pwc-archive/papers-with-abstracts huggingface dataset:
Multi-organ Self-supervised Contrastive Learning for Breast Lesion Segmentation
Authors: Hugo Figueiras, Helena Aidos, Nuno Cruz Garcia
Date: 2024-02-21 00:00:00
Tasks: Contrastive Learning, Lesion Segmentation, Self-Supervised Learning

Self-supervised learning has proven to be an effective way to learn representations in domains where annotated labels are scarce, such as medical imaging. A widely adopted framework for this purpose is contrastive learning and it has been applied to different scenarios. This paper seeks to advance our understanding of the contrastive learning framework by exploring a novel perspective: employing multi-organ datasets for pre-training models tailored to specific organ-related target tasks. More specifically, our target task is breast tumour segmentation in ultrasound images. The pre-training datasets include ultrasound images from other organs, such as the lungs and heart, and large datasets of natural images. Our results show that conventional contrastive learning pre-training improves performance compared to supervised baseline approaches. Furthermore, our pre-trained models achieve comparable performance when fine-tuned with only half of the available labelled data. Our findings also show the advantages of pre-training on diverse organ data for improving performance in the downstream task.
EXACT-Net:EHR-guided lung tumor auto-segmentation for non-small cell lung cancer radiotherapy
Authors: Hamed Hooshangnejad, Xue Feng, Gaofeng Huang, Rui Zhang, Katelyn Kelly, Quan Chen, Kai Ding
Date: 2024-02-21 00:00:00
Tasks: Computed Tomography (CT), Language Modelling, Large Language Model, Lung Nodule Detection, Segmentation, Tumor Segmentation, Zero-Shot Learning

Lung cancer is a devastating disease with the highest mortality rate among cancer types. Over 60% of non-small cell lung cancer (NSCLC) patients, which accounts for 87% of diagnoses, require radiation therapy. Rapid treatment initiation significantly increases the patient's survival rate and reduces the mortality rate. Accurate tumor segmentation is a critical step in the diagnosis and treatment of NSCLC. Manual segmentation is time and labor-consuming and causes delays in treatment initiation. Although many lung nodule detection methods, including deep learning-based models, have been proposed, there is still a long-standing problem of high false positives (FPs) with most of these methods. Here, we developed an electronic health record (EHR) guided lung tumor auto-segmentation called EXACT-Net (EHR-enhanced eXACtitude in Tumor segmentation), where the extracted information from EHRs using a pre-trained large language model (LLM), was used to remove the FPs and keep the TP nodules only. The auto-segmentation model was trained on NSCLC patients' computed tomography (CT), and the pre-trained LLM was used with the zero-shot learning approach. Our approach resulted in a 250% boost in successful nodule detection using the data from ten NSCLC patients treated in our institution.
Intriguing Properties of Modern GANs
Authors: Roy Friedman, Yair Weiss
Date: 2024-02-21 00:00:00

Modern GANs achieve remarkable performance in terms of generating realistic and diverse samples. This has led many to believe that ``GANs capture the training data manifold''. In this work we show that this interpretation is wrong. We empirically show that the manifold learned by modern GANs does not fit the training distribution: specifically the manifold does not pass through the training examples and passes closer to out-of-distribution images than to in-distribution images. We also investigate the distribution over images implied by the prior over the latent codes and study whether modern GANs learn a density that approximates the training distribution. Surprisingly, we find that the learned density is very far from the data distribution and that GANs tend to assign higher density to out-of-distribution images. Finally, we demonstrate that the set of images used to train modern GANs are often not part of the typical set described by the GANs' distribution.
A Systematic Review of Low-Rank and Local Low-Rank Matrix Approximation in Big Data Medical Imaging
Authors: Sisipho Hamlomo, Marcellin Atemkeng, Yusuf Brima, Chuneeta Nunhokee, Jeremy Baxter
Date: 2024-02-21 00:00:00
Tasks: Bayesian Optimization, Image Segmentation, Missing Values, Semantic Segmentation

The large volume and complexity of medical imaging datasets are bottlenecks for storage, transmission, and processing. To tackle these challenges, the application of low-rank matrix approximation (LRMA) and its derivative, local LRMA (LLRMA) has demonstrated potential. A detailed analysis of the literature identifies LRMA and LLRMA methods applied to various imaging modalities, and the challenges and limitations associated with existing LRMA and LLRMA methods are addressed. We note a significant shift towards a preference for LLRMA in the medical imaging field since 2015, demonstrating its potential and effectiveness in capturing complex structures in medical data compared to LRMA. Acknowledging the limitations of shallow similarity methods used with LLRMA, we suggest advanced semantic image segmentation for similarity measure, explaining in detail how it can be used to measure similar patches and its feasibility. We note that LRMA and LLRMA are mainly applied to unstructured medical data, and we propose extending their application to different medical data types, including structured and semi-structured. This paper also discusses how LRMA and LLRMA can be applied to regular data with missing entries and the impact of inaccuracies in predicting missing values and their effects. We discuss the impact of patch size and propose the use of random search (RS) to determine the optimal patch size. To enhance feasibility, a hybrid approach using Bayesian optimization and RS is proposed, which could improve the application of LRMA and LLRMA in medical imaging.
Fine-Tuning Enhances Existing Mechanisms: A Case Study on Entity Tracking
Authors: Nikhil Prakash, Tamar Rott Shaham, Tal Haklay, Yonatan Belinkov, David Bau
Date: 2024-02-22 00:00:00
Tasks: Code Generation, Instruction Following

Fine-tuning on generalized tasks such as instruction following, code generation, and mathematics has been shown to enhance language models' performance on a range of tasks. Nevertheless, explanations of how such fine-tuning influences the internal computations in these models remain elusive. We study how fine-tuning affects the internal mechanisms implemented in language models. As a case study, we explore the property of entity tracking, a crucial facet of language comprehension, where models fine-tuned on mathematics have substantial performance gains. We identify the mechanism that enables entity tracking and show that (i) in both the original model and its fine-tuned versions primarily the same circuit implements entity tracking. In fact, the entity tracking circuit of the original model on the fine-tuned versions performs better than the full original model. (ii) The circuits of all the models implement roughly the same functionality: Entity tracking is performed by tracking the position of the correct entity in both the original model and its fine-tuned versions. (iii) Performance boost in the fine-tuned models is primarily attributed to its improved ability to handle the augmented positional information. To uncover these findings, we employ: Patch Patching, DCM, which automatically detects model components responsible for specific semantics, and CMAP, a new approach for patching activations across models to reveal improved mechanisms. Our findings suggest that fine-tuning enhances, rather than fundamentally alters, the mechanistic operation of the model.
Difference Learning for Air Quality Forecasting Transport Emulation
Authors: Reed River Chen, Christopher Ribaudo, Jennifer Sleeman, Chace Ashcraft, Collin Kofroth, Marisa Hughes, Ivanka Stajner, Kevin Viner, Kai Wang
Date: 2024-02-22 00:00:00

Human health is negatively impacted by poor air quality including increased risk for respiratory and cardiovascular disease. Due to a recent increase in extreme air quality events, both globally and locally in the United States, finer resolution air quality forecasting guidance is needed to effectively adapt to these events. The National Oceanic and Atmospheric Administration provides air quality forecasting guidance for the Continental United States. Their air quality forecasting model is based on a 15 km spatial resolution; however, the goal is to reach a three km spatial resolution. This is currently not feasible due in part to prohibitive computational requirements for modeling the transport of chemical species. In this work, we describe a deep learning transport emulator that is able to reduce computations while maintaining skill comparable with the existing numerical model. We show how this method maintains skill in the presence of extreme air quality events, making it a potential candidate for operational use. We also explore evaluating how well this model maintains the physical properties of the modeled transport for a given set of species.
Link Prediction with Physics-Inspired Graph Neural Networks
Authors: Andrea Giuseppe Di Francesco, Francesco Caso, Maria Sofia Bucarelli, Fabrizio Silvestri
Date: 2024-02-22 00:00:00
Tasks: Graph Neural Network, Link Prediction, Node Classification, Prediction, Recommendation Systems

The message-passing mechanism underlying Graph Neural Networks (GNNs) is not naturally suited for heterophilic datasets, where adjacent nodes often have different labels. Most solutions to this problem remain confined to the task of node classification. In this article, we focus on the valuable task of link prediction under heterophily, an interesting problem for recommendation systems, social network analysis, and other applications. GNNs like GRAFF have improved node classification under heterophily by incorporating physics biases in the architecture. Similarly, we propose GRAFF-LP, an extension of GRAFF for link prediction. We show that GRAFF-LP effectively discriminates existing from non-existing edges by learning implicitly to separate the edge gradients. Based on this information, we propose a new readout function inspired by physics. Remarkably, this new function not only enhances the performance of GRAFF-LP but also improves that of other baseline models, leading us to reconsider how every link prediction experiment has been conducted so far. Finally, we provide evidence that even simple GNNs did not experience greater difficulty in predicting heterophilic links compared to homophilic ones. This leads us to believe in the necessity for heterophily measures specifically tailored for link prediction, distinct from those used in node classification. The code for reproducing our experiments is available at this URL https://anonymous.4open.science/r/Link_Prediction_with_PIGNN_IJCNN-F03F/.
Causal Imputation for Counterfactual SCMs: Bridging Graphs and Latent Factor Models
Authors: Alvaro Ribot, Chandler Squires, Caroline Uhler
Date: 2024-02-22 00:00:00
Tasks: counterfactual, Imputation, Matrix Completion

We consider the task of causal imputation, where we aim to predict the outcomes of some set of actions across a wide range of possible contexts. As a running example, we consider predicting how different drugs affect cells from different cell types. We study the index-only setting, where the actions and contexts are categorical variables with a finite number of possible values. Even in this simple setting, a practical challenge arises, since often only a small subset of possible action-context pairs have been studied. Thus, models must extrapolate to novel action-context pairs, which can be framed as a form of matrix completion with rows indexed by actions, columns indexed by contexts, and matrix entries corresponding to outcomes. We introduce a novel SCM-based model class, where the outcome is expressed as a counterfactual, actions are expressed as interventions on an instrumental variable, and contexts are defined based on the initial state of the system. We show that, under a linearity assumption, this setup induces a latent factor model over the matrix of outcomes, with an additional fixed effect term. To perform causal prediction based on this model class, we introduce simple extension to the Synthetic Interventions estimator (Agarwal et al., 2020). We evaluate several matrix completion approaches on the PRISM drug repurposing dataset, showing that our method outperforms all other considered matrix completion approaches.
2D Matryoshka Sentence Embeddings
Authors: Xianming Li, Zongxi Li, Jing Li, Haoran Xie, Qing Li
Date: 2024-02-22 00:00:00
Tasks: RAG, Representation Learning, Retrieval, Semantic Textual Similarity, Sentence, Sentence Embedding, Sentence-Embedding, Sentence Embeddings, STS

Common approaches rely on fixed-length embedding vectors from language models as sentence embeddings for downstream tasks such as semantic textual similarity (STS). Such methods are limited in their flexibility due to unknown computational constraints and budgets across various applications. Matryoshka Representation Learning (MRL) \cite{aditya2022matryoshka} encodes information at finer granularities, i.e., with lower embedding dimensions, to adaptively accommodate \emph{ad hoc} tasks. Similar accuracy can be achieved with a smaller embedding size, leading to speedups in downstream tasks. Despite its improved efficiency, MRL still requires traversing all Transformer layers before obtaining the embedding, which remains the dominant factor in time and memory consumption. This prompts consideration of whether the fixed number of Transformer layers affects representation quality and whether using intermediate layers for sentence representation is feasible. In this paper, we introduce a novel sentence embedding model called \textit{Two-dimensional Matryoshka Sentence Embedding} (2DMSE)\footnote{Our code is available at \url{https://github.com/SeanLee97/AnglE/blob/main/README_2DMSE.md}.}. It supports elastic settings for both embedding sizes and Transformer layers, offering greater flexibility and efficiency than MRL. We conduct extensive experiments on STS tasks and downstream applications. The experimental results demonstrate the effectiveness of our proposed model in dynamically supporting different embedding sizes and Transformer layers, allowing it to be highly adaptable to various scenarios.
Generalizing Reward Modeling for Out-of-Distribution Preference Learning
Authors: Chen Jia
Date: 2024-02-22 00:00:00
Tasks: Bilevel Optimization, Meta-Learning, Text Generation

Preference learning (PL) with large language models (LLMs) aims to align the LLMs' generations with human preferences. Previous work on reinforcement learning from human feedback (RLHF) has demonstrated promising results in in-distribution PL. However, due to the difficulty of obtaining human feedback, discretely training reward models for every encountered distribution is challenging. Thus, out-of-distribution (OOD) PL is practically useful for enhancing the generalization ability of LLMs with limited preference feedback. This work addresses OOD PL by optimizing a general reward model through a meta-learning approach. During meta-training, a bilevel optimization algorithm is utilized to learn a reward model capable of guiding policy learning to align with human preferences across various distributions. When encountering a test distribution, the meta-test procedure conducts regularized policy optimization using the learned reward model for PL. We theoretically demonstrate the convergence rate of the bilevel optimization algorithm under reasonable assumptions. Additionally, we conduct experiments on two text generation tasks across 20 held-out domains and outperform a variety of strong baselines across various evaluation metrics.
Scaling Efficient LLMs
Authors: B. N. Kausik
Date: 2024-02-22 00:00:00

Trained LLMs are typically sparse in that most of the parameters are zero, raising questions on efficiency. In response, we inquire into efficient LLMs, i.e. those with the fewest parameters that achieve the desired accuracy on a training corpus. Specifically, we compare theoretical and empirical estimates for training loss to obtain upper and lower bounds on the number of unique sequences in a natural training corpus as a function of its size. Our result implies (1) to double the number of skills represented in a training corpus, the corpus must scale more than four fold (2) for efficient LLMs, the number of parameters N and the size D of a natural training corpus scale as $N \propto D^{0.44}$; (3) if the number of parameters of an LLM is smaller than the number of unique sequences in the training corpus, scaling up can uncover emergent skills.
Back to Basics: Revisiting REINFORCE Style Optimization for Learning from Human Feedback in LLMs
Authors: Arash Ahmadian, Chris Cremer, Matthias Gallé, Marzieh Fadaee, Julia Kreutzer, Olivier Pietquin, Ahmet Üstün, Sara Hooker
Date: 2024-02-22 00:00:00

AI alignment in the shape of Reinforcement Learning from Human Feedback (RLHF) is increasingly treated as a crucial ingredient for high performance large language models. Proximal Policy Optimization (PPO) has been positioned by recent literature as the canonical method for the RL part of RLHF. However, it involves both high computational cost and sensitive hyperparameter tuning. We posit that most of the motivational principles that led to the development of PPO are less of a practical concern in RLHF and advocate for a less computationally expensive method that preserves and even increases performance. We revisit the formulation of alignment from human preferences in the context of RL. Keeping simplicity as a guiding principle, we show that many components of PPO are unnecessary in an RLHF context and that far simpler REINFORCE-style optimization variants outperform both PPO and newly proposed "RL-free" methods such as DPO and RAFT. Our work suggests that careful adaptation to LLMs alignment characteristics enables benefiting from online RL optimization at low cost.
How Transformers Learn Causal Structure with Gradient Descent
Authors: Eshaan Nichani, Alex Damian, Jason D. Lee
Date: 2024-02-22 00:00:00
Tasks: In-Context Learning

The incredible success of transformers on sequence modeling tasks can be largely attributed to the self-attention mechanism, which allows information to be transferred between different parts of a sequence. Self-attention allows transformers to encode causal structure which makes them particularly suitable for sequence modeling. However, the process by which transformers learn such causal structure via gradient-based training algorithms remains poorly understood. To better understand this process, we introduce an in-context learning task that requires learning latent causal structure. We prove that gradient descent on a simplified two-layer transformer learns to solve this task by encoding the latent causal graph in the first attention layer. The key insight of our proof is that the gradient of the attention matrix encodes the mutual information between tokens. As a consequence of the data processing inequality, the largest entries of this gradient correspond to edges in the latent causal graph. As a special case, when the sequences are generated from in-context Markov chains, we prove that transformers learn an induction head (Olsson et al., 2022). We confirm our theoretical findings by showing that transformers trained on our in-context learning task are able to recover a wide variety of causal structures.
A Quick Introduction to Quantum Machine Learning for Non-Practitioners
Authors: Ethan N. Evans, Dominic Byrne, Matthew G. Cook
Date: 2024-02-22 00:00:00
Tasks: Quantum Machine Learning

This paper provides an introduction to quantum machine learning, exploring the potential benefits of using quantum computing principles and algorithms that may improve upon classical machine learning approaches. Quantum computing utilizes particles governed by quantum mechanics for computational purposes, leveraging properties like superposition and entanglement for information representation and manipulation. Quantum machine learning applies these principles to enhance classical machine learning models, potentially reducing network size and training time on quantum hardware. The paper covers basic quantum mechanics principles, including superposition, phase space, and entanglement, and introduces the concept of quantum gates that exploit these properties. It also reviews classical deep learning concepts, such as artificial neural networks, gradient descent, and backpropagation, before delving into trainable quantum circuits as neural networks. An example problem demonstrates the potential advantages of quantum neural networks, and the appendices provide detailed derivations. The paper aims to help researchers new to quantum mechanics and machine learning develop their expertise more efficiently.
PeriodGrad: Towards Pitch-Controllable Neural Vocoder Based on a Diffusion Probabilistic Model
Authors: Yukiya Hono, Kei Hashimoto, Yoshihiko Nankaku, Keiichi Tokuda
Date: 2024-02-22 00:00:00
Tasks: Denoising, Pitch control, Singing Voice Synthesis

This paper presents a neural vocoder based on a denoising diffusion probabilistic model (DDPM) incorporating explicit periodic signals as auxiliary conditioning signals. Recently, DDPM-based neural vocoders have gained prominence as non-autoregressive models that can generate high-quality waveforms. The neural vocoders based on DDPM have the advantage of training with a simple time-domain loss. In practical applications, such as singing voice synthesis, there is a demand for neural vocoders to generate high-fidelity speech waveforms with flexible pitch control. However, conventional DDPM-based neural vocoders struggle to generate speech waveforms under such conditions. Our proposed model aims to accurately capture the periodic structure of speech waveforms by incorporating explicit periodic signals. Experimental results show that our model improves sound quality and provides better pitch control than conventional DDPM-based neural vocoders.
Q-Probe: A Lightweight Approach to Reward Maximization for Language Models
Authors: Kenneth Li, Samy Jelassi, Hugh Zhang, Sham Kakade, Martin Wattenberg, David Brandfonbrener
Date: 2024-02-22 00:00:00
Tasks: Code Generation, Language Modeling, Language Modelling

We present an approach called Q-probing to adapt a pre-trained language model to maximize a task-specific reward function. At a high level, Q-probing sits between heavier approaches such as finetuning and lighter approaches such as few shot prompting, but can also be combined with either. The idea is to learn a simple linear function on a model's embedding space that can be used to reweight candidate completions. We theoretically show that this sampling procedure is equivalent to a KL-constrained maximization of the Q-probe as the number of samples increases. To train the Q-probes we consider either reward modeling or a class of novel direct policy learning objectives based on importance weighted policy gradients. With this technique, we see gains in domains with ground-truth rewards (code generation) as well as implicit rewards defined by preference data, even outperforming finetuning in data-limited regimes. Moreover, a Q-probe can be trained on top of an API since it only assumes access to sampling and embeddings. Code: https://github.com/likenneth/q_probe .