hidden state corresponding to the final layer and token position are used to predict the answer label. In this work, we propose instead to learn a small separate neural network predictor module on a collection of training questions, that take the hidden states from all the layers at the last temporal position as input and outputs predictions. In effect, such a framework disentangles the representational abilities of LLMs from their predictive abilities. On a collection of hard benchmarks, our method achieves considerable improvements in performance, sometimes comparable to supervised fine-tuning procedures, but at a fraction of the computational cost.
Reinforcement-Learning Portfolio Allocation with Dynamic Embedding of Market Information
Authors: Jinghai He, Cheng Hua, Chunyang Zhou, Zeyu Zheng
Date: 2025-01-29 00:00:00
Tasks: Meta-Learning, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

We develop a portfolio allocation framework that leverages deep learning techniques to address challenges arising from high-dimensional, non-stationary, and low-signal-to-noise market information. Our approach includes a dynamic embedding method that reduces the non-stationary, high-dimensional state space into a lower-dimensional representation. We design a reinforcement learning (RL) framework that integrates generative autoencoders and online meta-learning to dynamically embed market information, enabling the RL agent to focus on the most impactful parts of the state space for portfolio allocation decisions. Empirical analysis based on the top 500 U.S. stocks demonstrates that our framework outperforms common portfolio benchmarks and the predict-then-optimize (PTO) approach using machine learning, particularly during periods of market stress. Traditional factor models do not fully explain this superior performance. The framework's ability to time volatility reduces its market exposure during turbulent times. Ablation studies confirm the robustness of this performance across various reinforcement learning algorithms. Additionally, the embedding and meta-learning techniques effectively manage the complexities of high-dimensional, noisy, and non-stationary financial data, enhancing both portfolio performance and risk management.
KoopAGRU: A Koopman-based Anomaly Detection in Time-Series using Gated Recurrent Units
Authors: Issam Ait Yahia, Ismail Berrada
Date: 2025-01-29 00:00:00
Tasks: Anomaly Detection, Time Series

Anomaly detection in real-world time-series data is a challenging task due to the complex and nonlinear temporal dynamics involved. This paper introduces KoopAGRU, a new deep learning model designed to tackle this problem by combining Fast Fourier Transform (FFT), Deep Dynamic Mode Decomposition (DeepDMD), and Koopman theory. FFT allows KoopAGRU to decompose temporal data into time-variant and time-invariant components providing precise modeling of complex patterns. To better control these two components, KoopAGRU utilizes Gate Recurrent Unit (GRU) encoders to learn Koopman observables, enhancing the detection capability across multiple temporal scales. KoopAGRU is trained in a single process and offers fast inference times. Extensive tests on various benchmark datasets show that KoopAGRU outperforms other leading methods, achieving a new average F1-score of 90.88\% on the well-known anomalies detection task of times series datasets, and proves to be efficient and reliable in detecting anomalies in real-world scenarios.
Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetics in Hyperbolic Space
Authors: Alex Chen, Philipe Chlenski, Kenneth Munyuza, Antonio Khalil Moretti, Christian A. Naesseth, Itsik Pe'er
Date: 2025-01-29 00:00:00
Tasks: Variational Inference

Hyperbolic space naturally encodes hierarchical structures such as phylogenies (binary trees), where inward-bending geodesics reflect paths through least common ancestors, and the exponential growth of neighborhoods mirrors the super-exponential scaling of topologies. This scaling challenge limits the efficiency of Euclidean-based approximate inference methods. Motivated by the geometric connections between trees and hyperbolic space, we develop novel hyperbolic extensions of two sequential search algorithms: Combinatorial and Nested Combinatorial Sequential Monte Carlo (\textsc{Csmc} and \textsc{Ncsmc}). Our approach introduces consistent and unbiased estimators, along with variational inference methods (\textsc{H-Vcsmc} and \textsc{H-Vncsmc}), which outperform their Euclidean counterparts. Empirical results demonstrate improved speed, scalability and performance in high-dimensional phylogenetic inference tasks.
A Robust Support Vector Machine Approach for Raman COVID-19 Data Classification
Authors: Marco Piazza, Andrea Spinelli, Francesca Maggioni, Marzia Bedoni, Enza Messina
Date: 2025-01-29 00:00:00

Recent advances in healthcare technologies have led to the availability of large amounts of biological samples across several techniques and applications. In particular, in the last few years, Raman spectroscopy analysis of biological samples has been successfully applied for early-stage diagnosis. However, spectra' inherent complexity and variability make the manual analysis challenging, even for domain experts. For the same reason, the use of traditional Statistical and Machine Learning (ML) techniques could not guarantee for accurate and reliable results. ML models, combined with robust optimization techniques, offer the possibility to improve the classification accuracy and enhance the resilience of predictive models. In this paper, we investigate the performance of a novel robust formulation for Support Vector Machine (SVM) in classifying COVID-19 samples obtained from Raman Spectroscopy. Given the noisy and perturbed nature of biological samples, we protect the classification process against uncertainty through the application of robust optimization techniques. Specifically, we derive robust counterpart models of deterministic formulations using bounded-by-norm uncertainty sets around each observation. We explore the cases of both linear and kernel-induced classifiers to address binary and multiclass classification tasks. The effectiveness of our approach is validated on real-world COVID-19 datasets provided by Italian hospitals by comparing the results of our simulations with a state-of-the-art classifier.
Molecular Fingerprints Are Strong Models for Peptide Function Prediction
Authors: Jakub Adamczyk, Piotr Ludynia, Wojciech Czech
Date: 2025-01-29 00:00:00
Tasks: Graph Classification, Graph Regression, Property Prediction

We study the effectiveness of molecular fingerprints for peptide property prediction and demonstrate that domain-specific feature extraction from molecular graphs can outperform complex and computationally expensive models such as GNNs, pretrained sequence-based transformers and multimodal ensembles, even without hyperparameter tuning. To this end, we perform a thorough evaluation on 126 datasets, achieving state-of-the-art results on LRGB and 5 other peptide function prediction benchmarks. We show that models based on count variants of ECFP, Topological Torsion, and RDKit molecular fingerprints and LightGBM as classification head are remarkably robust. The strong performance of molecular fingerprints, which are intrinsically very short-range feature encoders, challenges the presumed importance of long-range interactions in peptides. Our conclusion is that the use of molecular fingerprints for larger molecules, such as peptides, can be a computationally feasible, low-parameter, and versatile alternative to sophisticated deep learning models.
Shared DIFF Transformer
Authors: Yueyang Cang, Yuhang Liu, Xiaoteng Zhang, Xiangju Wang
Date: 2025-01-29 00:00:00
Tasks: In-Context Learning, Information Retrieval

DIFF Transformer improves attention allocation by enhancing focus on relevant context while suppressing noise. It introduces a differential attention mechanism that calculates the difference between two independently generated attention distributions, effectively reducing noise and promoting sparse attention patterns. However, the independent signal generation in DIFF Transformer results in parameter redundancy and suboptimal utilization of information. In this work, we propose Shared DIFF Transformer, which draws on the idea of a differential amplifier by introducing a shared base matrix to model global patterns and incorporating low-rank updates to enhance task-specific flexibility. This design significantly reduces parameter redundancy, improves efficiency, and retains strong noise suppression capabilities. Experimental results show that, compared to DIFF Transformer, our method achieves better performance in tasks such as long-sequence modeling, key information retrieval, and in-context learning. Our work provides a novel and efficient approach to optimizing differential attention mechanisms and advancing robust Transformer architectures.
Thoughts Are All Over the Place: On the Underthinking of o1-Like LLMs
Authors: Yue Wang, Qiuzhi Liu, Jiahao Xu, Tian Liang, Xingyu Chen, Zhiwei He, Linfeng Song, Dian Yu, Juntao Li, Zhuosheng Zhang, Rui Wang, Zhaopeng Tu, Haitao Mi, Dong Yu
Date: 2025-01-30 00:00:00
Tasks: All

Large language models (LLMs) such as OpenAI's o1 have demonstrated remarkable abilities in complex reasoning tasks by scaling test-time compute and exhibiting human-like deep thinking. However, we identify a phenomenon we term underthinking, where o1-like LLMs frequently switch between different reasoning thoughts without sufficiently exploring promising paths to reach a correct solution. This behavior leads to inadequate depth of reasoning and decreased performance, particularly on challenging mathematical problems. To systematically analyze this issue, we conduct experiments on three challenging test sets and two representative open-source o1-like models, revealing that frequent thought switching correlates with incorrect responses. We introduce a novel metric to quantify underthinking by measuring token efficiency in incorrect answers. To address underthinking, we propose a decoding strategy with thought switching penalty TIP that discourages premature transitions between thoughts, encouraging deeper exploration of each reasoning path. Experimental results demonstrate that our approach improves accuracy across challenging datasets without requiring model fine-tuning. Our findings contribute to understanding reasoning inefficiencies in o1-like LLMs and offer a practical solution to enhance their problem-solving capabilities.
Streaming DiLoCo with overlapping communication: Towards a Distributed Free Lunch
Authors: Arthur Douillard, Yanislav Donchev, Keith Rush, Satyen Kale, Zachary Charles, Zachary Garrett, Gabriel Teston, Dave Lacey, Ross Mcilroy, Jiajun Shen, Alexandre Ramé, Arthur Szlam, Marc'Aurelio Ranzato, Paul Barham
Date: 2025-01-30 00:00:00
Tasks: All

Training of large language models (LLMs) is typically distributed across a large number of accelerators to reduce training time. Since internal states and parameter gradients need to be exchanged at each and every single gradient step, all devices need to be co-located using low-latency high-bandwidth communication links to support the required high volume of exchanged bits. Recently, distributed algorithms like DiLoCo have relaxed such co-location constraint: accelerators can be grouped into ``workers'', where synchronizations between workers only occur infrequently. This in turn means that workers can afford being connected by lower bandwidth communication links without affecting learning quality. However, in these methods, communication across workers still requires the same peak bandwidth as before, as the synchronizations require all parameters to be exchanged across all workers. In this paper, we improve DiLoCo in three ways. First, we synchronize only subsets of parameters in sequence, rather than all at once, which greatly reduces peak bandwidth. Second, we allow workers to continue training while synchronizing, which decreases wall clock time. Third, we quantize the data exchanged by workers, which further reduces bandwidth across workers. By properly combining these modifications, we show experimentally that we can distribute training of billion-scale parameters and reach similar quality as before, but reducing required bandwidth by two orders of magnitude.
CALM: Unleashing the Cross-Lingual Self-Aligning Ability of Language Model Question Answering
Authors: Yumeng Wang, Zhiyuan Fan, Qingyun Wang, May Fung, Heng Ji
Date: 2025-01-30 00:00:00
Tasks: General Knowledge, Language Modeling, Language Modelling, MedQA, Question Answering

Large Language Models (LLMs) are pretrained on extensive multilingual corpora to acquire both language-specific cultural knowledge and general knowledge. Ideally, while LLMs should provide consistent responses to culture-independent questions across languages, we observe significant performance disparities. To address this, we explore the Cross-Lingual Self-Aligning ability of Language Models (CALM) to align knowledge across languages. Specifically, for a given question, we sample multiple responses across different languages, and select the most self-consistent response as the target, leaving the remaining responses as negative examples. We then employ direct preference optimization (DPO) to align the model's knowledge across different languages. Evaluations on the MEDQA and X-CSQA datasets demonstrate CALM's effectiveness in enhancing cross-lingual knowledge question answering, both in zero-shot and retrieval augmented settings. We also found that increasing the number of languages involved in CALM training leads to even higher accuracy and consistency. We offer a qualitative analysis of how cross-lingual consistency can enhance knowledge alignment and explore the method's generalizability. The source code and data of this paper are available on GitHub.
GENIE: Generative Note Information Extraction model for structuring EHR data
Authors: Huaiyuan Ying, Hongyi Yuan, Jinsen Lu, Zitian Qu, Yang Zhao, Zhengyun Zhao, Isaac Kohane, Tianxi Cai, Sheng Yu
Date: 2025-01-30 00:00:00
Tasks: Attribute, Attribute Extraction

Electronic Health Records (EHRs) hold immense potential for advancing healthcare, offering rich, longitudinal data that combines structured information with valuable insights from unstructured clinical notes. However, the unstructured nature of clinical text poses significant challenges for secondary applications. Traditional methods for structuring EHR free-text data, such as rule-based systems and multi-stage pipelines, are often limited by their time-consuming configurations and inability to adapt across clinical notes from diverse healthcare settings. Few systems provide a comprehensive attribute extraction for terminologies. While giant large language models (LLMs) like GPT-4 and LLaMA 405B excel at structuring tasks, they are slow, costly, and impractical for large-scale use. To overcome these limitations, we introduce GENIE, a Generative Note Information Extraction system that leverages LLMs to streamline the structuring of unstructured clinical text into usable data with standardized format. GENIE processes entire paragraphs in a single pass, extracting entities, assertion statuses, locations, modifiers, values, and purposes with high accuracy. Its unified, end-to-end approach simplifies workflows, reduces errors, and eliminates the need for extensive manual intervention. Using a robust data preparation pipeline and fine-tuned small scale LLMs, GENIE achieves competitive performance across multiple information extraction tasks, outperforming traditional tools like cTAKES and MetaMap and can handle extra attributes to be extracted. GENIE strongly enhances real-world applicability and scalability in healthcare systems. By open-sourcing the model and test data, we aim to encourage collaboration and drive further advancements in EHR structurization.
RbFT: Robust Fine-tuning for Retrieval-Augmented Generation against Retrieval Defects
Authors: Yiteng Tu, Weihang Su, Yujia Zhou, Yiqun Liu, Qingyao Ai
Date: 2025-01-30 00:00:00
Tasks: counterfactual, RAG, Retrieval, Retrieval-augmented Generation

Retrieval-augmented generation (RAG) enhances large language models (LLMs) by integrating external knowledge retrieved from a knowledge base. However, its effectiveness is fundamentally constrained by the reliability of both the retriever and the knowledge base. In real-world scenarios, imperfections in these components often lead to the retrieval of noisy, irrelevant, or misleading counterfactual information, ultimately undermining the trustworthiness of RAG systems. To address this challenge, we propose Robust Fine-Tuning (RbFT), a method designed to enhance the resilience of LLMs against retrieval defects through two targeted fine-tuning tasks. Experimental results demonstrate that RbFT significantly improves the robustness of RAG systems across diverse retrieval conditions, surpassing existing methods while maintaining high inference efficiency and compatibility with other robustness techniques.
Citation Recommendation based on Argumentative Zoning of User Queries
Authors: Shutian Ma, Chengzhi Zhang, Heng Zhang, Zheng Gao
Date: 2025-01-30 00:00:00
Tasks: Citation Recommendation, Multi-Task Learning, Sentence

Citation recommendation aims to locate the important papers for scholars to cite. When writing the citing sentences, the authors usually hold different citing intents, which are referred to citation function in citation analysis. Since argumentative zoning is to identify the argumentative and rhetorical structure in scientific literature, we want to use this information to improve the citation recommendation task. In this paper, a multi-task learning model is built for citation recommendation and argumentative zoning classification. We also generated an annotated corpus of the data from PubMed Central based on a new argumentative zoning schema. The experimental results show that, by considering the argumentative information in the citing sentence, citation recommendation model will get better performance.